US20230340013A1

US20230340013A1 - Polypeptides and methods

Info

Publication number: US20230340013A1
Application number: US18/198,205
Authority: US
Inventors: Jason Chin; Kathrin Lang
Original assignee: United Kingdom Research and Innovation
Current assignee: United Kingdom Research and Innovation
Priority date: 2012-05-18
Filing date: 2023-05-16
Publication date: 2023-10-26
Also published as: US20200271658A1; JP2015523965A; WO2013171485A1; BR112014028588A2; EP2852664A1; US20150148525A1; CA2873793C; CN108410827B; BR112014028588B1; CA2873793A1; CN108410827A; CN104718285A; HK1208704A1; IN2014DN09922A; JP6343604B2; EP2852664B1; BR112014028588A8; US11732001B2

Abstract

The invention relates to a polypeptide comprising an amino acid having a bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) group, particularly when said BCN group is present as: a residue of a lysine amino acid. The invention also relates to a method of producing a polypeptide comprising a BCN group, said method comprising genetically incorporating an amino acid comprising a BCN group into a polypeptide. The invention also relates to an amino acid comprising bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN), particularly and amino acid which is bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) lysine. In addition the invention relates to a PylRS tRNA synthetase comprising the mutations Y271M, L274G and C313A.

Description

FIELD OF THE INVENTION

The invention relates to site-specific incorporation of bio-orthogonal groups via the (expanded) genetic code. In particular the invention relates to incorporation of chemical groups into polypeptides via accelerated inverse electron demand Diels-Alder reactions between genetically incorporated amino acid groups such as dienophiles, and chemical groups such as tetrazines.

BACKGROUND TO THE INVENTION

The site-specific incorporation of bio-orthogonal groups via genetic code expansion provides a powerful general strategy for site specifically labelling proteins with any probe. However, the slow reactivity of the bio-orthogonal functional groups that can be genetically encoded has limited this strategy's utility.
The rapid, site-specific labeling of proteins with diverse probes remains an outstanding challenge for chemical biologists; enzyme mediated labeling approaches may be rapid, but use protein or peptide fusions that introduce perturbations into the protein under study and may limit the sites that can be labeled, while many ‘bio-orthogonal’ reactions for which a component can be genetically encoded are too slow to effect the quantitative and site specific labeling of proteins on a time-scale that is useful to study many biological processes.
There is a pressing need for general methods to site-specifically label proteins, in diverse contexts, with user-defined probes.
Inverse electron demand Diels-Alder reactions between strained alkenes including norbornenes and trans-cyclooctenes, and tetrazines have emerged as an important class of rapid bio-orthogonal reactions^1-4. The rates reported for some of these reactions are incredibly fast^3,5.
Very recently, three approaches have been reported for specifically labeling proteins using these reactions:

- A lipoic acid ligase variant that accepts a trans-cyclooctene substrate has been used to label proteins bearing a 13 amino acid lipoic acid ligase tag in a two step procedure⁵.
- A tetrazine has been introduced at a specific site in a protein expressed in E. coli via genetic code expansion, and derivatized with a strained trans-cyclooctene-diacetyl fluorescein⁶.
- The incorporation of a strained alkene (a norbornene containing amino acid) has been demonstrated via genetic code expansion and site-specific fluorogenic labeling with tetrazine fluorophores in vitro, in E. coli and on mammalian cells⁷. The incorporation of norbornene containing amino acids has also been recently reported.^8,9

The low-efficiency incorporation of a trans-cyclooctene containing amino acid (TCO) (2) has been reported, with detection of some fluorescent labelling in fixed cells.⁹
Recent work with model reactions in organic solvents suggests that the reaction between BCN (first described in strain promoted reactions with azides)¹⁰and tetrazines may proceed very rapidly¹¹. However, this reaction, unlike the much slower reaction of simple cyclooctynes with azides, nitrones^12-16and tetrazines^9,17, has not been explored in aqueous media or as a chemoselective route to labeling macromolecules.
The present invention seeks to overcome problem(s) associated with the prior art.

SUMMARY OF THE INVENTION

Certain techniques for the attachment of tetrazine compounds to polypeptides exist in the art. However, those techniques suffer from slow reaction rates. Moreover, those techniques allow for multiple chemical species to be produced as reaction products. This can lead to problems, for example in variable molecular distances between dye groups which can be problematic for fluorescence resonance energy transfer (FRET) analysis. This can also be problematic for the production of therapeutic molecules since heterogeneity of product can be a drawback in this area.
The present inventors have provided a new amino acid bearing a bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) group. This allows a dramatically increased reaction rate, which is advantageous. In addition, this allows a single-product addition reaction to be carried out. This leads to a homogeneous product, which is an advantage. This also eliminates isomeric variations (spatial isomers) in the product, which provides technical benefits in a range of applications as demonstrated herein. In addition, the product of the BCN addition reaction does not epimerise, whereas the products from (for example) norbornene and/or TCO reactions do give rise to epimers. Thus it is an advantage of the invention that the problems of epimers are also avoided.
Thus in one aspect the invention provides a polypeptide comprising an amino acid having a bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) group. This has the advantage of providing a single reaction product following addition of (for example) tetrazine compounds. Alternate techniques such as norbornene addition or TCO addition give a mixture of products comprising different isomers, such as regio or stereo isomers. One reason for this advantage is that the BCN part of the molecule has mirror symmetry so that the product is the same, whereas for TCO/norbornene that part of the molecule is chiral and so attachment can be to the ‘top face’ or ‘bottom face’ of the double bond, leading to different isomers in the products.
Thus the invention provides the advantage of homogeneity of product when used in the attachment of further groups to the polypeptide such as tetrazine compounds.
Suitably said BCN group is present as a residue of a lysine amino acid.
In another aspect, the invention relates to a method of producing a polypeptide comprising a BCN group, said method comprising genetically incorporating an amino acid comprising a BCN group into a polypeptide.
Suitably producing the polypeptide comprises

- (i) providing a nucleic acid encoding the polypeptide which nucleic acid comprises an orthogonal codon encoding the amino acid having a BCN group;
- (ii) translating said nucleic acid in the presence of an orthogonal tRNA synthetase/tRNA pair capable of recognising said orthogonal codon and incorporating said amino acid having a BCN group into the polypeptide chain.

Suitably said amino acid comprising a BCN group is a BCN lysine.
Suitably said orthogonal codon comprises an amber codon (TAG), said tRNA comprises MbtRNA_CUA. Suitably said amino acid having a BCN group comprises a bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) lysine. Suitably said tRNA synthetase comprises a PylRS synthetase having the mutations Y271M, L274G and C313A (BCNRS).
Suitably said amino acid having a BCN group is incorporated at a position corresponding to a lysine residue in the wild type polypeptide. This has the advantage of maintaining the closest possible structural relationship of the BCN containing polypeptide to the wild type polypeptide from which it is derived.
In another aspect, the invention relates to a polypeptide as described above which comprises a single BCN group. Thus suitably the polypeptide comprises a single BCN group. This has the advantage of maintaining specificity for any further chemical modifications which might be directed at the BCN group. For example when there is only a single BCN group in the polypeptide of interest then possible issues of partial modification (e.g. where only a subset of BCN groups in the polypeptide are subsequently modified), or issues of reaction microenvironments varying between alternate BCN groups in the same polypeptides (which could lead to unequal reactivity between different BCN group(s) at different locations in the polypeptide) are advantageously avoided.
A key advantage of incorporation of a BCN group is that is permits a range of extremely useful further compounds such as labels to be easily and specifically attached to the BCN group.
In another aspect, the invention relates to a polypeptide as described above wherein said BCN group is joined to a tetrazine group.
In another aspect, the invention relates to a polypeptide as described above wherein said tetrazine group is further joined to a fluorophore.
Suitably said fluorophore comprises fluorescein, tetramethyl rhodamine (TAMRA) or boron-dipyrromethene (BODIPY).
In another aspect, the invention relates to a novel unnatural amino acid comprising a BCN group.
In another aspect, the invention relates to an amino acid comprising bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN).
In another aspect, the invention relates to an amino acid which is bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) lysine.
Suitably BCN lysine as described above has the structure:
In another aspect, the invention relates to a method of producing a polypeptide comprising a tetrazine group, said method comprising providing a polypeptide as described above, contacting said polypeptide with a tetrazine compound, and incubating to allow joining of the tetrazine to the BCN group by an inverse electron demand Diels-Alder cycloaddition reaction.
Suitably the tetrazine is selected from 6 to 17 of FIG. 1 .
Suitably the pseudo first order rate constant for the reaction is at least 80 M⁻¹s⁻¹.
Suitably the tetrazine is selected from 6, 7, 8 and 9 of FIG. 1 and the pseudo first order rate constant for the reaction is at least 80 M⁻¹s⁻¹.
This chemistry has the advantage of speed of reaction.
Suitably said reaction is allowed to proceed for 10 minutes or less.
Suitably said reaction is allowed to proceed for 1 minute or less.
Suitably said reaction is allowed to proceed for 30 seconds or less.
It will be noted that certain reaction environments may affect reaction times. Most suitably the shortest times such as 30 seconds or less are applied to in vitro reactions.
Reactions in vivo, or in eukaryotic culture conditions such as tissue culture medium or other suitable media for eukaryotic cells, may need to be conducted for longer than 30 seconds to achieve maximal labelling. The skilled operator can determine optimum reaction limes by trial and error based on the guidance provided herein.
Suitably said tetrazine compound is a tetrazine compound selected from the group consisting of 11 and 17 of FIG. 1 .
In another aspect, the invention relates to a PylRS tRNA synthetase comprising the mutations Y271M, L274G and C313A.
Suitably said PylRS tRNA synthetase has a sequence corresponding to MbPylRS tRNA synthetase comprising the mutations Y271M, L274G and C313A.
In another aspect the invention relates to the use of the PylRS tRNA synthetase(s) of the invention for the incorporation of amino acid comprising bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) into a polypeptide.
In another aspect the invention relates to a method for the incorporation of amino acid comprising bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) into a polypeptide comprising use of the PylRS tRNA synthetase(s) of the invention to incorporate same.
In another aspect, the invention relates to a homogenous recombinant polypeptide as described above. Suitably said polypeptide is made by a method as described above.
Also disclosed is a polypeptide produced according to the method(s) described herein. As well as being the product of those new methods, such a polypeptide has the technical feature of comprising BCN.
Mutating has it normal meaning in the art and may refer to the substitution or truncation or deletion of the residue, motif or domain referred to. Mutation may be effected at the polypeptide level e.g. by synthesis of a polypeptide having the mutated sequence, or may be effected at the nucleotide level e.g. by making a nucleic acid encoding the mutated sequence, which nucleic acid may be subsequently translated to produce the mutated polypeptide. Where no amino acid is specified as the replacement amino acid for a given mutation site, suitably a randomisation of said site is used. As a default mutation, alanine (A) may be used. Suitably the mutations used at particular site(s) are as set out herein.
A fragment is suitably at least 10 amino acids in length, suitably at least 25 amino acids, suitably at least 50 amino acids, suitably at least 100 amino acids, suitably at least 200 amino acids, suitably at least 250 amino acids, suitably at least 300 amino acids, suitably at least 313 amino acids, or suitably the majority of the polypeptide of interest.

DETAILED DESCRIPTION OF THE INVENTION

Here we demonstrate a fluorogenic reaction between bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) and tetrazines. The rates for these reactions are 3-7 orders of magnitude faster than the rates for many ‘bio-orthogonal’ reactions. We describe aminoacyl-tRNA synthetase/tRNA pairs and their use for the efficient site-specific incorporation of a BCN-containing amino acid, 1, and a transcyclooctene-containing amino acid 2 (which also reacts extremely rapidly with tetrazines) into proteins expressed in E. coli and mammalian cells. We demonstrate the site-specific, fluorogenic labeling of proteins containing 1 and 2 in vitro, in E. coli and in live mammalian cells at the first measureable time point (after seconds or minutes). Moreover we demonstrate the specificity of tetrazine labeling with respect to a proteome as well as the advantages of the approach with respect to current ‘bio-orthogonal’ reactions for which a component can be encoded. The approaches developed may be applied to site-specific protein labeling in animals, and they find utility in labelling and imaging studies.
A polypeptide comprising an amino acid having a dienophile group, characterised in that said dienophile group comprises a bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) group.
We describe genetic encoding of bicyclononynes and trans-cyclooctenes for site-specific protein labelling in vitro and in live mammalian cells via fluorogenic Diels-Alder reactions.
The methods of the invention may be practiced in vivo or in vitro.
In one embodiment, suitably the methods of the invention are not applied to the human or animal body. Suitably the methods of the invention are in vitro methods. Suitably the methods do not require the presence of the human or animal body. Suitably the methods are not methods of diagnosis or of surgery or of therapy of the human or animal body.

Dienophile/Trans-Cyclooctene (TCO) Aspects

In a broad aspect the invention relates to a polypeptide comprising an amino acid having a dienophile group capable of reacting with a tetrazine group.
Suitably said dienophile group is present as a residue of a lysine amino acid.
In one embodiment, the invention relates to a method of producing a polypeptide comprising a dienophile group, said method comprising genetically incorporating an amino acid comprising a dienophile group into a polypeptide.
Suitably producing the polypeptide comprises

- (i) providing a nucleic acid encoding the polypeptide which nucleic acid comprises an orthogonal codon encoding the amino acid having a dienophile group;
- (ii) translating said nucleic acid in the presence of an orthogonal tRNA synthetase/tRNA pair capable of recognising said orthogonal codon and incorporating said amino acid having a dienophile group into the polypeptide chain. Suitably said amino acid comprising a dienophile group is a dienophile lysine.

Suitably said orthogonal codon comprises an amber codon (TAG), said tRNA comprises MbtRNA_CUA, said amino acid having a dienophile group comprises a trans-cyclooctene-4-ol (TCO) containing amino acid and said tRNA synthetase comprises a PylRS synthetase having the mutations Y271A, L274M and C313A (TCORS).
Suitably said PylRS tRNA synthetase has a sequence corresponding to MbPylRS tRNA synthetase comprising the mutations Y271A, L274M and C313A (TCORS). In another aspect the invention relates to the use of the PylRS tRNA synthetase(s) of the invention for the incorporation of amino acid comprising trans-cyclooctene-4-ol (TCO) into a polypeptide.
In another aspect the invention relates to a method for the incorporation of amino acid comprising trans-cyclooctene-4-ol (TCO) into a polypeptide comprising use of the PylRS tRNA synthetase(s) of the invention to incorporate same.
Aspects of the invention regarding the joining of tetrazine compounds to the unnatural amino acids discussed herein apply equally to TCO amino acids as they do to BCN amino acids unless otherwise indicated by the context.
We report the exceptionally rapid, fluorogenic, reaction of BCN with a range of tetrazines under aqueous conditions at room temperature. The rate constants for BCN-tetrazine reactions are 500 to 1000 times greater than for the reaction of norbornene with the same tetrazines. The rate constants for TCO-tetrazine reactions are 10-15 fold greater than those for BCN with the same tetrazine. The reaction between strained alkenes and tetrazines may lead to a mixture of diastereomers and regioisomers, as well as isomers from dihydropyridazine isomerization.^3,4
In contrast the BCN tetrazine reaction leads to the formation of a single product. This may be an advantage in applications where homogeneity in the orientation of probe attachment may be important, including single molecule spectroscopy, and FRET approaches.
We have described aminoacyl-tRNA synthetase/tRNA pairs and their uses to direct the efficient, site-specific incorporation of 1 and 2 into proteins in E. coli and mammalian cells.
We have demonstrated that the specific, quantitative labeling of proteins—a process that takes tens of minutes to hours with an encoded norbornene⁷and tens of hours with an encoded azide using copper-catalysed click chemistry with alkyne probes²¹—may be complete within seconds using the encoded amino acids 1 and 2. While we do not observe labeling of an azide incorporated into EGFR on the mammalian cell surface with cyclooctynes⁷and labeling of an encoded norbornene in EGFR allows labeling only after 2 hours with tetrazines⁷, strong and saturated labeling of EGFR incorporating 1 and 2 was observed at the first time point measured (2 min) using nanomolar concentrations of tetrazine-dye conjugates. These experiments confirm that the rapid BCN-tetrazine and TCO-tetrazine ligations characterized in small molecule experiments translate into substantial improvements in protein labeling in diverse contexts. While we have demonstrated the advantages of this approach in vitro, in E. coli and in live mammalian cells the ability to incorporate unnatural amino acids in C. elegans using the PylRS/tRNA_CUApairs suggests that it may be possible to extend the labeling approach described here to site-specific protein labeling in animals.

