EP0765334A1 - Purification de phosphorothioates d'oligodesoxynucleotides a l'aide de la chromatographie echangeuse d'anions deae 5pw et de la chromatographie hydrophobe - Google Patents
Purification de phosphorothioates d'oligodesoxynucleotides a l'aide de la chromatographie echangeuse d'anions deae 5pw et de la chromatographie hydrophobeInfo
- Publication number
- EP0765334A1 EP0765334A1 EP95925363A EP95925363A EP0765334A1 EP 0765334 A1 EP0765334 A1 EP 0765334A1 EP 95925363 A EP95925363 A EP 95925363A EP 95925363 A EP95925363 A EP 95925363A EP 0765334 A1 EP0765334 A1 EP 0765334A1
- Authority
- EP
- European Patent Office
- Prior art keywords
- oligonucleotide
- dmt
- column
- phosphorothioates
- oligonucleotides
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Withdrawn
Links
- RYYWUUFWQRZTIU-UHFFFAOYSA-N Thiophosphoric acid Chemical class OP(O)(S)=O RYYWUUFWQRZTIU-UHFFFAOYSA-N 0.000 title claims abstract description 35
- 238000004191 hydrophobic interaction chromatography Methods 0.000 title claims description 39
- 238000000746 purification Methods 0.000 title description 23
- 238000004255 ion exchange chromatography Methods 0.000 title description 18
- 229940046166 oligodeoxynucleotide Drugs 0.000 title description 15
- 150000001450 anions Chemical class 0.000 title description 4
- 108091034117 Oligonucleotide Proteins 0.000 claims abstract description 133
- FAPWRFPIFSIZLT-UHFFFAOYSA-M Sodium chloride Chemical compound [Na+].[Cl-] FAPWRFPIFSIZLT-UHFFFAOYSA-M 0.000 claims abstract description 66
- 238000000034 method Methods 0.000 claims abstract description 61
- JLCPHMBAVCMARE-UHFFFAOYSA-N [3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methyl [5-(6-aminopurin-9-yl)-2-(hydroxymethyl)oxolan-3-yl] hydrogen phosphate Polymers Cc1cn(C2CC(OP(O)(=O)OCC3OC(CC3OP(O)(=O)OCC3OC(CC3O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c3nc(N)[nH]c4=O)C(COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3CO)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cc(C)c(=O)[nH]c3=O)n3cc(C)c(=O)[nH]c3=O)n3ccc(N)nc3=O)n3cc(C)c(=O)[nH]c3=O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)O2)c(=O)[nH]c1=O JLCPHMBAVCMARE-UHFFFAOYSA-N 0.000 claims abstract description 37
- 239000011780 sodium chloride Substances 0.000 claims abstract description 33
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- USFZMSVCRYTOJT-UHFFFAOYSA-N Ammonium acetate Chemical group N.CC(O)=O USFZMSVCRYTOJT-UHFFFAOYSA-N 0.000 claims description 32
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- 229940043376 ammonium acetate Drugs 0.000 claims description 32
- 235000019257 ammonium acetate Nutrition 0.000 claims description 32
- VHUUQVKOLVNVRT-UHFFFAOYSA-N Ammonium hydroxide Chemical compound [NH4+].[OH-] VHUUQVKOLVNVRT-UHFFFAOYSA-N 0.000 claims description 24
- 239000000908 ammonium hydroxide Substances 0.000 claims description 24
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- 229920005989 resin Polymers 0.000 claims description 12
- NAGJZTKCGNOGPW-UHFFFAOYSA-N dithiophosphoric acid Chemical class OP(O)(S)=S NAGJZTKCGNOGPW-UHFFFAOYSA-N 0.000 claims description 9
- 238000011033 desalting Methods 0.000 claims description 8
- 238000011068 loading method Methods 0.000 claims description 5
