EP1311516A1 - Novel amidite derivatives for synthesising polymers on surfaces - Google Patents

Abstract

The invention relates to novel amidite derivatives and the use thereof as linker elements for synthesising polymers, especially biopolymers such as nucleic acids, peptides and saccharides, on the surface of solid carriers. The use of the inventive linker derivatives enables surfaces to be regenerated in a non-destructive manner.

Description

New amidite derivatives for the synthesis of polymers on surfaces

description

The invention relates to new amidite derivatives and their use as linker building blocks for the synthesis of polymers, in particular biopolymers such as nucleic acids, peptides and saccharides, on the surface of solid supports. The use of the linker derivatives according to the invention permits non-destructive regeneration of the surfaces.

Since Merryfield introduced the synthesis of biopolymers on solid surfaces in 1 965, a large number of publications on this technique have appeared. A recent development in this area is the production of so-called biopolymer arrays, in which a large number of different biopolymers, such as nucleic acids or peptides, are immobilized on a carrier in defined areas.

In the synthesis of biopolymers on a solid phase, a spacer, a so-called spacer, is generally used between the support and the actual biopolymer. The use of a spacer has the advantage that the biopolymer is further away from the surface of the solid support, so that its influences are suppressed, so that the immobilized biopolymer can undergo quasi-homogeneous reactions. The nature of the spacer, its length, polarity and its other physicochemical properties consequently have a decisive influence on the coupling yield in the polymer system on the support, and thus on the quality of the polymer and its later use.

In general, strategies based on the polycondensation of amino acid monomers in the broadest sense are used for the spacer construction or cyanoethyl- or otherwise protected phosphoramidites or H-phosphonates. Compounds with the following general structure are usually used:

R '

O

O Q

O

R

wherein R 'represents a protected linker group, R represents the predecessor synthetic building block or the functional group of a solid phase and Q represents H or an organic protective group such as cyanoethoxy or methoxy, which plays no role in anchoring on the surface.

A major disadvantage of the spacer molecules known hitherto are the negative charges which occur on the phosphate groups as the protective groups are split off. These additional potential coupling centers prevent possible recycling by suitable chemical or enzymatic procedures of the spacers.

The object on which the invention is based was therefore to provide new spacer units for the synthesis of polymers on solid supports. This object is achieved by a compound of the general formula (I) R ³ OOR ^A

.N

R ¹ R ²

wherein R ¹ and R ² each independently represent a C _r C ₁₀ hydrocarbon radical, for example a C _r C ₆ alkyl radical or the C ₃ -C ₄ cycloalkyl radical, or are linked to one another, for example to form a 5- or 6-membered ring surrender and

R ³ and R ^{4 are} each independently a protected linker group of the general formula (II):

L- (X> n

where L is a linker, X is a protecting group and n is an integer from 1-3.

in the compounds (I) R ¹ and R ^{2 are} preferably each methyl, ethyl or i-propyl radicals or together they form a morpholine radical. However, other alkyl or cycloalkyl radicals can of course also be used.

The linker group (II) generally contains linear or branched aliphatic, olefinic and / or aromatic hydrocarbon groups which are optionally substituted by heteroatoms. It preferably contains an alkylene chain in which one or more CH ₂ groups can optionally be replaced by heteroatoms such as O, S or NH. The chain length of the linker is preferably 1 to 100 atoms, preferably 10 to 45 atoms and particularly preferably 1 to 25 atoms. The chain can also contain one or more branches, a linker group preferably up to can contain three branches. The branches can be introduced into the linker group, for example by ω-bis- or tfishydroxy compounds such as tris (hydroxymethyl) aminomethane. In a particularly preferred embodiment, the linker group (II) contains a structure selected from (a) (CH ₂ ) _n -X, where n = 1 -1 2, preferably 3-6, or (b) [(CH ² ) _r O] _s -X where r = 1 -4, preferably 2-3 and s = 1 -1 00, preferably 3-9.

At the end or at the ends of the linker group there are one or more protective groups X which are suitable for the solid-phase synthesis of

Known protective groups can be selected from nucleic acids or peptides. X is preferably a protective group which can be cleaved from the linker by chemical or enzymatic reactions, with the cleavage resulting in a reactive group e.g. a hydroxyl or amino group is released. Examples of suitable protective groups are acid-labile protective groups such as dimethoxytrityl (DMT), MMT, Pixyl,

Fpmp, base-labile protective groups, such as benzyl, benzoyl, isobutyryl,

Phenoxyacetyl, laevulinyl etc., oxidation and / or reduction labile

Protecting groups, photolabile protecting groups such as NVOC, NPPOC, catalytic, e.g. Pd removable protecting groups such as allyl, AOC and fluoride removable protecting groups such as TMS and derivatives thereof e.g. TBDMS.