Genetic Incorporation and Polypeptide Production

In the method according to the invention, said genetic incorporation preferably uses an orthogonal or expanded genetic code, in which one or more specific orthogonal codons have been allocated to encode the specific amino acid residue with the BCN group so that it can be genetically incorporated by using an orthogonal tRNA synthetase/tRNA pair. The orthogonal tRNA synthetase/tRNA pair can in principle be any such pair capable of charging the tRNA with the amino acid comprising the BCN group and capable of incorporating that amino acid comprising the BCN group into the polypeptide chain in response to the orthogonal codon.
The orthogonal codon may be the orthogonal codon amber, ochre, opal or a quadruplet codon. The codon simply has to correspond to the orthogonal tRNA which will be used to carry the amino acid comprising the BCN group. Preferably the orthogonal codon is amber.
It should be noted that the specific examples shown herein have used the amber codon and the corresponding tRNA/tRNA synthetase. As noted above, these may be varied. Alternatively, in order to use other codons without going to the trouble of using or selecting alternative tRNA/tRNA synthetase pairs capable of working with the amino acid comprising the BCN group, the anticodon region of the tRNA may simply be swapped for the desired anticodon region for the codon of choice. The anticodon region is not involved in the charging or incorporation functions of the tRNA nor recognition by the tRNA synthetase so such swaps are entirely within the ambit of the skilled operator.
Thus alternative orthogonal tRNA synthetase/tRNA pairs may be used if desired.
Preferably the orthogonal synthetase/tRNA pair are Methanosarcina barkeri MS pyrrolysine tRNA synthetase (MbPylRS) and its cognate amber suppressor tRNA (MbtRNA_CUA).
The Methanosarcina barkeri PylT gene encodes the MbtRNA_CUAtRNA.
The Methanosarcina barkeri PylS gene encodes the MbPylRS tRNA synthetase protein.
When particular amino acid residues are referred to using numeric addresses, the numbering is taken using MbPylRS (Methanosarcina barkeri pyrrolysyl-tRNA synthetase) amino acid sequence as the reference sequence (i.e. as encoded by the publicly available wild type Methanosarcina barkeri PylS gene Accession number Q46E77).

	SEQ ID NO. 1:
	MDKKPLDVLI SATGLWMSRT GTLHKIKHYE VSRSKIYIEM

	ACGDHLVVNN SRSCRTARAF RHHKYRKTCK RCRVSDEDIN

	NFLTRSTEGK TSVKVKVVSA PKVKKAMPKS VSRAPKPLEN

	PVSAKASTDT SRSVPSPAKS TPNSPVPTSA PAPSLTRSQL

	DRVEALLSPE DKISLNIAKP FRELESELVT RRKNDFQRLY

	INDREDYLGK LERDITKFFV DRDFLEIKSP ILIPAEYVER

	MGINNDTELS KQIFRVDKNL CLRPMLAPTL YNYLRKLDRI

	LPDPIKIFEV GPCYRKESDG KEHLEEFTMV NFCQMGSGCT

	RENLESLIKE FLDYLEIDFE IVGDSCMVYG DILDIMHGDL

	ELSSAVVGPV PLDREWGIDK PWIGAGFGLE RLLKVMHGFK

	NIKRASRSES YYNGISTNL.

If required, the person skilled in the art may adapt MbPylRS tRNA synthetase protein by mutating it so as to optimise for the BCN amino acid to be used. The need for mutation depends on the BCN amino acid used. An example where the MbPylRS tRNA synthetase may need to be mutated is when the BCN amino acid is not processed by the MbPylRS tRNA synthetase protein.
Such mutation may be carried out by introducing mutations into the MbPylRS tRNA synthetase, for example at one or more of the following positions in the MbPylRS tRNA synthetase: M241, A267, Y271, L274 and C313.
An example is when said amino acid having a BCN group comprises a bicyclo[6,1,0]non-4-yn-9-ylmethanol (BCN) lysine. Suitably said tRNA synthetase comprises a PylRS synthetase such as MbPylRS having the mutations Y271M, L274G and C313A (BCNRS).
An example is when said amino acid having a dienophile group comprises a trans-cyclooctene-4-ol (TCO) containing amino acid. Suitably said tRNA synthetase comprises a PylRS synthetase such as MbPylRS having the mutations Y271A, L274M and C313A (TCORS).
tRNA Synthetases
The tRNA synthetase of the invention may be varied. Although specific tRNA synthetase sequences may have been used in the examples, the invention is not intended to be confined only to those examples.
In principle any tRNA synthetase which provides the same tRNA charging (aminoacylation) function can be employed in the invention.
For example the tRNA synthetase may be from any suitable species such as from archea, for example from Methanosarcina barkeri MS; Methanosarcina barkeri str. Fusaro; Methanosarcina mazei Gol; Methanosarcina acetivorans C2A; Methanosarcina thermophila; or Methanococcoides burtonii. Alternatively the tRNA synthetase may be from bacteria, for example from Desulfitobacterium hafniense DCB-2; Desulfitobacterium hafniense Y51; Desulfitobacterium hafniense PCP1; Desulfotomaculum acetoxidans DSM 771.
Exemplary sequences from these organisms are the publically available sequences. The following examples are provided as exemplary sequences for pyrrolysine tRNA synthetases:

	>M. barkeriMS/1-419/
	Methanosarcina barkeri MS
	VERSION Q6WRH6.1 GI:74501411
	SEQ ID NO. 2:
	MDKKPLDVLISATGLWMSRTGTLHKIKHHEVSRSKIYIEM

	ACGDHLVVNNSRSCRTARAFRHHKYRKTCKRCRVSDEDIN

	NFLTRSTESKNSVKVRVVSAPKVKKAMPKSVSRAPKPLEN

	SVSAKASTNTSRSVPSPAKSTPNSSVPASAPAPSLTRSQL

	DRVEALLSPEDKISLNMAKPFRELEPELVTRRKNDFQRLY

	INDREDYLGKLERDITKFFVDRGFLEIKSPILIPAEYVER

	MGINNDTELSKQIFRVDKNLCLRPMLAPTLYNYLRKLDRI

	LPGPIKIFEVGPCYRKESDGKEHLEEFTMVNFCQMGSGCT

	RENLEALIKEFLDYLEIDFEIVGDSCMVYGDTLDIMHGDL

	ELSSAVVGPVSLDREWGIDKPWIGAGFGLERLLKVMHGFK

	NIKRASRSESYYNGISTNL

	>M. barkeriF/1-419/
	Methanosarcina barkeri str. Fusaro
	VERSION YP_304395.1 GI:73668380
	SEQ ID NO. 3:
	MDKKPLDVLISATGLWMSRTGTLHKIKHYEVSRSKIYIEM

	ACGDHLVVNNSRSCRTARAFRHHKYRKTCKRCRVSDEDIN

	NFLTRSTEGKTSVKVKVVSAPKVKKAMPKSVSRAPKPLEN

	PVSAKASTDTSRSVPSPAKSTPNSPVPTSAPAPSLTRSQL

	DRVEALLSPEDKISLNIAKPFRELESELVTRRKNDFQRLY

	TNDREDYLGKLERDITKFFVDRDFLEIKSPILIPAEYVER

	MGINNDTELSKQIFRVDKNLCLRPMLAPTLYNYLRKLDRI

	LPDPIKIFEVGPCYRKESDGKEHLEEFTMVNFCQMGSGCT

	RENLESLIKEFLDYLEIDFEIVGDSCMVYGDTLDI

	>M. mazei/1-454
	Methanosarcina mazei Go 1
	VERSION NP_633469.1 GI:21227547
	SEQ ID NO. 4:
	MDKKPLNTLISATGLWMSRTGTIHKIKHHEVSRSKIYIEM

	ACGDHLVVNNSRSSRTARALRHHKYRKTCKRCRVSDEDLN

	KFLTKANEDQTSVKVKVVSAPTRIKKAMPKSVARAPKPLE

	NTEAAQAQPSGSKFSPAIPVSTQESVSVPASVSTSISSIS

	TGATASALVKGNINPITSMSAPVQASAPALTKSQTDRLEV

	LLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERE

	NYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDN

	DTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPI

	KIFEIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLE

	SIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGDLELSSA

	VVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRA

	ARSESYYNGISTNL

	>M. acetivorans/1-443
	Methanosarcina acetivorans C2A
	VERSION NP_615128.2 GI:161484944
	SEQ ID NO. 5:
	MDKKPLDTLISATGLWMSRTGMIHKIKHHEVSRSKIYIEM

	ACGERLVVNNSRSSRTARALRHHKYRKTCRHCRVSDEDIN

	NFLTKTSEEKTTVKVKVVSAPRVRKAMPKSVARAPKPLEA

	TAQVPLSGSKPAPATPVSAPAQAPAPSTGSASATSASAQR

	MANSAAAPAAPVPTSAPALTKGQLDRLEGLLSPKDEISLD

	SEKPFRELESELLSRRKKDLKRIYAEERENYLGKLEREIT

	KFFVDRGFLEIKSPILIPEYVERMGINSDTELSKQVFRID

	KNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKE

	SDGKEHLEEFTMLNFCQMGSGCTRENLEAIITEFLNHLGI

	DFEIIGDSCMVYGNTLDVMHDDLELSSAVVGPVPLDREWG

	IDKPWIGAGFGLERLLKVMHGFKNIKRAARSESYYNGIST

	NL

	>M. thermophila/1-478
	Methanosarcina thermophila,
	VERSION DQ017250.1 GI:67773308
	SEQ ID NO. 6:
	MDKKPLNTLISATGLWMSRTGKLHKIRHHEVSKRKIYIEM

	ECGERLVVNNSRSCRAARALRHHKYRKICKHCRVSDEDLN

	KFLTRINEDKSNAKVTVVSAPKIRKVMPKSVARTPKPLEN

	TAPVQTLPSESQPAPTTPISASTTAPASTSTTAPAPASTT

	APAPASTTAPASASTTISTSAMPASTSAQGTTKFNYISGG

	FPRPIPVQASAPALTKSQIDRLQGLLSPKDEISLDSGTPF

	RKLESELLSRRRKDLKQIYAEEREHYLGKLEREITKFFVD

	RGFLEIKSPILIPMEYIERMGIDNDKELSKQIFRYDNNFC

	LRPMLAPNLYNYLRKLNRALPDPIKIFEIGPCYRKESDGK

	EHLEEFTMLNFCQMGSGCTRENLEAHIKDFLDYLGIDFEI

	VGDSCMVYGDTLDVMHGDLELSSAVVGPVPMDRDWGINKP

	WIGAGFGLERLLKVMHNFKNIKRASRSESYYNGISTNL

	>M. burtonii/1-416
	Methanococcoides burtonii DSM 6242,
	VERSION YP_566710.1 GI:91774018
	SEQ ID NO. 7:
	MEKQLLDVLVELNGVWLSRSGLLHGIRNFEITTKHIHIET

	DCGARFTVRNSRSSRSARSLRHNKYRKPCKRCRPADEQID

	RFVKKTFKEKRQTVSVFSSPKKHVPKKPKVAVIKSFSIST

	PSPKEASVSNSIPTPSISVVKDEVKVPEVKY

	TPSQIERLKTLMSPDDKIPIQDELPEFKVLEKELIQRRRD

	DLKKMYEEDREDRLGKLERDITEFFVDRGFLEIKSPIMIP

	FEYIERMGIDKDDHLNKQIFRVDESMCLRPMLAPCLYNYL

	RKLDKVLPDPIRIFEIGPCYRKESDGSSHLEEFTMVNFCQ

	MGSGCTRENMEALIDEFLEHLGIEYEIEADNCMVYGDTID

	IMHGDLELSSAVVGPIPLDREWGVNKPWMGAGFGLERLLK

	VRHNYTNIRRASRSELYYNGINTNL

	>D. hafniense_DCB-2/1-279
	Desulfitobacterium hafniense DCB-2
	VERSION YP_002461289.1 GI:219670854
	SEQ ID NO. 8:
	MSSFWTKVQYQRLKELNASGEQLEMGFSDALSRDRAFQGI

	EHQLMSQGKRHLEQLRTVKHRPALLELEEGLAKALHQQGF

	VQVVTPTIITKSALAKMTIGEDHPLFSQVFWLDGKKCLRP

	MLAPNLYTLWRELERLWDKPIRIFEIGTCYRKESQGAQHL

	NEFTMLNLTELGTPLEERHQRLEDMARWVLEAAGIREFEL

	VTESSVVYGDTVDVMKGDLELASGAMGPHFLDEKWEIVDP

	WVGLGFGLERLLMIREGTQHVQSMARSLSYLDGVRLNIN

	>D. hafniense_Y51/1-312
	Desulfitobacterium hafniense Y51
	VERSION YP_521192.1 GI:89897705
	SEQ ID NO. 9:
	MDRIDHTDSKFVQAGETPVLPATFMFLTRRDPPLSSFWTK

	VQYQRLKELNASGEQLEMGFSDALSRDRAFQGIEHQLMSQ

	GKRHLEQLRTVKHRPALLELEEGLAKALHQQGFVQVVTPT

	IITKSALAKMTIGEDHPLFSQVFWLDGKKCLRPMLAPNLY

	TLWRELERLWDKPIRIFEIGTCYRKESQGAQHLNEFTMLN

	LTELGTPLEERHQRLEDMARWVLEAAGIREFELVTESSVV

	YGDTVDVMKGDLELASGAMGPHFLDEKWEIVDPWVGLGFG

	LERLLMIREGTQHVQSMARSLSYLDGVRLNIN

	>D. hafniensePCP1/1-288
	Desulfitobacterium hafniense
	VERSION AY692340.1 GI:53771772
	SEQ ID NO. 10:
	MFLTRRDPPLSSFWTKVQYQRLKELNASGEQLEMGFSDAL

	SRDRAFQGIEHQLMSQGKRHLEQLRTVKHRPALLELEEKL

	AKALHQQGFVQVVTPTIITKSALAKMTIGEDHPLFSQVFW

	LDGKKCLRPMLAPNLYTLWRELERLWDKPIRIFEIGTCYR

	KESQGAQHLNEFTMLNLTELGTPLEERHQRLEDMARWVLE

	AAGIREFELVTESSVVYGDTVDVMKGDLELASGAMGPHFL

	DEKWEIFDPWVGLGFGLERLLMIREGTQHVQSMARSLSYL

	DGVRLNIN

	>D. acefoxidans/1-277
	Desulfotomaculum acetoxidans DSM 771
	VERSION YP_003189614.1 GI:258513392
	SEQ ID NO. 11:
	AAALRGAGFVQVATPVILSKKLLGKMTITDEHALFSQVFW

	IEENKCLRPMLAPNLYYILKDLLRLWEKPVRIFEIGSCFR

	KESQGSNHLNEFTMLNLVEWGLPEEQRQKRISELAKLVMD

	ETGIDEYHLEHAESVVYGETVDVMHRDIELGSGALGPHFL

	DGRWGVVGPWVGIGFGLERLLMVEQGGQNVRSMGKSLTYL

	DGVRLNI

When the particular tRNA charging (aminoacylation) function has been provided by mutating the tRNA synthetase, then it may not be appropriate to simply use another wild-type tRNA sequence, for example one selected from the above. In this scenario, it will be important to preserve the same tRNA charging (aminoacylation) function. This is accomplished by transferring the mutation(s) in the exemplary tRNA synthetase into an alternate tRNA synthetase backbone, such as one selected from the above.
In this way it should be possible to transfer selected mutations to corresponding tRNA synthetase sequences such as corresponding pylS sequences from other organisms beyond exemplary M. barkeri and/or M. mazei sequences.
Target tRNA synthetase proteins/backbones, may be selected by alignment to known tRNA synthetases such as exemplary M. barkeri and/or M. mazei sequences.
This subject is now illustrated by reference to the pylS (pyrrolysine tRNA synthetase) sequences but the principles apply equally to the particular tRNA synthetase of interest.
For example, FIG. 6 provides an alignment of all PylS sequences. These can have a low overall % sequence identity. Thus it is important to study the sequence such as by aligning the sequence to known tRNA synthetases (rather than simply to use a low sequence identity score) to ensure that the sequence being used is indeed a tRNA synthetase.
Thus suitably when sequence identity is being considered, suitably it is considered across the tRNA synthetases as in FIG. 6 . Suitably the % identity may be as defined from FIG. 6 . FIG. 7 shows a diagram of sequence identities between the tRNA synthetases. Suitably the % identity may be as defined from FIG. 7 .
It may be useful to focus on the catalytic region. FIG. 8 aligns just the catalytic regions. The aim of this is to provide a tRNA catalytic region from which a high % identity can be defined to capture/identify backbone scaffolds suitable for accepting mutations transplanted in order to produce the same tRNA charging (aminoacylation) function, for example new or unnatural amino acid recognition.
Thus suitably when sequence identity is being considered, suitably it is considered across the catalytic region as in FIG. 8 . Suitably the % identity may be as defined from FIG. 8 . FIG. 9 shows a diagram of sequence identities between the catalytic regions. Suitably the % identity may be as defined from FIG. 9 .
‘Transferring’ or ‘transplanting’ mutations onto an alternate tRNA synthetase backbone can be accomplished by site directed mutagenesis of a nucleotide sequence encoding the tRNA synthetase backbone. This technique is well known in the art. Essentially the backbone pylS sequence is selected (for example using the active site alignment discussed above) and the selected mutations are transferred to (i.e. made in) the corresponding/homologous positions.
When particular amino acid residues are referred to using numeric addresses, unless otherwise apparent, the numbering is taken using MbPylRS (Methanosarcina barkeri pyrrolysyl-tRNA synthetase) amino acid sequence as the reference sequence (i.e. as encoded by the publicly available wild type Methanosarcina barkeri PylS gene Accession number Q46E77),