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- MTLZEBXFKNNOHO-UHFFFAOYSA-N 1-[5-[[[2-[[[2-[[[2-[[[2-[[[2-[[[2-[[[5-(2-amino-6-oxo-1h-purin-9-yl)-2-[[[5-(4-amino-2-oxopyrimidin-1-yl)-2-[[[2-[[[5-(4-amino-2-oxopyrimidin-1-yl)-2-[[[2-[[[5-(4-amino-2-oxopyrimidin-1-yl)-2-(hydroxymethyl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethy Chemical compound O=C1NC(=O)C(C)=CN1C1OC(COP(O)(=S)OC2C(OC(C2)N2C(N=C(N)C=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C(NC(=O)C(C)=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C(NC(=O)C(C)=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C(N=C(N)C=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C(N=C(N)C=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C(NC(=O)C(C)=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C(N=C(N)C=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C(NC(=O)C(C)=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C(N=C(N)C=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C(NC(=O)C(C)=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C(N=C(N)C=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C(NC(=O)C(C)=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C3=NC=NC(N)=C3N=C2)COP(O)(=S)OC2C(OC(C2)N2C(N=C(N)C=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C(N=C(N)C=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C(N=C(N)C=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C3=NC=NC(N)=C3N=C2)COP(O)(=S)OC2C(OC(C2)N2C(N=C(N)C=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C3=C(C(NC(N)=N3)=O)N=C2)COP(S)(=O)OC2C(OC(C2)N2C(N=C(N)C=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C(NC(=O)C(C)=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C(N=C(N)C=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C(NC(=O)C(C)=C2)=O)COP(O)(=S)OC2C(OC(C2)N2C(N=C(N)C=C2)=O)CO)C(O)C1 MTLZEBXFKNNOHO-UHFFFAOYSA-N 0.000 description 20
- 239000000047 product Substances 0.000 description 20
- WEVYAHXRMPXWCK-UHFFFAOYSA-N Acetonitrile Chemical compound CC#N WEVYAHXRMPXWCK-UHFFFAOYSA-N 0.000 description 18
- 238000004366 reverse phase liquid chromatography Methods 0.000 description 18
- 239000000243 solution Substances 0.000 description 16
- XLYOFNOQVPJJNP-UHFFFAOYSA-N water Substances O XLYOFNOQVPJJNP-UHFFFAOYSA-N 0.000 description 16
- 238000012856 packing Methods 0.000 description 11
- 238000004128 high performance liquid chromatography Methods 0.000 description 10
- 238000000926 separation method Methods 0.000 description 10
- -1 DEAE 5PW ANION Chemical class 0.000 description 9
- 238000001818 capillary gel electrophoresis Methods 0.000 description 9
- RYYWUUFWQRZTIU-UHFFFAOYSA-K thiophosphate Chemical compound [O-]P([O-])([O-])=S RYYWUUFWQRZTIU-UHFFFAOYSA-K 0.000 description 9
- QKNYBSVHEMOAJP-UHFFFAOYSA-N 2-amino-2-(hydroxymethyl)propane-1,3-diol;hydron;chloride Chemical compound Cl.OCC(N)(CO)CO QKNYBSVHEMOAJP-UHFFFAOYSA-N 0.000 description 8
- 238000004587 chromatography analysis Methods 0.000 description 8
- 238000004458 analytical method Methods 0.000 description 7
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- 238000001704 evaporation Methods 0.000 description 7
- 239000002773 nucleotide Substances 0.000 description 7
- 125000003729 nucleotide group Chemical group 0.000 description 7
- 238000006467 substitution reaction Methods 0.000 description 7
- HEMHJVSKTPXQMS-UHFFFAOYSA-M Sodium hydroxide Chemical compound [OH-].[Na+] HEMHJVSKTPXQMS-UHFFFAOYSA-M 0.000 description 6
- 239000006167 equilibration buffer Substances 0.000 description 6
- 239000011521 glass Substances 0.000 description 6
- 230000001225 therapeutic effect Effects 0.000 description 6
- KCXVZYZYPLLWCC-UHFFFAOYSA-N EDTA Chemical compound OC(=O)CN(CC(O)=O)CCN(CC(O)=O)CC(O)=O KCXVZYZYPLLWCC-UHFFFAOYSA-N 0.000 description 5