The compounds according to the invention are outstandingly suitable as spacers or spacer units for the synthesis of polymers on solid supports. One or more molecules of the compounds (I) can be used for the synthesis of a polymer molecule. The compounds (I) are usually first coupled to the support to build up the spacer and then the polymer is synthesized on the spacer using suitable synthesis components. Inorganic or organic carriers come into consideration as solid phases, for example functionalized controlled-pore glass (CPG), other glasses such as Foturan, Pyrex or ordinary soda-lime. Glasses, metallic supports such as silicon, or organic resins such as tentagel. The carrier is particularly preferably a chip which is used for the synthesis of polymer arrays.

The present invention thus also relates to a support for solid phase synthesis of the general formula (Ia)

wherein T is a solid support as previously indicated and R ³ and R ^{4 are} as previously defined. The carrier (Ia) is produced by coupling a compound (I) to a reactive group of the carrier, for example a hydroxyl group, with elimination of the - NR ¹ NR ² group. Possibly. For example, the support (Ia) can be oxidized with molecular l ₂ , the P atom being transferred from oxidation level III to oxidation level V.

At least one of the protective groups X can be split off at the linkers R ³ and R ⁴ . One or more polymers can be synthesized onto the reactive groups released after the protective groups X have been split off, these polymers being able to be selected from, for example, nucleic acids such as DNA or RNA, nucleic acid analogs such as PNA or LNA, peptides and saccharides.

The compounds (I) according to the invention are notable for the fact that they do not require a P (V) protective group and, after deblocking and, if appropriate, oxidation to give the phosphate, do not have a negative charge. In this way The compounds according to the invention can be used in conjunction with other synthetic building blocks, for example trifunctional sugar or nucleotide units which are provided with orthogonal protective groups, for the construction of polymers and for the non-destructive recycling of the surfaces, without disruptive charges occurring in subsequent syntheses.

The compound (I) according to the invention is first reacted

Group, e.g. a hydroxyl group of the solid support is coupled.

The protective group X is then split, the protective group

X is orthogonal to a protecting group Y on the polymer synthesis building block. After the end of the polymer synthesis and, if necessary, deblocking of the resulting polymers, it becomes the one used previously

Synthesis conditions cleaved orthogonal protecting group Y. On

An example of such a synthesis block with the general formula is as follows:

wherein X and Y are protective groups orthogonal to one another, where X is, for example, an acid- and / or photolabile protective group and Y is a protective group which can be split off by catalysis and R represents a nucleobase or a fluorophore, a chromophore or another labeling group. After Y has been split off in a basic medium, the 3'-phosphate is attacked by the 2'-hydroxy group to form a cyclic phosphate, which is equivalent to hydrolysis and leads to the restoration of the original hydroxy group. If an RNA section is used as a probe "base", chemical regeneration of the reaction carrier can take place. The synthesis is first carried out using 2'-OH-protected phosphitamide building blocks. After hybridization, the protective group of the RNA section is split off, resulting in a free 2'-OH group. The ribose sugar can then be cleaved in a subsequent chemical reaction step using periodate or other oxidizing agents and the probe can be removed from the reaction carrier by β-elimination.

The compound la according to the invention can also be used by means of suitable biochemical approaches without the coupling in of a special molecule for the non-destructive recycling of the surfaces. Here, the polymer or oligomer probes linked to the reaction carrier are cleaved with a DNA or RNA-degrading enzyme or a peptide-cleaving enzyme, which leads to partial or complete degradation of the probes. The reaction support can then be used again for the synthesis of new probes.

Suitable enzymes are nucleases such as exonucleases or endonucleases, which attack a strand of nucleic acid from the ends or within the probe strand and leave nucleotides or nucleosides as cleavage products. In the case of RNA, the use of RNAsen (such as RNAse H etc.) is possible, which selectively cut the RNA part when an RNA-DNA double strand is formed, as a result of which the entire probe is used as the predetermined breaking point in the case of RNA probes and in the case of RNA sections RNA section is cleaved. The regeneration of a reaction carrier with DNA probes can also be achieved by using DNAse (DNAse I, DNAse II, etc.), whereby both single-stranded and double-stranded DNA can be degraded. Peptide-cleaving enzymes can also be used as a predetermined breaking point for the degradation of peptide probes or peptide sequence sections.