	SEQ ID NO. 12:
	MDKKPLDVLI SATGLWMSRT GTLHKIKHYE VSRSKIYIEM

	ACGDHLVVNN SRSCRTARAF RHHKYRKICK RCRVSDEDIN

	NFLTRSTEGK TSVKVKVVSA PKVKKAMPKS VSRAPKPLEN

	PVSAKASTDT SRSVPSPAKS TPNSPVPTSA PAPSLTRSQL

	DRVEALLSPE DKISLNIAKP FRELESELVT RRKNDFQRLY

	INDREDYLGK LERDITKFFV DRDFLEIKSP ILIPAEYVER

	MGINNDTELS KQIFRVDKNL CLRPMLAPTL YNYLRKLDRI

	LPDPIKIFEV GPCYRKESDG KEHLEEFTMV NFCQMGSGCT

	RENLESLIKE FLDYLEIDFE IVGDSCMVYG DILDIMHGDL

	ELSSAVVGPV PLDREWGIDK PWIGAGFGLE RLLKVMHGFK

	NIKRASRSES YYNGISTNL

This is to be used as is well understood in the art to locate the residue of interest. This is not always a strict counting exercise—attention must be paid to the context or alignment. For example, if the protein of interest is of a slightly different length, then location of the correct residue in that sequence corresponding to (for example) L266 may require the sequences to be aligned and the equivalent or corresponding residue picked, rather than simply taking the 266th residue of the sequence of interest. This is well within the ambit of the skilled reader.
Notation for mutations used herein is the standard in the art. For example L266M means that the amino acid corresponding to L at position 266 of the wild type sequence is replaced with M.
The transplantation of mutations between alternate tRNA backbones is now illustrated with reference to exemplary M. barkeri and M. mazei sequences, but the same principles apply equally to transplantation onto or from other backbones.
For example Mb AcKRS is an engineered synthetase for the incorporation of AcK

- Parental protein/backbone: M. barkeri PylS
- Mutations: L266V, L270I, Y271F, L274A, C317F
- Mb PCKRS: engineered synthetase for the incorporation of PCK
- Parental protein/backbone: M. barkeri PylS
- Mutations: M241F, A267S, Y271C, L274M

Synthetases with the same substrate specificities can be obtained by transplanting these mutations into M. mazei PylS. The sequence homology of the two synthetases can be seen in FIG. 10 . Thus the following synthetases may be generated by transplantation of the mutations from the Mb backbone onto the Mm tRNA backbone:

- Mm AcKRS introducing mutations L301V, L3051, Y306F, L309A, C348F into M. mazei PylS, and
- Mm PCKRS introducing mutations M276F, A302S, Y306C, L309M into M. mazei PylS.

Full length sequences of these exemplary transplanted mutation synthetases are given below.

	>Mb_PylS/1-419
	SEQ ID NO. 13:
	MDKKPLDVLISATGLWMSRTGTLHKIKHHEVSRSKIYIEM

	ACGDHLVVNNSRSCRTARAFRHHKYRKTCKRCRVSDEDIN

	NFLTRSTESKNSVKVRVVSAPKVKKAMPKSVSRAPKPLEN

	SVSAKASTNTSRSVPSPAKSTPNSSVPASAPAPSLTRSQL

	DRVEALLSPEDKISINMAKPFRELEPELVTRRKNDFQRLY

	TNDREDYLGKLERDITKFFVDRGFLEIKSPILIPAEYVER

	MGINNDTELSKQIFRVDKNLCLRPMLAPTLYNYLRKLDRI

	LPGPIKIFEVGPCYRKESDGKEHLEEFTMVNFCQMGSGCT

	RENLEALIKEFLDYLEIDFEIVGDSCMVYGDTLDIMHGDL

	ELSSAVVGPVSLDREWGIDKPWIGAGFGLERLLKVMHGFK

	NIKRASRSESYYNGISTNL

	>Mb_ACKRS/1-419
	SEQ ID NO. 14:
	MDKKPLDVLISATGLWMSRTGTLHKIKHHEVSRSKIYIEM

	ACGDHLVVNNSRSCRTARAFRHHKYRKTCKRCRVSGEDIN

	NFLTRSTESKNSVKVRVVSAPKVKKAMPKSVSRAPKPLEN

	SVSAKASTNTSRSVPSPAKSTPNSSVPASAPAPSLTRSQL

	DRVEALLSPEDKISLNMAKPFRELEPELVTRRKNDFQRLY

	TNDREDYLGKLERDITKFFVDRGFLEIKSPILIPAEYVER

	MGINNDTELSKQIFRVDKNLCLRPMVAPTIFNYARKLDRI

	LPGPIKIFEVGPCYRKESDGKEHLEEFTMVNFFQMGSGCT

	RENLEALIKEFLDYLEIDFEIVGDSCMVYGDTLDIMHGDL

	ELSSAVVGPVSLDREWGIDKPWIGAGFGLERLLKVMHGFK

	NIKRASRSESYYNGISTNL

	>Mb_PCKRS/1-419
	SEQ ID NO. 15:
	MDKKPLDVLISATGLWMSRTGTLHKIKHHEVSRSKIYIEM

	ACGDHLVVNNSRSCRTARAFRHHKYRKTCKRCRVSDEDIN

	NFLTRSTESKNSVKVRVVSAPKVKKAMPKSVSRAPKPLEN

	SVSAKASTNTSRSVPSPAKSTPNSSVPASAPAPSLTRSQL

	DRVEALLSPEDKISLNMAKPFRELEPELVTRRKNDFQRLY

	INDREDYLGKLERDITKFFVDRGFLEIKSPILIPAEYVER

	FGINNDTELSKQIFRVDKNLCLRPMLSPTLCNYMRKLDRI

	LPGPIKIFEVGPCYRKESDGKEHLEEFTMVNFCQMGSGCT

	RENLEALIKEFLDYLEIDFEIVGDSCMVYGDTLDIMHGDL

	ELSSAVVGPVSLDREWGIDKPWIGAGFGLERLLKVMHGFK

	NIKRASRSESYYNGISTNL

	>Mm_PyIS/1-454
	SEQ ID NO. 16:
	MDKKPLNTLISATGLWMSRIGTIHKIKHHEVSRSKIYIEM

	ACGDHLVVNNSRSSRTARALRHHKYRKTCKRCRVSDEDLN

	KFLTKANEDQTSVKVKVVSAPTRTKKAMPKSVARAPKPLE

	NTEAAQAQPSGSKFSPAIPVSTQESVSVPASVSTSISSIS

	TGATASALVKGNTNPITSMSAPVQASAPALTKSQTDRLEV

	LLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERE

	NYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDN

	DTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPI

	KIFEIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLE

	SIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGDLELSSA

	VVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRA

	ARSESYYNGISTNL

	>Mm_ACKRS/1-454
	SEQ ID NO. 17:
	MDKKPLNTLISATGLWMSRIGTIHKIKHHEVSRSKIYIEM

	ACGDHLVVNNSRSSRTARALRHHKYRKTCKRCRVSDEDLN

	KFLTKANEDQTSVKVKVVSAPTRIKKAMPKSVARAPKPLE

	NTEAAQAQPSGSKFSPAIPVSTQESVSVPASVSTSISSIS

	TGATASALVKGNTNPITSMSAPVQASAPALTKSQTDRLEV

	LLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERE

	NYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDN

	DTELSKQIFRVDKNFCLRPMVAPNIFNYARKLDRALPDPI

	KIFEIGPCYRKESDGKEHLEEFTMLNFFQMGSGCTRENLE

	SIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGDLELSSA

	VVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRA

	ARSESYYNGISTNL

	>Mm_PCKRS/1-454
	SEQ ID NO. 18:
	MDKKPLNTLISATGLWMSRTGTIHKIKHHEVSRSKIYIEM

	ACGDHLVVNNSRSSRTARALRHHKYRKTCKRCRVSDEDLN

	KFLTKANEDQTSVKVKVVSAPTRTKKAMPKSVARAPKPLE

	NTEAAQAQPSGSKFSPAIPVSTQESVSVPASVSTSISSIS

	TGATASALVKGNINPITSMSAPVQASAPALTKSQTDRLEV

	LLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERE

	NYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERFGIDN

	DTELSKQIFRVDKNFCLRPMLSPNLCNYMRKLDRALPDPI

	KIFEIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLE

	SIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGDLELSSA

	VVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRA

	ARSESYYNGISTNL

The same principle applies equally to other mutations and/or to other backbones.
Transplanted polypeptides produced in this manner should advantageously be tested to ensure that the desired function/substrate specificities have been preserved.
Polynucleotides encoding the polypeptide of interest for the method described above can be incorporated into a recombinant replicable vector. The vector may be used to replicate the nucleic acid in a compatible host cell. Thus in a further embodiment, the invention provides a method of making polynucleotides of the invention by introducing a polynucleotide of the invention into a replicable vector, introducing the vector into a compatible host cell, and growing the host cell under conditions which bring about replication of the vector. The vector may be recovered from the host cell. Suitable host cells include bacteria such as E. coli.
Preferably, a polynucleotide of the invention in a vector is operably linked to a control sequence that is capable of providing for the expression of the coding sequence by the host cell, i.e. the vector is an expression vector. The term “operably linked” means that the components described are in a relationship permitting them to function in their intended manner. A regulatory sequence “operably linked” to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under condition compatible with the control sequences.
Vectors of the invention may be transformed or transfected into a suitable host cell as described to provide for expression of a protein of the invention. This process may comprise culturing a host cell transformed with an expression vector as described above under conditions to provide for expression by the vector of a coding sequence encoding the protein, and optionally recovering the expressed protein.
The vectors may be for example, plasmid or virus vectors provided with an origin of replication, optionally a promoter for the expression of the said polynucleotide and optionally a regulator of the promoter. The vectors may contain one or more selectable marker genes, for example an ampicillin resistance gene in the case of a bacterial plasmid. Vectors may be used, for example, to transfect or transform a host cell. Control sequences operably linked to sequences encoding the protein of the invention include promoters/enhancers and other expression regulation signals. These control sequences may be selected to be compatible with the host cell for which the expression vector is designed to be used in. The term promoter is well-known in the art and encompasses nucleic acid regions ranging in size and complexity from minimal promoters to promoters including upstream elements and enhancers.
Another aspect of the invention is a method, such as an in vitro method, of incorporating the BCN containing amino acid(s) genetically and site-specifically into the protein of choice, suitably in a eukaryotic cell. One advantage of incorporating genetically by said method is that it obviates the need to deliver the proteins comprising the BCN amino acid into a cell once formed, since in this embodiment they may be synthesised directly in the target cell. The method comprises the following steps:

- i) introducing, or replacing a specific codon with, an orthogonal codon such as an amber codon at the desired site in the nucleotide sequence encoding the protein
- ii) introducing an expression system of orthogonal tRNA synthetase/tRNA pair in the cell, such as a pyrollysyl-tRNA synthetase/tRNA pair
- iii) growing the cells in a medium with the BCN containing amino acid according to the invention.

Step (i) entails or replacing a specific codon with an orthogonal codon such as an amber codon at the desired site in the genetic sequence of the protein. This can be achieved by simply introducing a construct, such as a plasmid, with the nucleotide sequence encoding the protein, wherein the site where the BCN containing amino acid is desired to be introduced/replaced is altered to comprise an orthogonal codon such as an amber codon. This is well within the person skilled in the art's ability and examples of such are given here below.
Step (ii) requires an orthogonal expression system to specifically incorporate the BCN containing amino add at the desired location (e.g. the amber codon). Thus a specific orthogonal tRNA synthetase such as an orthogonal pyrollysyl-tRNA synthetase and a specific corresponding orthogonal tRNA pair which are together capable of charging said tRNA with the BCN containing amino acid are required. Examples of these are provided herein.

Protein Expression and Purification

Host cells comprising polynucleotides of the invention may be used to express proteins of the invention. Host cells may be cultured under suitable conditions which allow expression of the proteins of the invention. Expression of the proteins of the invention may be constitutive such that they are continually produced, or inducible, requiring a stimulus to initiate expression. In the case of inducible expression, protein production can be initiated when required by, for example, addition of an inducer substance to the culture medium, for example dexamethasone or IPTG.
Proteins of the invention can be extracted from host cells by a variety of techniques known in the art, including enzymatic, chemical and/or osmotic lysis and physical disruption.
Proteins of the invention can be purified by standard techniques known in the art such as preparative chromatography, affinity purification or any other suitable technique.

Definitions

The term ‘comprises’ (comprise, comprising) should be understood to have its normal meaning in the art, i.e. that the stated feature or group of features is included, but that the term does not exclude any other stated feature or group of features from also being present.

BRIEF DESCRIPTION OF THE FIGURES

The application contains al least one drawing executed in color. Copies of this patent or patent application publication with color drawings will be provided by the Office upon request and payment of the necessary fee.

FIG. 1 shows structural formulae of unnatural amino acids 1 to 5 and tetrazine derivatives (6-17) used in this study. TAMRA-X, Bodipy TMR-X, Bodipy-FL and CFDA are common names for fluorophores; their structural formulae are shown in Supplementary Figure S4).

FIG. 2 shows kinetic and spectrometric characterization of the BCN-tetrazine reaction. a) Stopped flow kinetics of the reaction; the inset shows the conjugation of tetrazine 7 to 5-norbornen-2-ol (Nor), note different timescales; conditions: c₇=0.05 mM, c_8CN=c_Nor=5 mM in McOH/H₂O (55/45), 25° C. b) The second order rate constant k for the reaction of 7 and BCN. c) The fluorogenic reaction of 11 with BCN.

FIG. 3 shows efficient, genetically encoded incorporation of unnatural amino acids using the BCNRS/tRNA_CUAor TCORS/tRNA_CUApair in E. coli, a) Amino, acid dependent overexpression of sfGFP-His₆bearing an amber codon at position 150. The expressed protein was detected in lysates using an anti-His₆antibody. b) Coomassie stained gel showing purified proteins. c-e) Mass spectrometry of amino acid incorporation: sfGFP-1-His₆, found: 28017.54 Da, calculated: 28017.62 Da; sfGFP-2-His₆, found: 27993.36 Da, calculated: 27992.82 Da; sfGFP-His₆produced in the presence of 3, as described in the text, found: 28019.34 Da, calculated: 28019.63 Da. Smaller grey peaks in all mass spectra denote a loss of 131 Da, which corresponds to the proteolytic cleavage of the N-terminal Methionine.

FIG. 4 shows rapid and specific labeling of recombinant proteins with tetrazine-fluorophores. a) Specific labeling of sfGFP bearing 1, 2 and 4 with tetrazine-dye conjugate 11 (10 eq) demonstrated by SDS-PAGE and in-gel fluorescence. For sfGFP-His₆produced in the presence of 3 only very faint, sub-stoichiometric labeling is visible. b) Quantitative labeling of sfGFP-1 with 11 demonstrated by ESI-MS (before bioconjugation (blue spectrum, found: 28018.1±2 Da, calculated: 28017.6 Da) and after bioconjugation (red spectrum, found 28824.2±2 Da, calculated: 28823.2 Da)). c) Quantitative labeling of sfGFP-2 with 11 demonstrated by ESI-MS (before bioconjugation (blue spectrum, found: 27993.2±2 Da, calculated: 27992.8 Da) and after bioconjugation (red spectrum, found 28799.4±2 Da, calculated: 28799.1 Da)). d) No labeling of sfGFP-His₆(expressed in the presence of 3) with 11 could be detected by MS. e) Very rapid labeling of proteins containing site-specifically incorporated

amino acid

1 and 2. sfGFP-1 (left) and sfGFP-2 (middle) are quantitatively labeled with 11 in the few seconds it takes to load the gel while it takes 1 h to completely label sfGFP-4 under the same conditions (right).

FIG. 5 shows site specific incorporation of 1 and 2 into proteins in mammalian cells and the rapid and specific labeling of cell surface and intracellular mammalian proteins with 11. a) Western blots demonstrate that the expression of full length mCherry(TAG)eGFP-HA is dependent on the presence of 1 or 2 and tRNA_CUA. BCNRS, TCORS are FLAG tagged. b) Specific and ultra-rapid labeling of a cell surface protein in live mammalian cells. EGFR-

GFP bearing

1, 2 or 5 at position 128 is visible as green fluorescence at the membrane of transfected cells (left panels). Treatment of cells with 11 (400 nM) leads to selective labeling of EGFR that contains 1 or 2 (middle panels). Right panels show merged green and red fluorescence images, DIC=differential interference contrast. Cells were imaged 2 minutes after the addition of 11. c) Specific and rapid labeling of a nuclear protein in live mammalian cells. Jun-1-mCherry is visible as red fluorescence in the nuclei of transfected cells (left panels). Treatment of cells with the cell permeable tetrazine dye 17 (200 nM) leads to selective labeling of jun-1-mCherry (middle panel). Right panels show merged red and green fluorescence. No labeling was observed for cells bearing jun-5-mCherry.