- 229920005654 Sephadex Polymers 0.000 description 5
- 239000012507 Sephadex™ Substances 0.000 description 5
- VYPSYNLAJGMNEJ-UHFFFAOYSA-N Silicium dioxide Chemical compound O=[Si]=O VYPSYNLAJGMNEJ-UHFFFAOYSA-N 0.000 description 5
- 229940124276 oligodeoxyribonucleotide Drugs 0.000 description 5
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- 125000006239 protecting group Chemical group 0.000 description 5
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- BFSVOASYOCHEOV-UHFFFAOYSA-N 2-diethylaminoethanol Chemical compound CCN(CC)CCO BFSVOASYOCHEOV-UHFFFAOYSA-N 0.000 description 4
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- BJDCWCLMFKKGEE-CMDXXVQNSA-N chembl252518 Chemical compound C([C@@](OO1)(C)O2)C[C@H]3[C@H](C)CC[C@@H]4[C@@]31[C@@H]2O[C@H](O)[C@@H]4C BJDCWCLMFKKGEE-CMDXXVQNSA-N 0.000 description 3
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- 108020004707 nucleic acids Proteins 0.000 description 3
- 150000007523 nucleic acids Chemical class 0.000 description 3
- 102000039446 nucleic acids Human genes 0.000 description 3
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- 150000004713 phosphodiesters Chemical class 0.000 description 3
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- 229910002027 silica gel Inorganic materials 0.000 description 3
- 159000000000 sodium salts Chemical group 0.000 description 3
- 208000030507 AIDS Diseases 0.000 description 2
- 108020000948 Antisense Oligonucleotides Proteins 0.000 description 2
- LFQSCWFLJHTTHZ-UHFFFAOYSA-N Ethanol Chemical compound CCO LFQSCWFLJHTTHZ-UHFFFAOYSA-N 0.000 description 2
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- 125000002221 trityl group Chemical group [H]C1=C([H])C([H])=C([H])C([H])=C1C([*])(C1=C(C(=C(C(=C1[H])[H])[H])[H])[H])C1=C([H])C([H])=C([H])C([H])=C1[H] 0.000 description 2
- 239000011534 wash buffer Substances 0.000 description 2
- CHRJZRDFSQHIFI-UHFFFAOYSA-N 1,2-bis(ethenyl)benzene;styrene Chemical compound C=CC1=CC=CC=C1.C=CC1=CC=CC=C1C=C CHRJZRDFSQHIFI-UHFFFAOYSA-N 0.000 description 1
- 229920000936 Agarose Polymers 0.000 description 1
- 108020004491 Antisense DNA Proteins 0.000 description 1
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- 206010061598 Immunodeficiency Diseases 0.000 description 1
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- 102000000589 Interleukin-1 Human genes 0.000 description 1
- 108010002352 Interleukin-1 Proteins 0.000 description 1
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- YACKEPLHDIMKIO-UHFFFAOYSA-N methylphosphonic acid Chemical compound CP(O)(O)=O YACKEPLHDIMKIO-UHFFFAOYSA-N 0.000 description 1
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- 125000002467 phosphate group Chemical group [H]OP(=O)(O[H])O[*] 0.000 description 1
- PTMHPRAIXMAOOB-UHFFFAOYSA-L phosphoramidate Chemical compound NP([O-])([O-])=O PTMHPRAIXMAOOB-UHFFFAOYSA-L 0.000 description 1
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Classifications
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
- C07H1/00—Processes for the preparation of sugar derivatives
- C07H1/06—Separation; Purification
Definitions
- This invention relates to the field of purification of oligodeoxynucleotides, and in particular, the purification of oligodeoxynucleotide phosphorothioates.
- modified phosphate backbone oligodeoxynucleotides as antisense oligonucleotides in the field of selective gene regulation for therapeutic purposes has received increasing attention over the last several years.