Another advantage of the compounds according to the invention is that signal amplification takes place due to the branching, since the doping density of the functional groups on the surface is increased. Furthermore, the compounds according to the invention are distinguished by the fact that they enable more cost-effective polymer synthesis and can be easily integrated into the DNA solid-phase synthesis, while at the same time reducing the required amidite ports compared to the use of commercially available amidites.

The compounds according to the invention are prepared by reacting the mono-protected basic spacer molecules with phosphorus trichloride to give the bisubstituted monochloro derivative. The secondary amine is then introduced into the molecule.

The invention is further illustrated by the following example.

Example 1 :

Preparation of bis (9-O-dimethoxytrityltriethylene glycol) - [N, N-diisopropyI] - phosphoramidite

1.37 g (10 mmol) of PCI ₃ and 5 equivalents of N-ethyldiisopropylamine or pyridine are taken up under protective gas in absolute ether. Monotritylated triethylene glycol, dissolved in ether and N-ethyldiisopropylamine, is slowly added dropwise to this cooled solution. After stirring for two hours at room temperature, 3 equivalents of diisopropylamine, dissolved in ether, are slowly added dropwise to the reaction mixture. The mixture is then left for a further 1 2 h at room temperature stir. After concentration, the mixture is taken up in methylene chloride and extracted several times with the customary solutions before the substance is then isolated by chromatography on silica gel.

The synthesis scheme is shown in Fig. 1A.

Example 2:

As an alternative to the procedure described in Example 1, PCI _{3 can} also be reacted with heterocyclic nitrogen bases, such as pyrrole, triazole or imidazole, and then only with monotritylated triethylene glycol, if appropriate in the presence of an activator, such as tetrazole.

The corresponding synthesis schemes are shown in Fig. 1 B and 1 C.

Claims

Expectations 1 . Compound of the general formula (I) wherein R and R ² each independently represent a C, -C ₁₀ hydrocarbon radical or are bonded together to form a 5- or 6-membered ring and R ³ and R ^{4 are} each independently a protected linker group of the general formula (II): - L- (X) _n (II) where L is a linker, X is a protecting group and n is an integer from 1-3. 2. A compound according to claim 1, characterized in that R ¹ and R ² each independently represent a C _r C ₆ alkyl radical or a C ₃ -C ₄ cycloalkyl radical. 3. A compound according to claim 1 or 2, characterized in that R ¹ and R ^{2 are} each methyl, ethyl or i-propyl or together form a morpholine residue. 4. A compound according to any one of claims 1 to 3, characterized in that the linker group (II) contains linear or branched aliphatic, olefinic and / or aromatic hydrocarbon groups, which are optionally partially substituted by heteroatoms. 5. A compound according to any one of claims 1 to 4, characterized in that the linker group (II) (a) a structure - (CH ₂ ) _m -X where m = 1 - 1 2 or (b) a structure - [(CH ₂ ) _r O] _s -X where r = 1-4 and s = 1-100 contains. 6. Compound according to one of claims 1 to 5, characterized in that X is a protective group selected from protective groups which can be split off by chemical or enzymatic reactions. 7. A compound according to claim 6, characterized in that X is an acid-labile protective group. 8. A compound according to claim 6, characterized in that X is a base-labile protective group. , A compound according to claim 6, characterized in that X is an oxidation and / or reduction labile protective group. 0. A compound according to claim 6, characterized in that X is a photolabile protecting group. 1 . A compound according to claim 6, characterized in that X is a protective group which can be split off catalytically. 2. Compound according to claim 6, characterized in that X is a protective group which can be split off by fluoride. 3. Carrier for solid phase synthesis of the general formula (Ia) wherein T is a solid support and R ³ and R ^{4 are} as defined in any one of claims 1 and 4 to 1 2. 4. Carrier according to claim 1 3, characterized in that at least one protective group X is split off in the linker groups R ³ and R ⁴ . 5. A carrier according to claim 14, characterized in that one or more polymers are synthesized on the reactive groups released after the protective groups X have been split off. 6. Carrier according to claim 1 5, characterized in that the polymer is selected from nucleic acids, nucleic acid analogs, peptides and saccharides. 7. A process for the synthesis of polymers on a solid support, characterized in that a compound of the formula (I) as defined in claims 1 to 1 2 is covalently coupled to the solid support and then on the compound (I) from synthesis building blocks Polymer builds up. 8. The method according to claim 1 7, characterized in that the compound (I) is coupled to a hydroxyl group on the solid support. 9. The method according to claim 17 or 1 8, characterized in that the polymers are selected from nucleic acids, nucleic acid analogs, peptides and saccharides.