FIG. 6 shows alignment of PylS sequences.

FIG. 7 shows sequence identity of PylS sequences.

FIG. 8 shows alignment of the catalytic domain of PylS sequences (from 350 to 480; numbering from alignment of FIG. 6 ).

FIG. 9 shows sequence identity of the catalytic domains of PylS sequences.

FIG. 10 shows alignment of synthetases with transplanted mutations based on M. barkeri PylS or M. mazei PylS. The red asterisks indicate the mutated positions.

FIG. 11 shows scheme 1. We demonstrate the synthesis, genetic encoding and fluorogenic labeling of

unnatural amino acids

1 and 2 in vitro, in E. coli and in mammalian cells.

FIG. 12 (Supplementary Figure S1) shows LC/MS traces (254 nm) showing the formation of pyridazine products (6-BCN, 7-BCN, 9-BCN, 8-BCN) from reaction of the corresponding tetrazines (6, 7, 9 and 8) with 2 equivalents of BCN (exo/endo mixture—4/1) in McOH. All masses are given in Daltons. The HPLC traces were taken after incubating the reactions for 10 to 30 minutes at room temperature. The overall yield for conversion to pyridazine products was >98%.

FIG. 13 (Supplementary Figure S2) shows determination of rate constants k for the reaction of various tetrazines with BCN by UV-spectroscopy using a stopped-flow device. (a) Response of the UV absorbance at 320 nm of compound 6 upon BCN addition (100 eq=5 mM); by fitting the data to a single exponential equation, k′ values were determined (left panel); each measurement was carried out three to five times and the mean of the observed rates k′ was plotted against the concentration of BCN to obtain the rate constant k from the slope of the plot. For all four tetrazines complete measurement sets were done in duplicate (middle and right panel) and the mean of values is reported in Supplementary Table 1. (b-d) same as (a) for

tetrazines

7, 9 and 8. Conditions: c_tetrazine=0.05 mM in 9/1 H₂O/MeOH, c_BCN=0.5 to 5 mM in McOH, resulting in a final 55/45 McOH/H₂O mixture. All experiments were recorded at 25° C.

FIG. 14 (Supplementary Figure S3) shows determination of rate constants k for the reaction of

tetrazines

6 and 7 with TCO by UV-spectroscopy using a stopped-flow device. (a) Response of the UV absorbance at 320 nm of compound 6 upon TCO addition (100 eq=5 mM); by fitting the data to the sum of two single exponential equations, k′ values for the fast single exponential equations were determined (left panel); each measurement was carried out three to five times and observed rates k′ were plotted against the concentration of TCO to obtain the rate constant k from the slope of the plot. For both tetrazines complete measurement sets were done at least in duplicate (middle and right panel) and the mean of values is reported in Supplementary Table 1. (b) same as (a) for tetrazine 7. Conditions: c_tetrazine=0.05 mM in 9/1 H₂O/MeOH, cr_CO=0.5 to 5 mM in McOH, resulting in a final 55/45 McOH/H₂O mixture. All experiments were recorded at 25° C.

FIG. 15 (Supplementary Figure S4) shows structural formulae of various tetrazine-fluorophores used in this study. Details on synthesis and characterization of these tetrazine-fluorophores can be found in reference 2.

FIG. 16 (Supplementary Figure S5) shows “Turn on” fluorescence of tetrazine-fluorophores upon reaction with 9-hydroxymethylbicyclo[6.1.0]nonyne (BCN). A 2microM solution of the corresponding tetrazine-fluorophore in water (2 mM in DMSO) was reacted with 300 equivalents of BCN. Emission spectra were recorded before and 30 min after the addition of BCN. Excitation wavelengths: TAMRA-dyes and Bodipy-TMR-X: 550 nm; Bodipy-FL: 490 nm.

FIG. 17 (Supplementary Figure S6) shows amino acid dependent expression of sfGFP-His₆bearing an amber codon at position 150. The expressed protein was detected in lysates using an anti-His₆antibody. Using purified exo or endo diastereomers of amino acid 1 demonstrated that the exo form is preferentially incorporated into sfGFP by BCNRS/tRNA_CUA.

FIG. 18 (Supplementary Figure S7) shows LC-MS characterization of the labelling reaction of sfGFP-1 with various tetrazines. Black peaks denote the found mass of sfGFP-1 before labelling, colored peaks the found masses after reaction of sfGFP-1 with 6, 7, 9 and 8. All masses are given in Daltons. Labelling with all tetrazines is specific and quantitative. Reaction conditions: to a ˜10 □M solution of sfGFP-1 (in 20 mM Tris-HCl, 100 mM NaCl, 2 mM EDTA, pH 7.4) 10 equivalents of the corresponding tetrazine (1 mM stock solution in methanol) were added and the reaction mixture incubated for 10 to 30 minutes at room temperature.

FIG. 19 (Supplementary Figure S8) shows LC-MS shows specific and quantitative labelling of sfGFP-1 with tetrazine fluorophore conjugates 12, 16, 13 and 14. Red peaks denote the found mass of sfGFP-1 before labelling, colored peaks the found masses after reaction of sfGFP-1 with 12 (a), 16 (b), 13 (c) and 14 (d). Expected and found mass values are given in Daltons. Labelling with all tetrazine-fluorophores is specific and quantitative. Reaction conditions: to a ˜10 □M solution of sfGFP-1 (in 20 mM Tris-HCl, 100 mM NaCl, 2 mM EDTA, pH 7.4) 10 equivalents of the corresponding tetrazine dye (2 mM stock solution in DMSO) were added and the reaction mixture incubated for 10 to 30 minutes at room temperature.

FIG. 20 (Supplementary Figure S9) shows specificity of

labeling

1 and 2 in sfGFP versus the E. coli proteome. The coomassie stained gel shows proteins from E. coli producing sfGFP in the presence of the indicated concentration of

unnatural amino acids

1, 2, 3 (both exo and endo diastereomers) and 5. In gel fluorescence gels show specific labeling with tetrazine-dye conjugate 11. Though

amino acids

1, 2 and 3-exo are incorporated at a similar level (as judged from coomassie stained gels and western blots), we observe only very faint, sub-stoichiometric labeling of sfGFP produced in the presence of 3-exo and 3-endo. These observations are consistent with the in vivo conversion of a fraction of the trans-alkene in 3 to its cis-isomer.

FIG. 21 (Supplementary Figure S10) shows specificity of labeling 1 in sfGFP versus the E. coli proteome. Lanes 1-5: Coomassie stained gel showing proteins from E. coli producing sfGFP in the presence of the indicated concentration of

unnatural amino acids

1 and 5. Lanes 6-10: The expressed protein was detected in lysates using an anti-His6 antibody. Lanes 11-15: fluorescence images of protein labeled with the indicated fluorophore 11.

FIG. 22 (Supplementary Figure S11) shows specific and ultra-rapid labelling of EGFR-GFP with tetrazine-fluorophore conjugate 11 for 2 minutes. EGFR-GFP bearing 1 at position 128 is visible as green fluorescence at the membrane of transfected cells (left panels). Treatments of cells with 11 (400 nM) leads to selective labelling of EGFR-GFP containing 1 (middle panels). Right panels show merged green and red fluorescence images, DIC=differential interference contrast. Cells were imaged 2 minutes after addition of 11. No labelling was observed for cells in the same sample that did not express EGFR-GFP, and cells bearing EGFR-5-GFP were not labeled with 11.

FIG. 23 (Supplementary Figure S12) shows specific and ultra-rapid labelling of EGFR-GFP with tetrazine-fluorophore conjugate 11 for 5 minutes. EGFR-GFP bearing 1 at position 128 is visible as green fluorescence at the membrane of transfected cells (left panels). Treatments of cells with 11 (400 nM) leads to selective labelling of EGFR-GFP containing 1 (middle panels). Right panels show merged green and red fluorescence images, DIC=differential interference contrast. Cells were imaged 5 minutes after addition of 11. No labelling was observed for cells in the same sample that did not express EGFR-GFP, and cells bearing EGFR-5-GFP were not labeled with 11.

FIG. 24 (Supplementary Figure S13) shows specific and ultra-rapid labelling of EGFR-GFP with tetrazine-fluorophore conjugate 11 for 10 minutes. EGFR-GFP bearing 1 at position 128 is visible as green fluorescence at the membrane of transfected cells (left panels). Treatments of cells with 11 (400 nM) leads to selective labelling of EGFR-GFP containing 1 (middle panels). Right panels show merged green and red fluorescence images, DIC=differential interference contrast. Cells were imaged 10 minutes after addition of 11. No labelling was observed for cells in the same sample that did not express EGFR-GFP, and cells bearing EGFR-5-GFP were not labeled with 11.

FIG. 25 (Supplementary Figure S14) shows that in contrast to the ultra-rapid labelling of EGFR-GFP containing amino acid 1, it took 2 hours to specifically label cells bearing EGFR-4-GFP with tetrazine-fluorophore conjugate 11.²

EGFR-GFP bearing 4 at position 128 is visible as green fluorescence at the membrane of transfected cells (left panels). Treatments of cells with 11 (200 nM) leads to labelling of EGFR-GFP containing 4 (middle panels). Right panels show merged green and red fluorescence images, DIC=differential interference contrast. Cells were imaged 2 hours after addition of 11.

FIG. 26 (Supplementary Figure S15) shows specific and ultra-rapid labelling of EGFR-GFP with tetrazine-fluorophore conjugate 11 for 2 minutes. EGFR-GFP bearing 2 at position 128 is visible as green fluorescence at the membrane of transfected cells (left panels). Treatments of cells with 11 (400 nM) leads to selective labelling of EGFR-GFP containing 2 (middle panels). Right panels show merged green and red fluorescence images, DIC=differential interference contrast. Cells were imaged 2 minutes after addition of 11. No labelling was observed for cells in the same sample that did not express EGFR-GFP, and cells bearing EGFR-5-GFP were not labeled with 11.

FIG. 27 (Supplementary Figure S16) shows specific and ultra-rapid labelling of EGFR-GFP with tetrazine-fluorophore conjugate 11 for 5 minutes. EGFR-GFP bearing 2 at position 128 is visible as green fluorescence at the membrane of transfected cells (left panels). Treatments of cells with 11 (400 nM) leads to selective labelling of EGFR-GFP containing 2 (middle panels). Right panels show merged green and red fluorescence images, DIC=differential interference contrast. Cells were imaged 5 minutes after addition of 11. No labelling was observed for cells in the same sample that did not express EGFR-GFP, and cells bearing EGFR-5-GFP were not labeled with 11.

FIG. 28 (Supplementary Figure S17) shows site specific incorporation of 3 in mammalian cells and the labeling of EGFR-GFP with tetrazine-fluorophore conjugate 11 for 30 and 60 minutes. a) Western blots demonstrate that the expression of full length mCherry(TAG)eGFP-HA is dependent on the presence of 3 or 5 and tRNA_CUA. BCNRS and PylRS are FLAG tagged. B and c) EGFR-GFP in the presence 3 at position 128 is visible as green fluorescence at the membrane of transfected cells (left panels). Treatments of cells with 11 (400 nM) leads to faint, but measurable labelling of EGFR-GFP containing 3 (middle panels) This observation is consistent with the isomerization of the trans-alkene bond to its cis form of a fraction of 3 in mammalian cells. Right panels show merged green and red fluorescence images, DIC=differential interference contrast. Cells were imaged 30 or 60 minutes after addition of 11, No labelling was observed for cells in the same sample that did not express EGFR-GFP.

FIG. 29 (Supplementary Figure S18) shows specific and ultra-rapid labelling of a nuclear protein in live mammalian cells. Jun-1-mCherry is visible as red fluorescence in the nuclei of transfected cells (left panels). Treatment of cells with the cell permeable tetrazine dye 17 (200 nM) leads to selective labeling of jun-1-mCherry (middle panel). Right panels show merged red and green fluorescence. DIC=differential interference contrast. Cells were imaged 15 minutes after addition of 11. No labelling was observed for cells in the same sample that did not express jun-mCherry, and cells bearing jun-5-mCherry were not labeled with 11

The invention is now described by way of example. These examples are intended to be illustrative, and are not intended to limit the appended claims.

EXAMPLES

Here we develop a rapid and fluorogenic reaction between tetrazines and BCN and demonstrate the genetic encoding of both BCN and transcyclooctene containing amino acids 1 and 2 in E. coli and mammalian cells. We show the specific and rapid labeling of proteins in E. coli and in live mammalian cells with tetrazine probes, and explicitly demonstrate the advantages of the approach with respect to previously reported bioorthogonal labeling strategies (FIG. 11 —Scheme 1).

Example 1: Chemistry and Addition Reactions

The rate constants for the reactions of various dienophiles (BCN, TCO (trans-cyclooctene-4-ol) and sTCO (bicyclo[6.1.0]non-4-ene-9-ylmethanol)) with tetrazines have been determined^3-5,9,11. However, in many cases, researchers have used different tetrazines, solvent systems or measurement methods making it challenging to quantitatively compare the reactivity of each dienophile with tetrazines of interest. Our initial experiments confirmed that the rates for the reactions of each dienophile with tetrazine 6 (FIG. 1 ) were too fast to study by manual mixing under pseudo first order conditions. We therefore turned to stopped-flow techniques to directly determine the pseudo first order rate constants for these reactions. By following the exponential decay in absorbance at 320 nm upon reaction with a 10- to 100-fold excess of BCN in a methanol/water (55/45) mixture we determined the rate constants for the reaction of BCN with 6 and 7 as 437 M⁻¹s⁻¹(+/−13) and 1245 M⁻¹s⁻¹(+/−45), respectively. LC-MS and NMR confirm the formation of the expected products (Supplementary Information and Supplementary Figure 1). Under the same conditions we determined the rate constant of TCO with 6 and 7 as 5235 M⁻¹s⁻¹(+/−258) and 17248 M⁻¹s⁻¹(+/−3132), respectively. These data demonstrate that the reaction between BCN and 6 is approximately 1000 times faster than the reaction between 5-norbornene-2-ol and 6⁷, while the TCO rate is approximately 10-15 times faster than the BCN rate. The sTCO rate was too fast to be measured accurately by stopped flow techniques and we estimate that it is at least 50 times faster than the TCO rate. Similar rate accelerations were observed for the reaction of BCN with tetrazines 8 and 9 (FIG. 1 , FIGS. 2 a and 2 b , Supplementary Table 1 and Supplementary Figures S2 and S3).


Tetrazine	BCN k₂[M⁻¹s⁻¹]ª	Nor k₂[M⁻¹s⁻¹]ª	TCO k₂[M⁻¹s⁻¹]^a

6	437 ± 13	0.47 ± 0.0069	5235 ± 258
7	1245 ± 45	1.70 ± 0.048	17248 ± 3132
9	80	0.15	n.d.
8	2672 ± 95	5.00 ± 0.096	n.d.

Supplementary Table 1: Rate constants k for the reaction of various tetrazines (6, 7, 9 and 8) with BCN and TCO at 25° C. measured under pseudo first order conditions using a stopped-flow device in comparison to rate constants for the reaction of the same tetrazines with 5-norbornene-2-ol at 21° C.²Values were determined from at least two independent measurements. Solvent system: 55/45 methanol/water. The cycloaddition reaction of BCN to tetrazines is 500 to 1000 times faster than the one of 5-norbornene-2-ol, the reaction between TCO and tetrazines is 10 to 15 times faster than the one between BCN and tetrazines.

Several tetrazine fluorophore conjugates, including 11, 13, 14 and 16 (FIG. 1 , Supplementary Figure S4) are substantially quenched with respect to the free fluorophore, an observation that results from energy transfer of the fluorophore's emission to a proximal tetrazine chromophore with an absorption maximum between 510 and 530 nm^7,18. We find that the reaction of BCN with tetrazine fluorophore conjugates 11, 13, 14 and 16 leads to a 5-10 fold increase in fluorescence, suggesting that the formation of the pyridazine product efficiently relieves fluorophore quenching (FIG. 2 c and Supplementary Figure S5). The fluorogenic reaction between BCN and these tetrazines, like the reaction between strained alkenes and these tetrazines^7,18, is advantageous for imaging experiments since it maximizes the labeling signal while minimizing fluorescence arising from the free tetrazine fluorophore.