- modified phosphate linkages e.g. , methylphosphonate, phosphorothioate, phosphoramidate, that have been incorporated into antisense oligonucleotides and studied.
- Oligodeoxyribonucleotide phosphorothioates have been found to inhibit immunodeficiency virus (Agrawal et al. , Proc Natl. Acad. Sci. Usa 85, 7079 (1988); Agrawal et al. , Proc Natl. Acad. Sci. USA 86, 7790 (1989); Agrawal et al. , in Advanced Drug Delivery Reviews 6, 251 (R. Juliano, Ed. , Elsevier, Amsterdam, 1991); Agrawal et al. in Prospects for Antisense Nucleic Acid Therapy of Cancer and AIDS, 143 (E.
- Oligonucleotides are produced step wise, with the addition of one monomer at a time to the nascent oligonucleotide chain. 2-3 % of the reactions fail during each cycle in which a nucleotide monomer is to be added however. Consequently, the resulting products are generally a heterogenous mixture of oligonucleotides of varying length. For example, in a typical 20mer synthesis, the 20mer product represents only 50- 60% of the recovered oligonucleotide product.
- oligodeoxynucleotides on a solid phase support requires that the oligodeoxynucleotide be cleaved from the support. Cleavage of the oligo from the support is typically accomplished by treating the solid phase with concentrated ammonium hydroxide.
- the ammonium hydroxide is conventionally removed under reduced pressure using, for example, a rotary evaporator. This method for removing the ammonium hydroxide, however, is not ideal for use in large scale isolation of oligodeoxynucleotides.
- the present invention provides improved methods for purifying oligodeoxynucleotide phosphorothioates.
- the invention provides purification techniques suitable for large scale separation of oligonucleotide phosphorothioates.
- the purification methods of the invention do not require the use of reduced pressure to remove ammonium hydroxide or the use of conventional C-18 silica gel reverse-phase liquid chromatography.
- the inventive methods replace these procedures with hydrophobic interaction chromatography or DEAE-5PW anion ion-exchange chromatography.
- the oligodeoxynucleotides are purified using hydrophobic interaction chromatography.
- Ammonium hydroxide is used to cleave oligonuc-leotides from the solid support on which they were synthesized.
- roto- evaporation under reduced pressure has been used to remove most of the ammonium hydroxide.
- reversed phase chromatography is then typically followed with reversed phase chromatography to separate the DMT-on oligonucleotides from the DMT-off oligonucleotides.
- hydrophobic interaction chromatography is used in place of roto-evaporation alone or both roto-evaporation and reversed phase chromatography.
- HIC is preferable to roto- evaporation because it simplifies and accelerates ammonium hydroxide removal and can be used for large scale purification. If it is to be followed by RPLC, HIC increases the purity of the oligonucleotide relative to roto-evaporation, resulting in less potential for fouling the RPLC column and reducing the purification challenge presented to the RPLC column.
- HIC When used in place of roto-evaporation and RPLC, HIC provides the benefit of accomplishing two tasks (removal of ammonium hydroxide and separation of DMT-on Oligos from DMT-off oligos) at once. Substitution of RPLC with HIC also reduces the resin cost, eliminates the need for organic solvents (which require more stringent handling, including special disposal, explosion-proof environment, and evaporative equipment), provides for more rapid elimination of contaminants (e.g. , unreacted monomers and failure sequences), and increases throughput. This increase in throughput is made possible by use of short columns and high linear velocities.
- HIC also reduces both the expense (in terms of column packing and equipment) and potential problems that can arise with HPLC, e.g., difficulties in packing and maintaining HPLC columns.
- Suitable HIC columns that can be used in the present invention include, but are not limited to, phenyl-sepharose fast flow (high substitution) and TSK-gel phenyl- 5PW.
- HIC and DEAE-5PW chromatography are mechanistically quite different, they can be used interchangeably to serve the same purpose. They both can be used to purify DMT-off oligonucleotides, although, as demonstrated below, DEAE- 5PW results in better yields when purifying 25mers.