Example 2: Amino Acid Design

Next, we aimed to design, synthesize and genetically encode amino acids bearing BCN, TCO and sTCO for site-specific protein labeling with a diverse range of probes both in vitro and in cells. The Pyrrolysyl-tRNA synthetase (PylRS)/tRNA_CUApairs from Methanosarcina species, including M. barkeri (Mb) and M. mazei (Mm), and their evolved derivatives have been used to direct the site-specific incorporation of a growing list of structurally diverse unnatural amino acids in response to the amber codon^19-26. The PylRS/tRNA_CUApair is emerging as perhaps the most versatile system for incorporating unnatural amino acids into proteins since it is orthogonal in a range of hosts, allowing synthetases evolved in E. coli to be used for genetic code expansion in a growing list of cells and organisms, including: E. coli, Salmonella typhimurium, yeast, human cells and C. elegans ^7,27-31. We designed the unnatural amino acids 1, 2 and 3 (FIG. 1 ) with the goal of incorporating them into proteins using the PylRS/tRNA_CUApair or an evolved derivative. The amino acids were synthesized as described in the Supplementary Information.

Example 3: Genetic Incorporation into Polypeptides and tRNA Synthetases

We screened the MbPylRS/tRNA_CUApair along with a panel of mutants of MbPylRS, previously generated in our laboratory for the site-specific incorporation of diverse unnatural amino acids into proteins, for their ability to direct the incorporation of 1, 2 and 3 in response to an amber codon introduced at position 150 in a C-terminally hexahistidine-(His₆) tagged superfolder green fluorescent protein (sfGFP). The MbPylRS/tRNA_CUApair did not direct the incorporation of any of the unnatural amino acids tested, as judged by western blot against the C-terminal His₆tag. However, cells containing a mutant of MbPylRS, containing three amino acid substitutions Y271M, L274G, C313³²in the enzyme active site (which we named BCN-tRNA synthetase, BCNRS), and a plasmid that encodes MbtRNA_CUAand sfGFP-His₆with an amber codon at position 150 (psfGFP150TAGPylT-His₆) led to amino acid dependent synthesis of full length sfGFP-His₆, as judged by anti-His₆western blot and coomassie staining (FIG. 3 a ). Additional protein expression experiments using 1, and its endo isomer demonstrated that the exo form is preferentially incorporated into proteins by BCNRS/tRNA_CUA(Supplementary Figure S6). We found an additional synthetase mutant, bearing the mutations Y271A, L274M and C313A³², which we named TCO-tRNA synthetase, TCORS. The TCORS/tRNA_CUApair led to amino acid dependent synthesis of sfGFP from psfGFP150TAGPylT-His₆in the presence of 2. Finally we found that both the BCNRS/tRNA_CUApair as well as the TCORS/tRNA_CUApair led to amino acid dependent synthesis of sfGFP from psfGFP150TAGPylT-His₆in the presence of 3. For each amino acid sfGFP was isolated in good yield after His-tag and gel filtration purification (6-12 mg per L of culture, FIG. 3 b ). This is comparable to the yields obtained for other well-incorporated unnatural amino acids, including 5. Electrospray ionization mass spectrometry (ESI-MS) of sfGFP produced from psfGFP150TAGPylT-His₆in the presence of each unnatural amino acid is consistent with their site-specific incorporation (FIG. 3 c-3 e ).

Example 4: Site-Specific Incorporation

To demonstrate that the tetrazine-dye-probes react efficiently and specifically with recombinant proteins that bear site-specifically incorporated 1 we labeled purified sfGFP-1-His₆with 10 equivalents of tetrazine fluorophore conjugate 11 for 1 hour at room temperature. SDS-page and ESI-MS analysis confirmed quantitative labeling of sfGFP containing 1 (FIGS. 4 a and 4 b ). Control experiments demonstrated that sfGFP-4 is labeled under the same conditions used to label sfGFP-1, and that no non-specific labeling is detected with sfGFP-5. ESI-MS demonstrates that sfGFP-1 can be efficiently and specifically derivatized with a range of tetrazines 6, 7, 8 and 9 (Supplementary Figure S7), and with tetrazine fluorophore conjugates 12, 13, 14 and 16 (Supplementary Figure S8). We also demonstrated that purified sfGFP-2-His₆can be quantitatively labeled with tetrazine fluorophore 11 (FIGS. 4 a and 4 c ). Interestingly we observe only very faint labeling of sfGFP-His₆purified from cells expressing the TCORS/tRNA_CUAand psfGFP150TAGPylT-His₆and grown in the presence of 3 (FIGS. 4 a and 4 d ) and sub-stoichiometric labeling of this protein prior to purification (Supplementary Figure S9). Since the sfGFP expressed in the presence of 3 has a mass corresponding to the incorporation of 3, these observations are consistent with the in vivo conversion of a fraction of the trans-alkene in 3 to its unreactive cis isomer. This isomerization is known to occur in the presence of thiols.⁴

Example 5: Specificity and Selectivity of Reactions

To further demonstrate that the reaction between BCN and various tetrazine-based dyes is not only highly efficient and specific, but also highly selective within a cellular context, we performed the reaction on E. coli expressing sfGFP-1-His₆(Supplementary Figure S10). Cells expressing sfGFP-1 at a range of levels (controlled by adjusting the concentration of 1 added to cells) were harvested 4 hours after induction of protein expression, washed with PBS and incubated with tetrazine dye 11 for 30 min at room temperature. After adding an excess of BCN in order to quench non-reacted tetrazine-dye, the cells were lysed and the reaction mixtures were analyzed. In-gel fluorescence demonstrated specific labeling of recombinant sfGFP bearing 1 with tetrazine-conjugated TAMRA dye 11. While many proteins in the lysates were present at a comparable abundance to sfGFP-1 we observe very little background labeling, suggesting that the reaction is specific with respect to the E. coli proteome.

Example 6: Speed of Labelling

To investigate whether the rate of reaction for the BCN- and TCO-tetrazine cycloadditions observed on small molecules translates into exceptionally rapid protein labeling we compared the labeling of purified sfGFP bearing 1, 2 or 4 with 10 equivalents of tetrazine-fluorophore conjugate 11. In-gel fluorescence imaging of the labeling reaction as a function of time (FIG. 4 e ) indicates that the reaction of sfGFP-4 reaches completion in approximately 1 h. In contrast the labeling of sfGFP-1 and sfGFP-2 was complete within the few seconds it took to measure the first time point, demonstrating that the rate acceleration of the BCN- and TCO-tetrazine reaction translates into much more rapid protein labeling.

Example 7: Application to Mammalian Cells

To demonstrate the incorporation of amino acids 1 and 2 in mammalian cells we created mammalian optimized versions of BCNRS and TCORS by transplanting the mutations that allow the incorporation of 1 or 2 into a mammalian optimized MbPylRS. By western blot we demonstrated that both 1 and 2 can be genetically encoded with high efficiency into proteins in mammalian cells using the BCNRS/tRNA_CUApair or TCORS/tRNA_CUA(FIG. 5 a ).
To investigate whether the rapid BCN-tetrazine ligation provides advantages for site-specifically labeling proteins on mammalian cells we expressed an epidermal growth factor receptor (EGFR)-green fluorescent protein (GFP) fusion bearing an amber codon at position 128 (EGFR(128TAG)GFP) in HEK-293 cells containing the BCNRS/tRNA_CUApair, cultured in the presence of 1 (0.5 mM). Full-length EGFR-1-GFP was produced in the presence of 1 resulting in bright green fluorescence at the cell membrane. To label 1 at position 128 of EGFR, which is on the extracellular domain of the receptor, with tetrazine-fluorophore conjugates we incubated cells with 11 (400 nM), changed the media and imaged the red fluorescence arising from TAMRA labeling as well as the green fluorescence arising from expression of full-length EGFR-GFP. TAMRA fluorescence co-localized nicely with cell-surface EGFR-GFP fluorescence. Clear labeling of cells that bear EGFR-1-GFP was observed within 2 minutes, the first time point we could measure; additional time points demonstrated that labeling was saturated within 2 minutes (FIG. 5 b and Supplementary Figures S11-S14); similar results were obtained with tetrazine fluorophore 12. Incorporation of 2 into the EGFR-GFP fusion led to similarly rapid and efficient labeling with tetrazine fluorophore 11 (FIG. 5 b and Supplementary Figure S15-S16). In contrast it took 2 hours before we observed any specific labeling of cells bearing EGFR-1-GFP under identical conditions (Supplementary Figure S14)⁷. In control experiments we observed no labeling for cells bearing EGFR-5-GFP and no non-specific labeling was detected for cells that did not express EGFR-GFP. We observe weak but measureable labeling of EGFR-GFP expressed in HEK 293 cells from (EGFR(128TAG)GFP) in the presence of the BCNRS/tRNA_CUApair and 3 (Supplementary Figure S17). These observations are consistent with the isomerization of a fraction of 3 in mammalian cells, and with our observations in E. coli.
To demonstrate the rapid labeling of an intracellular protein in mammalian cells we expressed a transcription factor, jun, with a C-terminal mCherry fusion from a gene bearing an amber codon in the linker between JunB (jun) and mCherry. In the presence of amino acid 1 and the BCNKRS/tRNA_CUApair the jun-1-mCherry protein was produced in HEK cells and, as expected, localized to the nuclei of cells (FIG. 5 c and Supplementary Figure S18). Labeling with a cell permeable diacetyl fluorescein tetrazine conjugate (200 nM) resulted in green fluorescence that co-localizes nicely with the mCherry signal at the first time point analyzed (15 min labeling followed by 90 min washing). No specific labeling was observed in non-transfected cells in the same sample or in control cells expressing jun-5-mCherry, further confirming the specificity of intracellular labeling.

Supplementary Examples

Protein Expression and Purification

To express sfGFP with incorporated unnatural amino acid 1, we transformed E. coli DH10B cells with pBKBCNRS (which encodes MbBCNRS) and psfGFP150TAGPylT-His₆(which encodes MbtRNA_CUAand a C-terminally hexahistidine tagged sfGFP gene with an amber codon at position 150). Cells were recovered in 1 ml of S.O.B media (supplemented with 0.2% glucose) for 1 h at 37° C., before incubation (16 h, 37° C., 230 r.p.m) in 100 ml of LB containing ampicillin (100 μg/mL) and tetracycline (25 μg/mL). 20 ml of this overnight culture was used to inoculate 1 L of LB supplemented with ampicillin (50 μg/mL) and tetracycline (12 μg/mL) and incubated at 37° C. At OD₆₀₀=0.4 to 0.5, a solution of 1 in H₂O was added to a final concentration of 2 mM. After 30 min, protein expression was induced by the addition of arabinose to a final concentration of 0.2%. After 3 h of induction, cells were harvested by centrifugation and frozen at −80° C. until required. Cells were thawed on ice and suspended in 30 ml of lysis buffer (10 mM Tris-HCl, 20 mM imidazole, 200 mM NaCl, pH 8, 1 mM phenylmethanesulfonylfluoride, 1 mg/mL lysozyme, 100 μg/mL DNaseA, Roche protease inhibitor). Proteins were extracted by sonication at 4° C. The extract was clarified by centrifugation (20 min, 21.000 g, 4° C.), 600 μL of Ni²⁺-NTA beads (Qiagen) were added to the extract and the mixture was incubated with agitation for 1 h at 4° C. Beads were collected by centrifugation (10 min, 1000 g). The beads were three times resuspended in 30 mL wash buffer (20 mM Tris-HCl, 30 mM imidazole, 300 mM NaCl, pH 8) and spun down at 1000 g. Subsequently, the beads were resuspended in 10 mL of wash buffer and transferred to a column. The protein was eluted with 3 ml of wash buffer supplemented with 200 mM imidazole and further purified by size-exclusion chromatography employing a HiLoad 16/60 Superdex 75 Prep Grade column (GE Life Sciences) at a flow rate of 1 mL/min (buffer: 20 mM Tris-HCl, 100 mM NaCl, 2 mM EDTA, pH 7.4). Fractions containing the protein were pooled and concentrated with an Amicon Ultra-15 3 kDa MWCO centrifugal filter device (Millipore). Purified proteins were analyzed by 4-12% SDS-PAGE and their mass confirmed by mass spectrometry (see Supplementary Information). SfGFP with incorporated 2 and 3, sfGFP-2, sfGFP-3 were prepared in the same way, expect that cells were transformed with pBKTCORS (which encodes MbTCORS) and psfGFP150TAGPylT-His₆(which encodes MbtRNA_CUAand a C-terminally hexahistidine tagged sfGFP gene with an amber codon at position 150). SfGFP with incorporated 4 and 5, sfGFP-4, sfGFP-5 were prepared in the same way, expect that cells were transformed with pBKPylRS (which encodes MbPylRS) and psfGFP150TAGPylT-His₆(which encodes MbtRNA_CUAand a C-terminally hexahistidine tagged sfGFP gene with an amber codon at position 150). Yields of purified proteins were up to 6-12 mg/L.

Protein Mass Spectrometry

Using an Agilent 1200 LC-MS system, ESI-MS was carried out with a 6130 Quadrupole spectrometer. The solvent system consisted of 0.2% formic acid in H₂O as buffer A, and 0.2% formic acid in acetonitrile (MeCN) as buffer B. LC-ESI-MS on proteins was carried out using a Phenomenex Jupiter C4 column (150×2 mm, 5 μm) and samples were analyzed in the positive mode, following protein UV absorbance at 214 and 280 nm. Total protein masses were calculated by deconvolution within the MS Chemstation software (Agilent Technologies).
Additionally, protein total mass was determined on an LCT time-of-flight mass spectrometer with electrospray ionization (ESI, Micromass). Proteins were rebuffered in 20 mM of ammonium bicarbonate and mixed 1:1 acetonitrile, containing 1% formic acid. Alternatively samples were prepared with a C4 Ziptip (Millipore) and infused directly in 50% aqueous acetonitrile containing 1% formic acid. Samples were injected at 10 μL min⁻¹and calibration was performed in positive ion mode using horse heart myoglobin. 30 scans were averaged and molecular masses obtained by maximum entropy deconvolution with MassLynx version 4.1 (Micromass). Theoretical masses of wild-type proteins were calculated using Protparam (http://us.expasy.org/tools/protparam.html), and theoretical masses for unnatural amino acid containing proteins were adjusted manually.

Protein Labelling Via Tetrazine-BCN or Tetrazine-TCO Cycloaddition

In Vitro Labelling of Purified Proteins with Different Tetrazines
To 40 μL of purified recombinant protein (˜10 μM in 20 mM Tris-HCl, 100 mM NaCl, 2 mM EDTA, pH 7.4) 4 μL of a 1 mM solution of tetrazine compounds 6, 7, 8, or 9 in McOH were added (˜10 or 20 equivalents). After 30 minutes of incubation at room temperature, the solutions were analyzed by LC-ESI-MS. (Supplementary Figure S9)
In Vitro Labelling of Purified Proteins with Tetrazines and Tetrazine-Dye Conjugates:
Purified recombinant sfGFP with site-specifically incorporated 1 or 2, sfGFP-1 or sfGFP-2 (˜10 μM in 20 mM Tris-HCl, 100 mM NaCl, 2 mM EDTA, pH 7.4), was incubated with 10 equivalents of the tetrazine- dye conjugates 11, 12, 13, 14, 15 or 16, respectively (2 mM in DMSO). The solution was incubated at room temperature and aliquots were taken after 30 min to 3 hours and analyzed by SDS PAGE and—after desalting with a C4-ZIPTIP—by ESI-MS. The SDS PAGE gels were either stained with coomassie or scanned with a Typhoon imager to visualize in-gel fluorescence (FIG. 4 and Supplementary Figure S8).
In Vitro Labelling of Purified Proteins with Tetrazines-Dye Conjugates as a Function of Time:
2 nmol of purified sfGFP-1, sfGFP-2 or sfGFP-4 (10 μM in 20 mM Tris-HCl, 100 mM NaCl, 2 mM EDTA, pH 7.4) were incubated with 20 nmol of tetrazine-dye conjugate 11 (10 μl of a 2 mM solution in DMSO). At different time points (0, 30 s, 1 min, 2 min, 5 min, 10 min, 30 min, 1 h, 2 h, 3 h) 8 aliquots were taken from the solution and quenched with a 700-fold excess of BCN or TCO and plunged into liquid nitrogen. Samples were mixed with NuPAGE LDS sample buffer supplemented with 5% β-mercaptoethanol, heated for 10 min to 90° C. and analyzed by 4-12% SDS page. The amounts of labelled proteins were quantified by scanning the fluorescent bands with a Typhoon Trio phosphorimager (GE Life Sciences). Bands were quantified with the ImageQuant™ TL software (GE Life Sciences) using rubber band background subtraction. In gel fluorescence shows that labelling is complete within 1 h for sfGFP-4 using 10 equivalents tetrazine-fluorophore 11 (FIG. 4 e ), whereas the labelling of sfGFP-1 and sfGFP-2 was complete within the few seconds it took to measure the first time point.
Labelling of the Whole E. coli Proteome with Tetrazine-Dye Conjugates:
E. coli DH10B cells containing either psfGFP150TAGPylT-His₆and pBKBCNRS or psfGFP150TAGPylT-His₆and pBKPylRS were inoculated into LB containing ampicillin (for pBKBCNRS, 100 μg/mL) or kanamycin (for pBKPylRS 50 μg/mL) and tetracycline (25 μg/mL). The cells were incubated with shaking overnight at 37° C., 250 rpm. 2 mL of overnight culture was used to inoculate into 100 mL of LB supplemented with ampicillin (50 μg/mL) and tetracycline (12 μg/mL) or kanamycin (25 μg/mL) and tetracycline (12 μg/mL) and incubated at 37° C. At OD₆₀₀=0.5, 3 ml culture aliquots were removed and supplemented with different concentrations (1 mM, 2 mM and 5 mM) of 1 and 1 mM of 5. After 30 min of incubation with shaking at 37° C., protein expression was induced by the addition of 30 μL of 20% arabinose. After 3.5 h of expression, cells were collected by centrifugation (16000 g, 5 min) of 1 mL of cell suspension. The cells were resuspended in PBS buffer, spun down again and the supernatant was discarded. This process was repeated twice more. Finally, the washed cell pellet was suspended in 100 μL PBS and incubated with 3 μL of tetrazine-dye conjugate 11 (2 mM in DMSO) at rt for 30 minutes. After adding a 200-fold excess of BCN in order to quench non-reacted tetrazine-dye, the cells were resuspended in 100 μL of NuPAGE LDS sample buffer supplemented with 5% β-mercaptoethanol, heated at 90° C. for 10 min and centrifuged at 16000 g for 10 min. The crude cell lysate was analyzed by 4-12% SDS-PAGE to assess protein levels. Gels were either Coomassie stained or scanned with a Typhoon imager to make fluorescent bands visible (Supplementary Figures S9 and S10). Western blots were performed with antibodies against the hexahistidine tag (Cell Signaling Technology, His tag 27E8 mouse mAb #2366).

Stopped-Flow Determination of Kinetic Rate Constants for Small Molecule Cycloadditions

Rate constants k for different tetrazines were measured under pseudo first order conditions with a 10- to 100-fold excess of BCN or TCO in methanol/water mixtures by following the exponential decay in UV absorbance of the tetrazine at 320, 300 or 280 nm over time with a stopped-flow device (Applied Photophysics, Supplementary Figures S2 and S3 and Supplementary Table 1). Stock solutions were prepared for each tetrazine (0.1 mM in 9/1 water/methanol) and for BCN and TCO (1 to 10 mM in methanol). Both tetrazine and BCN and TCO solutions were thermostated in the syringes of the stopped flow device before measuring. Mixing equal volumes of the prepared stock solutions via the stopped-flow apparatus resulted in a final concentration of 0.05 mM tetrazine and of 0.5 to 5 mM BCN or TCO, corresponding to 10 to 100 equivalents of BCN or TCO. Spectra were recorded using the following instrumental parameters: wavelength, 320 nm for 6 and 7; 300 nm for 8, 280 nm for 9; 500 to 5000 datapoints per second). All measurements were conducted at 25° C. Data were fit to a single-exponential equation for BCN-tetrazine reactions and to a sum of two single exponential equations for TCO-tetrazine reactions. Each measurement was carried out three to five times and the mean of the observed rates k′ (the first exponential equation in case of the TCO-tetrazine reaction) was plotted against the concentration of BCN or TCO to obtain the rate constant k from the slope of the plot. For all four tetrazines complete measurement sets were done in duplicate and the mean of values is reported in Supplementary Table 1. All data processing was performed using Kaleidagraph software (Synergy Software, Reading, UK).

Cloning for Mammalian Cell Applications

The plasmids pMmPylS-mCherry-TAG-EGFP-HA^1,2and pMmPylRS-EGFR-(128TAG)-GFP-HA²were both digested with the enzymes AflII and EcoRV (NEB) to remove the wild-type MmPylRS. A synthetic gene of the mutant synthetase MbBCNRS and MbTCORS was made by GeneArt with the same flanking sites. The synthetic MbBCNRS and MbTCORS were also digested with AflII and EcoRV and cloned in place of the wild-type synthetase (MmPylS). Using a rapid ligation kit (Roche) vectors pMbBCNRS-mCherry-TAG-EGFP-HA, pMbBCNRS-EGFR(128TAG)-GFP-HA and pMbTCORS-EGFR(128TAG)-GFP-HA were created. The pCMV-cJun-TAG-mCherry-MbBCNRS plasmid was created from a pCMV-cJun-TAG-mCherry-MmPylRS plasmid (created by Fiona Townsley) by exchanging MmPylRS for MbBCNRS. This was carried out as for the pMbBCNRS-mCherry-TAG-EGFP-HA plasmid.

Incorporation of

Amino Acid

1, 2 and 3 in HEK293 Cells

HEK293 cells were plated on poly-lysine coated μ-dishes (Ibidi). After growing to near confluence in 10% fetal bovine serum (FBS) Dulbecco's modified eagle medium (DMEM) cells were transfected with 2 μg of pMbBCNRS-EGFR(128TAG)-GFP-HA and 2 μg of p4CMVE-U6-PylT (which contains four copies of the wild-type pyrrolysyl tRNA)^1,2using lipofectamin 2000 (Life Technologies). After transfection cells were left to grow overnight in 10% FBS DMEM at 37° C. and 5% CO₂. For a western blot, cells were plated on 24 well plates and grown to near confluence. Cells were transfected using lipofectamine 2000 with the pMbBCNRS-mCherry-TAG-EGFP-HA or pMmPylRS-mCherry-TAG-EGFP-HA or pTCORS-mCherry-TAG-EGFP-HA construct and the p4CMVE-U6-PylT plasmid. After 16 hours growth with or without 0.5 mM 1, 1 mM 2 or 1 mM 5 cells were lysed on ice using RIPA buffer (Sigma). The lysates were spun down and the supernatant was added to 4×LDS sample buffer (Life technologies). The samples were run out by SUS-PAGE, transferred to a nitrocellulose membrane and blotted using primary rat anti-HA (Roche) and mouse anti-FLAG (Ab frontier), secondary antibodies were anti-rat (Santa Cruz Biotech) and anti-mouse (Cell Signaling) respectively.

Labelling of Mammalian Cell Surface Protein

Cells were plated onto a poly-lysine coated μ-dish and after growing to near confluence were transfected with 2 μg each of pMbBCNRS-EGFR(128TAG)-GFP-HA or pMbTCORS-EGFR(128TAG)-GFP-HA and p4CMVE-U6 PylT. After 8-16 hours growth at 37° C. and at 5% CO₂in DMEM with 0.1% FBS in the presence of 0.5 mM 1 (0.5% DMSO), 1 mM 2 or 1 mM 3 cells were washed in DMEM with 0.1% FBS and then incubated in DMEM with 0.1% FBS overnight. The following day cells were washed once more before 400 nM terazine-dye conjugate 11 was added for 2-60 minutes. The media was exchanged twice and cells were then imaged. Imaging was carried out on a Zeiss 780 laser scanning microscope with a Plan apochromat 63× oil immersion objective; scan zoom: 1× or 2×; scan resolution: 512×512; scan speed: 9; averaging: 16×. EGFP was excited at 488 nm and imaged at 493 to 554 nm; TAMRA was excited and detected at 561 nm and 566-685 nm respectively.
Controls were performed similarly but transfected with pMmPylRS-EGFR(128TAG)-GFP-HA instead of pMbBCNRS-EGFR(128TAG)-GFP-HA. Cells were grown overnight in the presence of 1 mM 5 and in the absence or presence of 0.5% DMSO (as would be the case for amino acid 1).

Labeling of Mammalian Nuclear Protein

Cells were plated onto a poly-lysine coated μ-dish and after growing to near confluence were transfected with 2 μg each of pCMV-cJun-TAG-mCherry and p4CMVE-U6-PylT. After approximately 16 hrs growth at 37° C. and at 5% CO₂in DMEM with 0.1% FBS in the presence of 0.5 mM 1 (0.5% DMSO) cells were washed in DMEM 0.1% FBS and then incubated in DMEM 0.1% FBS overnight. The following day cells were washed repeatedly, using two media exchanges followed by 30 minutes incubation over 2 hours. 200 nM tetrazine-dye conjugate 11 was added for 15 minutes, the cells were then repeatedly washed again for 90 mins. Imaging was carried out as for the cell surface labeling

Chemical Syntheses:

General Methods:

NMR spectra were recorded on a Bruker Ultrashield™ 400 Plus spectrometer (¹H: 400 MHz, ¹³C: 101 MHz, ³¹P: 162 MHz). Chemical shifts (δ) are reported in ppm and are referenced to the residual non-deuterated solvent peak: CDCl₃(7.26 ppm), d₆-DMSO (2.50 ppm) for ¹H-NMR spectra, CDCl₃(77.0 ppm), d₆-DMSO (39.5 ppm) for ¹³C-NMR spectra. ¹³C- and ³¹P-NMR resonances are proton decoupled. Coupling constants (J) are measured to the nearest 0.1 Hz and are presented as observed. Splitting patterns are designated as follows: s, singlet; d, doublet; t, triplet; q, quartet; quin, quintet; sext, sextet; m, multiplet. Analytical thin-layer chromatography (TLC) was carried out on silica 60E-254 plates. The spots were visualized by UV light (254 nm) and/or by potassium permanganate staining. Flash column chromatography was carried out on silica gel 60 (230-400 mesh or 70-230 mesh). ESI-MS was carried out using an Agilent 1200 LC-MS system with a 6130 Quadrupole spectrometer. The solvent system consisted of 0.2% formic acid in H₂O as buffer A, and 0.2% formic acid in acetonitrile (MeCN) as buffer B. Small molecule LC-MS was carried out using a Phenomenex Jupiter C18 column (150×2 mm, 5 μm). Variable wavelengths were used and MS acquisitions were carried out in positive and negative ion modes. Preparative HPLC purification was carried out using a Varian PrepStar/ProStar HPLC system, with automated fraction collection from a Phenomenex C18 column (250×30 mm, 5 μm). Compounds were identified by UV absorbance at 191 nm. All solvents and chemical reagents were purchased from commercial suppliers and used without further purification. Bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN, exo/endo mixture ˜4/1) was purchased from SynAffix, Netherlands. Non-aqueous reactions were carried out in oven-dried glassware under an inert atmosphere of argon unless stated otherwise. All water used experimentally was distilled. Brine refers to a saturated solution of sodium chloride in water.
exo-Bicyclo[6.1.0]non-4-yn-9-ylmethanol (exo-BCN, S18) was synthesised according to a literature procedure.³
N,N′-disuccinimidyl carbonate (1.38 g, 5.37 mmol) was added to a stirring solution of exo-BCN-OH S18 (538 mg, 3.58 mmol) and triethylamine (2.0 mL, 14.3 mmol) in MeCN (10 mL) at 0° C. The solution was warmed to room temperature and stirred for 3 h and concentrated under reduced pressure. The crude oil was purified through a short pad of silica gel chromatography (eluting with 60% EtOAc in hexane) to yield the exo-BCN-succinimidyl carbonate, which was used without further purification. exo-BCN-OSu (1.25 g, 4.29 mmol) in DMF (4 mL) was added via cannula to a stirring solution of Fmoc-Lys-OH·HCl (2.61 g, 6.45 mmol) and DIPEA (1.49 mL, 8.58 mmol) in DMF (10 mL). The solution was stirred at room temperature for 14 h, diluted with Et₂O (100 mL) and washed with H₂O (3×100 mL). The organic phase was dried over sodium sulfate, filtered and concentrated under reduced pressure. The crude oil was purified by silica gel chromatography (0-5% McOH-1 in DCM (0.1% AcOH)) to yield exo-Fmoc-BCNK-OH S19 as a white solid (1.65 g, 85% over 2 steps). δ_H(400 MHz, d₆-DMSO) 12.67-12.31 (1H, brs), 7.90 (2H, d, J 7.5), 7.73 (2H, d, J 7.4), 7.63 (1H, d, J 7.8), 7.42 (2H, t, J 7.4), 7.34 (2H, t, J 7.4), 7.10 (1H, t, J 5.7), 4.31-4.19 (3H, m), 3.95-3.87 (1H, m), 3.84 (1H, d, J 6.4), 3.45-3.25 (br s, 1H), 3.01-2.91 (2H, m), 2.52-2.50 (1H, m), 2.33-2.15 (4H, m), 2.11-2.02 (2H, m), 1.75-1.54 (2H, m), 1.46-1.23 (6H, m), 0.70-0.58 (2H, m); δ_C(101 MHz, d₆-DMSO) 174.4, 156.9, 156.6, 144.30, 144.27, 141.2, 128.1, 127.5, 125.7, 120.6, 99.4, 68.1, 66.1, 54.3, 47.1, 33.3, 30.9, 29.5, 23.9, 23.4, 22.7, 21.3; LRMS (ESI⁺): m/z 543 (100% [M−H]⁻).
Polymer-bound piperazine (1.28 g, 1.28 mmol, 200-400 mesh, extent of labeling: 1.0-2.0 mmol/g loading, 2% cross-linked with divinylbenzene) was added to a stirring solution of exo-Fmoc-BCNK-OH S19 (174 mg, 0.32 mmol) in DCM (10 mL). The resulting mixture was stirred for 4 h at room temperature, filtered and the reagent washed with CHCl₃/MeOH (3:1, 3×50 mL). The filtrate was evaporated under reduced pressure, dissolved in H₂O (100 mL) and washed with EtOAc (3×100 mL). The aqueous phase was evaporated under reduced pressure and freeze-dried to yield exo-H-BCNK-OH 1 as a white solid (101 mg, 98%). For all subsequent labeling experiments using mammalian cells exo-H-BCNK-OH 1 was further purified by reverse-phase HPLC (0:1 H₂O:MeCN to 9:1 H₂O:MeCN gradient). δ_H(400 MHz, d₆-DMSO/D₂O (1:1)) 4.14-3.76 (m, 3H), 3.56-3.29 (m, 2H), 3.18-2.81 (m, 3H), 2.31-1.98 (m, 5H), 1.71-1.52 (m, 4H), 1.51-1.29 (m, 4H), 1.29-1.08 (m, 3H), 0.95-0.66 (m, 2H); δC (101 MHz, d₆-DMSO/D₂O (1:1)) 169.4, 165.9, 101.3, 76.0, 55.8, 31.8, 30.1, 29.9, 25.2, 23.2, 22.1, 21.0, 18.7; LRMS (ESI⁺): m/z 323 (100% [M+H]⁺). endo-Bicyclo[6.1.0]non-4-yn-9-ylmethanol (endo-BCN) was synthesised according to a literature procedure³and elaborated to the corresponding amino acid in an analogous fashion to 1.
A glass vial (Biotage® Ltd.) equipped with a magnetic stirring bar was charged with compound 6 (39.2 mg, 0.096 mmol) and was sealed with an air-tight aluminium/rubber septum. The contents in the vial were dried in vacuo and purged with argon gas (×3). McOH (1 ml) was added to the vial, followed by addition of a solution of exo-Bicyclo[6.1.0]non-4-yn-9-ylmethanol (exo-BCN, S18) (20.2 mg in 1 ml of McOH, 0.1344 mmol). The mixture was stirred at room temperature. Within 2 min, the reaction mixture decolorised and the contents were left stirring for additional 1 min. The mixture was then evaporated under reduced pressure and purified by silica gel chromatography (5% McOH in DCM) to afford pyridazine S20 as a faint yellow semi-solid (49 mg, 96%). δ_H(400 MHz, CDCl₃) 9.16 (1H, br s), 8.77-8.71 (1H, m), 8.67 (1H, app. d, J 2.1), 8.01 (1H, br s), 7.97 (1H, d, J 7.8), 7.89 (1H, ddd, J 7.8, 7.6, 1.7), 7.75 (1H, app. d, J 8.4), 7.40 (1H, ddd, J 7.4, 4.9, 1.1), 5.93 (1H, br s), 4.02 (2H, d, J 5.0), 3.49-3.31 (2H, m), 3.12-2.88 (4H, m), 2.68-2.49 (2H, m), 1.88-1.60 (1H, br s), 1.60-1.50 (1H, m), 1.48 (9H, s), 0.92-0.72 (4H, m); δ_C(101 MHz, CDCl₃) 169.0, 159.2, 159.0, 156.9, 156.8, 155.7, 152.1, 148.9, 143.0, 140.9, 137.0, 134.4, 128.0, 125.1, 124.9, 123.5, 80.7, 66.4, 45.7, 30.7, 29.9, 29.6, 29.5, 28.5 (3×CH₃(^tBu)), 28.0, 27.8, 21.7; LRMS (ESI⁺): m/z 531 (100% [M+H]⁺).
Commercially available 4-(Aminomethyl)benzonitrile hydrochloride S21 (2.11 g, 12.50 mmol) in H₂O (10 mL) was added to a stirring solution of NaOH (1.50 g, 37.50 mmol) and di-tert-butyl dicarbonate (3.00 g, 13.75 mmol) in H₂O (10 mL) at room temperature. The mixture was stirred for 16 h, after which time a white precipitate had formed. The mixture was filtered, washed with H₂O (50 mL), and the resulting solid dried under vacuum to yield tort-butylcarbamate S22 as a white solid (2.78 g, 96%). δ_H(400 MHz, CDCl₃) 7.62 (2H, d, J 8.2), 7.39 (2H, d, J 8.2), 5.00 (1H, br s), 4.37 (2H, d, J 5.8), 1.46 (9H, s); δ_C(101 MHz, CDCl₃) 155.9, 144.7, 132.4, 127.8, 118.9, 111.1, 80.1, 44.2, 28.4; LRMS (ESI⁺): m/z 233 (100% [M+H]⁺).
Tetrazine 10 was synthesised by modification of a literature procedure.⁴Hydrazine monohydrate (1.024 mL, 21.10 mmol) was added to a stirring suspension of tert-butylcarbamate S22 (98 mg, 0.44 mmol), formamidine acetate (439 mg, 4.22 mmol), and Zn(OTf)₂(77 mg, 0.22 mmol) in 1,4-dioxane (0.5 mL) at room temperature. The reaction was heated to 60° C. and stirred for 16 h. The reaction was cooled to room temperature and diluted with EtOAc (10 mL). The reaction was washed with 1M HCl (10 mL) and the aqueous phase extracted with EtOAc (2×5 mL). The organic phase was dried over sodium sulfate, filtered and evaporated under reduced pressure. The resulting crude residue was dissolved in a mixture of DCM and acetic acid (1:1, 5 mL), and NaNO₂(584 mg, 8.44 mmol) was added slowly over a period of 15 minutes, during which time the reaction turned bright red. The nitrous fumes were chased with an active air purge and the reaction then diluted with DCM (25 mL). The reaction mixture was washed with sodium bicarbonate (sat., aq., 25 mL) and the aqueous phase extracted with DCM (2×10 mL). The organic phase was dried over sodium sulfate, filtered and evaporated under reduced pressure. The resulting residue was purified by silica gel chromatography (20% EtOAc in hexane) to yield tetrazine 10 as a pink solid (85 mg, 70%). δ_H(400 MHz, CDCl₃) 10.21 (1H, s), 8.60 (2H, d, J 8.2), 7.53 (2H, d, J 8.2), 4.97 (1H, br s), 4.45 (2H, d, J 6.0), 1.49 (9H, s); δ_C(101 MHz, CDCl₃) 149.4, 142.6, 141.1, 132.1, 120.8, 119.2, 118.8, 51.8, 39.0; LRMS (ESI⁺): m/z 188 (100% [(M-Boc)+2H]⁺).
4M HCl in dioxane (2 mL, 8.0 mmol) was added to a stirring solution of tetrazine 10 (75 mg, 0.26 mmol) in DCM (4 mL). After 1 h the reaction was complete and the solvent was removed under reduced pressure to yield primary amine hydrochloride S23 as a pink solid (61 mg, 100%). δ_H(400 MHz, d₆-DMSO) 10.64 (1H, s), 8.54 (2H, d, J 8.4), 7.79 (2H, d, J 8.4), 4.18 (2H, d, J 5.5); δ_C(101 MHz, d₆-DMSO) 165.2, 158.2, 138.9, 131.9, 129.8, 127.9, 41.8; LRMS (ESI⁺): m/z 188 (100% [M+H]⁺).
E-5-hydroxycyclooctene and E-exo-Bicyclo[6.1.0]non-4-ene-9-ylmethanol were either made by previously described photochemical procedures^5,6, or by the non-photochemical protocols described below.
Diisobutylaluminium hydride (1.0 M solution in cyclohexane, 89 mL, 89 mmol) was added drop-wise to a stirring solution of commercially available 9-oxabicyclo[6.1.0]non-4-ene S24 (10 g, 80.53 mmol) in DCM (300 mL) at 0° C. The solution was stirred at 0° C. for 30 min, warmed to room temperature and stirred for 16 h. After this time, the reaction was cooled to 0° C. and propan-2-ol (50 mL) was added slowly followed by HCl (1 M, aq., 100 mL). The aqueous phase was extracted with DCM (3×200 mL). The combined organics were washed with brine, dried over sodium sulfate, filtered and concentrated under reduced pressure. The crude material was purified by silica gel chromatography (10-20% EtOAC in hexanes) to yield cyclooctene-4-ol S25 as a colorless oil (8.42 g, 83%). Spectral data was in accordance with the literature.⁷
tert-Butyl(chloro)dimethylsilane (13.3 g, 88.0 mmol) was added to a stirring solution of cyclooctene-4-ol S25 (5.6 g, 44.0 mmol), imidazole (7.5 g, 0.11 mol) and DMAP (1 crystal) in DCM (30 mL) at 0° C. The solution was warmed to room temperature and stirred for 90 min, during which time a white precipitate formed. The reaction was cooled to 0° C., diluted with DCM (100 mL) and sodium bicarbonate (sat., aq., 100 mL) was added. The phases were separated and the aqueous phase was extracted with DCM (3×100 mL). The combined organics were washed with brine (200 mL), dried over sodium sulfate, filtered and concentrated under reduced pressure. The crude material was purified by silica gel chromatography (10-20% DCM in hexane) to yield silyl ether S26 as colorless oil (10.55 g, quant.). δ_H(400 MHz, CDCl₃) 5.71-5.63 (1H, m), 5.60-5.52 (1H, m), 3.80 (1H, app td, J 8.6, 4.2), 2.34 (1H, dtd, J 13.8, 8.2, 3.8), 2.25-2.15 (1H, m), 2.13-2.05 (1H, m), 2.02-1.93 (1H, m), 1.87-1.52 (5H, m), 1.47-1.35 (1H, m), 0.88 (9H, s), 0.04 (3H, s), 0.03 (3H, s); δ_C(101 MHz, CDCl₃) 130.4, 129.4, 73.1, 38.0, 36.5, 26.1, 25.8, 25.1, 22.7, 18.4, −3.4; LRMS (ESI⁺): m/z 241 (11% [M+H]⁺).
Peracetic acid (39% in acetic acid, 10.3 ml, 52.7 mmol) was added drop-wise to a stirred solution of silyl ether S26 (10.6 g, 43.9 mmol) and sodium carbonate (7.0 g, 65.8 mmol) in DCM (80 mL) at 0° C. The mixture was warmed to room temperature and stirred for 14 h. The reaction was cooled to 0° C., diluted with DCM (50 mL) and sodium thiosulfate (sat., aq., 100 ml.) was added. The mixture was stirred at room temperature for 10 min and then basified to pH 12 with NaOH (2M, aq.). The phases were separated and the organic phase washed with H₂O (100 mL), brine (100 mL), dried over sodium sulfate, filtered and concentrated under reduced pressure. The crude material was purified by silica gel chromatography (80%-90% DCM in hexane) to yield epoxides S27/S28, as an inseparable mixture of diastereomers (2.3:1 by ¹H-NMR) and as a colorless oil (10.2 g, 91%). Major diastereomer: δ_H(400 MHz, CDCl₃) 3.90 (1H, app sext, J 4.2), 2.90 (2H, ddd, J 16.7, 8.3, 4.4), 2.21-2.09 (1H, m), 1.85-1.60 (6H, m), 1.50-1.38 (2H, m), 1.34-1.23 (1H, m), 0.88 (9H, s), 0.04 (3H, s), 0.03 (3H, s); δ_C(101 MHz, CDCl₃) 171.9, 55.5, 55.4, 36.3, 34.3, 27.7, 26.0, 25.8, 22.6, 18.3, −3.4; LRMS (ESI⁺): m/z 257 (β% [M+H]⁺).
n-Butyllithium (2.5 M in hexanes, 14.8 mL, 37.0 mmol) was added drop-wise over 15 min to a stirring solution of epoxides S27/S28 (7.9 g, 30.8 mmol) and diphenylphosphine (6.43 mL, 37.0 mmol) in THF (80 mL) at −78° C. The resulting mixture was stirred at −78° C. for 1 h, warmed to room temperature and stirred for 14 h. The reaction mixture was diluted with THF (80 mL) and cooled to 0° C. Acetic acid (5.54 mL, 92.4 mmol) was added followed by hydrogen peroxide (30% solution in H₂O, 7.68 mL, 67.7 mmol). The reaction mixture was warmed to room temperature and stirred for 4 h. Sodium thiosulfate (sat., aq., 100 mL) was added and the mixture stirred for 10 min. The aqueous phase was extracted with EtOAc (3×200 mL). The combined organics were washed with brine (3×200 mL), dried over sodium sulfate, filtered and concentrated under reduced pressure to yield phosphine oxides S29/S30/S31/S32 as a mixture of four diastereomers, which were used without further purification. δ_P(162 MHz, CDCl₃) 45.2, 44.8, 44.4, 43.8; LRMS (ESI⁺): m/z 459 (100% [M+H]⁺).
Sodium hydride (60% dispersion in mineral oil, 2.46 g, 61.5 mmol) was added to a stirring solution of crude hydroxyl phosphine oxides S29/S30/S31/S32 in DMF (100 mL) at 0° C. The resulting mixture was warmed to room temperature, wrapped in tin foil and stirred for 2 h. The reaction was cooled to 0° C., diluted with Et₂O (200 mL) and 1-120 (200 mL) was added. The phases were separated and the combined organics washed with brine (2×200 mL), dried over sodium sulfate, filtered and concentrated under reduced pressure. The crude mixture was purified by silica gel chromatography (1-15% DCM in hexane) to yield trans-cyclooctenes S33/S34 as a separable mixture of diastereomers, with exclusive E-selectivity, and as colorless oils (2.78 g, 1.2:1 dr, 38% over 3 steps). S33: δ_H(400 MHz, CDCl₃) 5.64 (1H, ddd, J 16.0, 10.8, 3.6), 5.45 (1H, ddd, J 15.9, 11.1, 3.2), 4.01 (1H, app dd, J 10.2, 5.4), 2.41 (1H, qd, J 11.5, 4.4), 2.26-2.19 (1H, m), 2.09-1.94 (31-1, m), 1.92-1.73 (2H, m), 1.71-1.63 (1H, m), 1.54 (1H, tdd, J 14.0, 4.7, 1.1), 1.30-1.08 (1H, m), 0.94 (9H, s), 0.03 (3H, s), 0.01 (3H, s); δ_C(101 MHz, CDCl₃) 135.9, 131.5, 67.6, 44.0, 35.2, 34.8, 29.7, 27.7, 26.2, 18.4, −4.7, −4.8; LRMS (ESI⁺): m/z 241 (8% [M+H]⁺). S34: δ_H(400 MHz, CDCl₃) 5.55 (1H, ddd, J 15.9, 11.0, 3.6), 5.36 (1H, ddd, J 16.1, 10.8, 3.4), 3.42-3.37 (1H, m), 2.36-2.28 (2H, m), 2.22 (1H, app qd, J 11.2, 6.3), 2.02-1.87 (4H, m), 1.73 (1H, dd, J 14.9, 6.2), 1.67-1.45 (2H, m), 0.87 (9H, s), 0.03 (6H, s); δ_C(101 MHz, CDCl₃) 135.5, 132.5, 78.6, 44.9, 42.0, 34.6, 33.0, 31.3, 26.1, 18.3, −4.4, −4.5; LRMS (ESI⁺): m/z 241 (12% [M+H]⁺). For all further experiments trans-cyclooctene S34 was used, where the C4-oxygen substituent occupies an equatorial position.
Tetrabutylammonium fluoride (1M solution in THF, 23.8 mL. 23.8 mmol) and cesium fluoride (1.08 g, 7.14 mmol) were added to a stirring solution of silyl ether S34 (573 mg, 2.38 mmol) in MeCN (5 mL) at room temperature. The resulting mixture was wrapped in tin foil and stirred at room temperature for 36 h. After this period the reaction was cooled to 0° C., diluted with DCM (100 mL) and H₂O (100 mL) was added. The phases were separated, the organic phase washed with brine (2×100 mL), dried over sodium sulfate, filtered and concentrated under reduced pressure. The crude material was purified by silica gel chromatography (20% EtOAc in hexane) to yield secondary alcohol S35 as a colorless oil (289 mg, 96%) δ_H(400 MHz, CDCl₃) 5.60 (1H, ddd, J 16.0, 10.7, 4.2), 5.41 (1H, ddd, J 16.0, 11.1, 3.7), 3.52-3.45 (2H, m), 2.40-2.25 (3H, m), 2.03-1.90 (4H, m), 1.75-1.53 (3H, m), 1.25-1.18 (1H, m); δ_C(101 MHz, CDCl₃) 135.1, 132.8, 77.7, 44.6, 41.1, 34.3, 32.6, 32.1; LRMS (ESI⁺): m/z 127 (14% [M+H]⁺).
Succimidyl carbonate S36 (200 mg, 0.75 mmol) was added to a stirring solution of Fmoc-Lys-OH·HCl (303 mg, 0.75 mmol) and DIPEA (0.19 g, 1.50 mmol) in DMF (7.5 mL) at 0° C. The solution was warmed to room temperature, wrapped in tin foil and stirred for 12 h. After this period the solution was concentrated under reduced pressure and purified by silica gel chromatography (0-10% MeOH in DCM) to yield Fmoc-TCOK-OH S37/S38 as a yellow oil that still contained DMF (350 mg, 81%). δ_H(400 MHz, CDCl₃) 7.75-7.69 (2H, m), 7.63-7.52 (2H, m), 7.41-7.33 (2H, m), 7.32-7.25 (2H, m), 5.82-5.34 (3H, m), 5.27 (1H, br s), 4.90-4.50 (1H, m), 4.47-4.01 (5H, m), 3.32-3.30 (1H, m), 2.39-1.08 (17H, m); δ_C(100 MHz, CDCl₃) 174.3, 156.3, 155.9, 143.8, 143.6, 141.1, 135.0, 134.8, 132.8, 132.6, 127.5, 126.9, 125.0, 119.8, 80.3, 66.8, 53.4, 47.0, 41.0, 40.4, 38.5, 34.1, 32.5, 32.3, 32.1, 30.8, 29.3, 22.3; ESI-MS (m/z): [M+Na]+ calcd. for C₃₀H₃₆N₂O₆Na 543.2471, found 543.2466.
Piperidine (1 mL) was added to a stirring solution of Fmoc-TCOK-OH S37/S38 (0.269 g, 0.517 mmol) in DCM (4 mL). The mixture was wrapped in tin foil and stirred at room temperature for 30 min. The reaction mixture was concentrated under reduced pressure and the crude material was purified by silica gel chromatography (30-50% McOH in DCM) to yield H-TCOK-OH 1 as an ivory-colored solid. δ_H(400 MHz, d₄-MeOD) 5.63-5.56 (1H, m), 5.50-5.43 (1H, m), 4.31-4.25 (1H, m), 3.60-3.53 (1H, m), 3.11-3.03 (2H, m), 2.37-2.26 (3H, m), 2.02-1.36 (13H, m); δ_C(100 MHz, d₄-MeOD) 174.3, 159.0, 136.3, 133.9, 81.8, 56.0, 42.4, 41.4, 39.8, 35.4, 33.7, 32.3, 32.1, 30.9, 23.6; ESI-MS (m/z): [M−H]⁻ calcd. for C₁₅H₂₅N₂O₄297.1814, found 297.1811.
exo-Bicyclo[6.1.0]non-4-ene-9-ylmethanol S18 was synthesised according to a literature procedure.
tert-Butyl(chloro)diphenylsilane (7.45 g, 27.1 mmol) was added to a stirring solution of exo-bicyclo[6.1.0]non-4-ene-9-ylmethanol S18 (2.75 g, 18.1 mmol), imidazole (2.15 g, 31.6 mmol) and DMAP (2.21 g, 18.1 mmol) in DCM (35 ml) at 0° C. The solution was warmed to room temperature and stirred for 24 h, during which a white precipitate formed. The reaction was cooled to 0° C., diluted with DCM (100 mL) and sodium bicarbonate (sat., aq., 100 mL) was added. The phases were separated and the aqueous phase was extracted with DCM (3×100 mL). The combined organics were washed with brine (200 mL), dried over sodium sulfate, filtered and concentrated under reduced pressure. The crude material was purified by silica gel chromatography (20% DCM in hexane) to yield silyl ether S39 as a colorless oil (6.85 g, 97%), δ_H(400 MHz, CDCl₃) 7.79-7.64 (4H, m), 7.50-7.32 (6H, m), 5.63 (2H, dm, J 11.5), 3.59 (2H, d, J 6.2), 2.40-2.21 (2H, m), 2.18-1.96 (4H, m), 1.45-1.33 (2H, m), 1.07 (9H, s), 0.72-0.56 (3H, m); δ_C(101 MHz, CDCl₃) 135.7, 134.3, 130.2, 129.5, 127.6, 67.9, 29.1, 28.6, 27.2, 26.9, 22.0, 19.3; LRMS (ESI⁺): m/z 408 (10%, [M+NH₄]⁺).
Peracetic acid (3.38 ml, 39% in acetic acid, 19.9 mmol) was added to a stirred solution of silyl ether S39 (6.49 g, 16.6 mmol) and anhydrous sodium carbonate (2.64 g, 24.9 mmol) in DCM (65 mL) at 0° C. The mixture was warmed to room temperature and stirred for 24 h. The reaction was then cooled to 0° C., diluted with DCM (100 mL) and sodium thiosulfate (sat., aq., 150 mL) was added. The mixture was stirred at room temperature for 30 min and then basified to pH 12 with NaOH (2M, aq.). The phases were separated and the organic phase was washed with H₂O (200 mL), brine (200 mL), dried over sodium sulfate, filtered and concentrated under reduced pressure. The crude material was purified by silica gel chromatography (100% DCM) to yield epoxides S40 and S41 as an inseparable mixture of diastereomers (1:1 by ¹H NMR spectroscopy) and as a colorless oil (5.97 g, 88%). δ_H(400 MHz, CDCl₃) 7.72-7.63 (8H, m), 7.47-7.34 (12H, m), 3.57 (2H, d, J 5.6), 3.54 (2H, d, J 5.9), 3.03-3.10 (2H, m), 3.02-2.91 (2H, m), 2.36-2.24 (2H, m), 2.21-2.08 (2H, m), 2.06-1.85 (6H, m), 1.35-1.12 (4H, m), 1.06 (9H, s), 1.05 (9H, s), 0.92-0.80 (2H, m), 0.78-0.47 (6H, m); δ_C(101 MHz, CDCl₃) 135.65, 135.63, 134.2, 134.1, 129.6 (2×CH), 127.6 (2×CH), 67.4, 67.0, 56.91, 56.85, 29.7, 27.7, 26.9 (2×3CH₃), 26.6, 26.5, 23.31, 23.25, 21.7, 20.4, 19.2 (2×2C); LRMS (ESI⁺): m/z 407 (9%, [M+H]⁺).
n-Butyllithium (2.5 M in hexanes, 5.92 mL, 14.8 mmol) was added drop wise over 15 min to a stirring solution of epoxides S40/S41 (5.47 g, 13.5 mmol) and diphenylphosphine (2.57 mL, 14.80 mmol) in THF (50 mL) at −78° C. The resulting mixture was stirred at −78° C. for 1 h, warmed to room temperature and stirred for additional 14 h. The reaction mixture was diluted with THF (80 mL) and cooled to 0° C. Acetic acid (1.54 mL, 26.9 mmol) was added followed by addition of hydrogen peroxide (30% solution in H₂O, 3.05 mL, 26.9 mmol). The reaction mixture was warmed to room temperature and stirred for 4 h. Sodium thiosulfate (sat., aq., 100 mL) was added and the mixture stirred for 10 min. The aqueous phase was extracted with EtOAc (3×200 mL). The combined organics were washed with brine (3×200 mL), dried over sodium sulfate, filtered and concentrated under reduced pressure. The crude mixture was purified by silica gel chromatography (40-100% EtOAc in hexane) to yield phosphine oxides S42/S43/S44/S45 as a 51:18 mixture of two diastereoisomers (5.61 g, 69% over 2 steps), each of which is a 1:1 mixture of regioisomers (S42/S45 and S43/S44). Major diastereomer: δ_H(400 MHz, CDCl₃) 7.82-7.68 (4H, m), 7.68-7.58 (4H, m), 7.52-7.32 (12H, m), 4.58-4.45 (1H, m), 4.16 (1H, d, J 5.3), 3.54 (2H, d, J 6.0), 2.47 (1H, ddd, J 12.0, 11.7, 4.3), 2.21-2.07 (1H, m), 2.05-1.85 (2H, m), 1.78-1.55 (31-1, m), 1.22-1.05 (1H, m), 1.03 (9H, s), 0.91-0.75 (1H, m), 0.62-0.35 (3H, m); δ_P(162 MHz, CDCl₃) 39.7; LRMS (ESI⁺): m/z 609 [100%, (M+H)+]. Minor diastereomer: δ_H(400 MHz, CDCl₃) 7.87-7.77 (2H, m), 7.74-7.60 (6H, m), 7.52-7.30 (12H, m), 4.26 (1H, d, J 4.0), 3.89-3.78 (1H, m), 3.63 (1H, dd, J 10.7, 5.8), 3.54 (1H, dd, J 10.7, 6.2), 3.26-3.10 (1H, m), 2.22-2.12 (1H, m), 2.00-1.78 (3H, m), 1.70-1.62 (1H, m), 1.42-1.28 (1H, m), 1.04 (9H, s), 1.04-0.92 (2H, m), 0.79-0.65 (1H, m), 0.55-0.41 (1H, m), 0.27-0.12 (1H, m); δ_P(162 MHz, CDCl₃) 39.6; LRMS (ESI⁺): m/z 609 [100%, (M+H)⁺].
Sodium hydride (60% dispersion in mineral oil, 0.46 g, 11.5 mmol) was added to a stirring solution of hydroxyl phosphine oxides S42/S43/S44/S45 (4.68 g, 7.69 mol) in anhydrous DMF (60 mL) at 0° C. The resulting mixture was warmed to room temperature, wrapped in tin foil and stirred for 2 h. The reaction mixture was cooled to 0° C., diluted with Et₂O (200 mL) and H₂O (200 mL), the phases were separated and aqueous phase was extracted with hexane (150 mL). The combined organics were washed with brine (sat., aq., 5×250 mL), dried over sodium sulfate, filtered and concentrated under reduced pressure. The crude mixture was purified by silica gel chromatography (1-20% DCM in hexane) to yield trans-cyclooctene S46 as a single diastereomer and with exclusive E-selectivity (2.08 g, 69%); δ_H(400 MHz, CDCl₃) 7.72-7.62 (4H, m), 7.46-7.34 (6H, m), 5.83 (1H, ddd, J 16.1, 9.2, 6.2), 5.11 (1H, ddd, J 16.1, 10.6, 3.3), 3.59 (2H, d, J 5.7), 2.28-2.40 (1H, m), 2.12-2.27 (3H, m), 1.80-1.95 (2H, m), 1.04 (9H, s), 0.74-0.90 (1H, m), 0.46-0.60 (1H, dm, J 14.0), 0.31-0.42 (2H, m), 0.18-0.29 (1H, m); (101 MHz, CDCl₃) 138.6, 135.8, 134.4, 131.3, 129.6, 127.7, 68.1, 39.0, 34.1, 32.9, 28.2, 27.9, 27.0, 21.6, 20.5, 19.4.
Tetrabutylammonium fluoride (1M solution in THF, 10.0 ml, 10.0 mmol) was added to a stirring solution of silyl ether S46 (0.78 g, 2 mmol) in THF (5 mL) at room temperature, wrapped in tin foil and stirred for 45 min. After this period, the reaction mixture was concentrated under reduced pressure, diluted with DCM (100 mL) and washed with brine (100 ml.). The phases were separated and the organic phase washed with brine (2×100 mL). The combined organics were dried over sodium sulfate, filtered and concentrated under reduced pressure. The crude material was purified by silica gel chromatography (20% EtOAc in hexane) to yield primary alcohol S47 as a colorless oil (0.29 g, 96%); δ_H(400 MHz, d₄-MeOD) 5.87 (1H, ddd, J 16.5, 9.3, 6.2), 5.13 (1H, dddd, J 16.5, 10.4, 3.9, 0.8), 3.39-3.47 (2H, dd, J 6.2, 1.5), 2.34-2.44 (1H, m), 2.12-2.33 (3H, m), 1.82-1.98 (2H; m), 0.90 (1H, dtd, J 12.5, 12.5, 7.1), 0.55-0.70 (1H, m), 0.41-0.55 (1H, m), 0.27-0.41 (2H, m); δ_C(101 MHz, d₄-MeOD) 139.3, 132.2, 67.5, 39.9, 34.8, 33.8, 29.2, 28.7, 23.0, 21.9; MS-CI (NH₃): m/z [M−OH] calcd. for C₁₀H₁₅, 135.1174; found 135.1173.
pNO₂-phenyl carbonate 548 (250 mg, 0.79 mmol) was added to a stirring solution of Fmoc-Lys-OH·HCl (478 mg, 1.18 mmol) and DIPEA (0.27 mL, 1.58 mmol) in DMF (3 mL) at 0° C. The solution was warmed to room temperature, wrapped in tin foil and stirred for 16 h. After this period the solution was concentrated under reduced pressure and purified by silica gel chromatography (0-5% McOH in DCM) to yield Fmoc-exo-sTCOK S49 as a white foam (373 mg, 87%). δ_H(400 MHz, d₆-DMSO) 13.09-12.06 (1H, br s), 7.90 (2H, d, J 7.5), 7.73 (2H, d, J 7.5), 7.66-7.56 (1H, m), 7.43 (2H, t, J 7.4), 7.34 (2H, J 7.4), 7.08 (1H, t, J 5.4), 5.84-5.72 (1H, m), 5.13-5.01 (1H, m), 4.31-4.19 (3H, m), 3.93-3.79 (3H, m), 3.00-2.90 (2H, m), 2.31-2.07 (4H, m), 1.91-1.78 (2H, m), 1.75-1.49 (2H, m), 1.45-1.22 (4H, m), 0.91-0.75 (1H, m), 0.62-0.45 (2H, m), 0.43-0.32 (2H, m); δ_C(101 MHz, d₆-DMSO) 173.9, 156.4, 156.1, 143.8, 140.7, 137.9, 131.0, 127.6, 127.0, 125.2, 120.1, 79.1, 67.9, 65.6, 53.8, 46.6, 38.1, 33.4, 31.9, 30.4, 29.0, 27.2, 24.3, 22.8, 21.2, 20.2; LRMS (ESI⁺): m/z 545 (100% [M−H]⁻).
Lithium hydroxide monohydrate (94 mg, 0.75 mmol) was added to a stirring solution of exo-sTCOK S49 in THF:H₂O (3:1, 8 mL). The solution was wrapped in tin foil, stirred for 4 h at room temperature and EtOAc (100 mL) and H₂O (100 mL) were added. The aqueous phase was carefully acidified to pH 4 by the addition of AcOH and extracted with EtOAc (4×100 mL). The aqueous phase was evaporated under reduced pressure and freeze-dried to yield exo-sTCOK 3 as a white solid. For all subsequent labeling experiments using mammalian cells exo-H-bcnK-OH 1 was further purified by reverse-phase HPLC (0:1 H₂O:MeCN to 9:1 H₂O:MeCN gradient). δ_H(400 MHz, d₆-DMSO) 7.21-7.09 (1H, br m), 5.85-5.72 (1H, m), 5.14-5.02 (1H, m), 3.80 (2H, d, J 2.6), 3.14-3.05 (1H, m), 2.98-2.86 (2H, m), 2.31-2.08 (4H, m), 1.92-1.78 (2H, m), 1.73-1.65 (1H, m), 1.55-1.44 (1H, m), 1.41-1.25 (4H, m), 0.90-0.62 (1H, m), 0.65-0.45 (2H, m), 0.43-0.32 (2H, m); δ_C(101 MHz, d₆-DMSO) 175.5, 156.3, 137.9, 131.1, 67.8, 54.5, 38.1, 33.4, 32.1, 32.0, 29.2, 27.2, 24.7, 24.3, 22.5, 21.2, 20.2; LRMS (ESI⁺): m/z 325 (100% [M+H]⁺).

REFERENCES TO SUPPLEMENTARY EXAMPLES

1. Gautier, A. et al. Genetically encoded photocontrol of protein localization in mammalian cells. J Am Chem Soc 132, 4086-8 (2010).
2. Lang, K. et al. Genetically encoded norbornene directs site-specific cellular protein labelling via a rapid bioorthogonal reaction. Nature chemistry 4, 298-304 (2012).
3. Dommerholt, J. et al. Readily Accessible Bicyclononynes for Bioorthogonal Labeling and Three-Dimensional Imaging of Living Cells. Angewandte Chemie-International Edition 49, 9422-9425 (2010).
4. Yang, J., Karver, M. R., Li, W., Sahu, S. & Devaraj, N. K. Metal-catalyzed one-pot synthesis of tetrazines directly from aliphatic nitriles and hydrazine. Angewandte Chemie 51, 5222-5 (2012).
5. Taylor, M. T., Blackman, M. L., Dmitrenko, O. & Fox, J. M. Design and synthesis of highly reactive dienophiles for the tetrazine-trans-cyclooctene ligation. Journal of the American Chemical Society 133, 9646-9 (2011).
6. Royzen, M., Yap, G. P. & Fox, J. M. A photochemical synthesis of functionalized trans-cyclooctenes driven by metal complexation. Journal of the American Chemical Society 130, 3760-1 (2008).
7. Zhang, K., Lackey, M. A., Cui, J. & Tew, G. N. Gels based on cyclic polymers. Journal of the American Chemical Society 133, 4140-8 (2011).

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All publications mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described aspects and embodiments of the present invention will be apparent to those skilled in the art without departing from the scope of the present invention. Although the present invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are apparent to those skilled in the art are intended to be within the scope of the following claims.

Claims

1-17. (canceled)

18. A polypeptide characterized by comprising an amino acid having a bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) group.

19. The polypeptide according to claim 18, wherein said BCN group is present as a residue of a lysine amino acid.

20. The polypeptide according to claim 18, which comprises a single BCN group.

21. The polypeptide according to claim 18, wherein said BCN group is joined to a tetrazine group.

22. The polypeptide according to claim 21, wherein said tetrazine group is further joined to a fluorophore.

23. The polypeptide according to claim 22, wherein said fluorophore comprises fluorescein, tetramethyl rhodamine (TAMRA) or boron-dipyrromethene (BODIPY).

24. The polypeptide according to claim 18, wherein the BCN group is BCN lysine and has the structure:

25. An amino acid incorporated into a polypeptide, wherein the amino acid comprises bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN).

26. The amino acid according to claim 25, characterized by the fact that it is bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) lysine.

27. The amino acid according to claim 26, wherein the BCN lysine has the structure:

28. A method of producing a polypeptide comprising a bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) group in a cell, said method comprising genetically incorporating an amino acid comprising a BCN group into a polypeptide in a cell, wherein said amino acid comprising a BCN group is a BCN lysine, and wherein producing the polypeptide comprises:

(i) providing a nucleic acid encoding the polypeptide which nucleic acid comprises an orthogonal codon encoding the amino acid having a BCN group; and

(ii) translating said nucleic acid in the cell,

wherein said BCN group is in the exo form,

wherein said BCN lysine has the structure:

29. The method according to claim 28, wherein the nucleic acid is translated in the presence of an orthogonal tRNA synthetase/tRNA pair capable of recognizing said orthogonal codon and incorporating said amino acid having a BCN group into the polypeptide chain.

30. The method according to claim 28, wherein said orthogonal codon comprises an amber codon (TAG) and said tRNA is mbtRNA_CUA.

31. The method according to claim 28, wherein said amino acid having a BCN group is incorporated at a position corresponding to a lysine residue in the wild type polypeptide.

32. The method according to claim 28, wherein the method produces a polypeptide comprising a single BCN group.

33. The method according to claim 28, further comprising:

(iii) contacting the translated polypeptide with a tetrazine compound, and incubating to allow joining of the tetrazine compound to the BCN group by an inverse electron demand Diels-Alder cycloaddition reaction.

34. The method according to claim 33, wherein the tetrazine compound has the chemical formula of

a) Formula VI, wherein:

(i) X=CH, R=BOC (Formula VI-1);

(ii) X=N, R=BOC (Formula VI-2);

(iii) X=CH, R=TAMRA-X (Formula VI-3);

(iv) X=N, R=TAMRA-X (Formula VI-4);

(v) X=CH, R=BODIPY TMR-X (Formula VI-5); or

(vi) X=CH, R=TAMRA (Formula VI-6),

b) Formula VII, wherein:

(i) R=BOC (Formula VII-1):

(ii) R=TAMRA-X (Formula VII-2); or

(iii) R=BODIPY-FL (Formula VII-3),

c) Formula VIII, wherein R=BOC (Formula VIII-I), or

d) Formula IX, wherein:

(i) R=BOC (Formula IX-I); or

(ii) R=5-(6)-carboxyfluorescein diacetate (CFDA) (Formula IX-2).

35. The method according to claim 34, wherein the tetrazine compound has the chemical formula selected from the group consisting of Formula VI-1, Formula VI-2, Formula VII-1 and Formula VIII-1, and wherein the pseudo first order rate constant for the reaction is at least 80 M⁻¹S⁻¹.

36. The method according to claim 33, wherein said reaction of step (iii) is allowed to proceed for 10 minutes or less.

37. The method according to claim 33, wherein said reaction of step (iii) is allowed to proceed for 1 minute or less.

38. The method according to claim 33, wherein said reaction of step (iii) is allowed to proceed for 30 seconds or less.

39. The method according to claim 34, wherein said tetrazine compound has the chemical formula selected from the group consisting of Formula VI-3, Formula VI-4, Formula VI-5, Formula VI-6, Formula VII-2, Formula VII-3, and Formula IX-2.

40. The method according to claim 33, wherein said tetrazine compound is further joined to a fluorophore.

41. The method according to claim 40, wherein said fluorophore comprises fluorescein, tetramethyl rhodamine (TAMRA) or boron-dipyrromethene (BODIPY).