- Oligonucleotide mixtures having purities of about 98% can regularly be obtained using these techniques.
- the use of DEAE-5PW column to purify DMT-off oligonucleotides, like HIC columns, does not require HPLC and, therefore, offers the same advantages as described accomplished on a relatively short column, which increases throughput and eases packing, and requires simple step gradients for elution, which simplifies equipment requirements and the chance for error.
- ion-exchange is accomplished with a DEAE-5PW column.
- oligonucleotides intended for therapeutic use it is essential that all ammonium cations be replaced with, for example sodium cations.
- This can be accomplished with a Dowex cation ion exchange column followed by desalting with sephadex gel filtration.
- standard ion-exchange methods are replaced by the DEAE-5PW column.
- the resin is relatively cheap compared to the more recently introduced anion ion-exchange styrene divinylbenzene polymer supports (e.g. , PerSeptive Biosytems, Polymer Labs), yet is sturdy enough (in terms of particle size and resistance to currently used cleaning procedures) for production use.
- the eluate generally has a very high salt concentration, rendering typical sephadex gel filtration desalting inpractical or impossible.
- other salt removal techniques e.g. , RPLC and tangential flow filtration (TFF)
- the DEAE-5PW oligonucleotide mixture is desalted using tangential flow filtration.
- the present invention provides improved methods for purifying oligodeoxynucleotide phosphorothioates.
- the invention provides purification techniques suitable for large scale separation of oligonucleotide phosphorothioates.
- the purification methods of the invention do not require the use of reduced pressure to remove ammonium hydroxide or the use of conventional C-18 silica gel reverse-phase liquid chromatography.
- the inventive methods replace these procedures with hydrophobic interaction chromatography or DEAE-5PW anion ion-exchange chromatography.
- oligonucleotides are cleaved from the solid support by incubating the support in ammonium hydroxide.
- failure sequences i.e. , olgionucleotide sequences being fewer than the desired number of nucleotides in length.
- failure sequences arise from less than complete coupling of mononucleosides to the growing oligonucleotide chain and less than complete capping of unreacted functional sites.
- the desired oligonucleotide must be separated from failure sequences if it is to be used effectively for therapeutic or other purposes.
- the bulk of the ammonium hydroxide is driven off by roto- evaporation. This is then followed by separating the desired DMT-on oligos (i.e. , oligonucleotides having a 5 ' dimethoxytrityl protecting group) from undesired DMT-off oligos (i.e. , oligonucleotides not having a 5' protecting group) by reversed phase liquid chromatography.
- the DMT-on oligos being more hydrophobic, bind to the reverse phase column more tightly than DMT-off oligos.
- any ammonium cations complexed with the oligonucleotide must be exchanged with, for example, sodium cations. This is generally accomplished by ion exchange chromatography followed by desalting using sephadex gel.
- the present invention comprises improved methods for separating or purifying oligonucleotide phosphorothioates.
- separating and “purifying” are intended to be used interchangeably and mean a process by which oligonucleotides having a particular molecular structure are physically segregated from oligonucleotides have a different molecular structure and by which ammonium hydroxide and/or other salts are removed from the oligonucleotide mixture.
- the present invention comprises the use of hydrophobic interaction chromatography (HIC) and DEAE- 5PW ion exchange chromatography to separate and purify oligonucleotide phosphorothioates .
- HIC hydrophobic interaction chromatography
- DEAE- 5PW ion exchange chromatography to separate and purify oligonucleotide phosphorothioates .
- the desired oligonucleotide is separated from excess ammonium hydroxide and prepared for treatment by reverse phase liquid chromatography by subjecting the oligonucleotide-containing ammonium hydroxide solution to hydrophobic interaction chromatography.
- the HIC comprises passing the oligonucleotide-containing ammonium hydroxide through a phenyl-sepharose fast flow chromatography resin or a phenyl-5PW chromatography resin.
- the desired oligonucleotide is separated from excess ammonium hydroxide and DMT-off oligos by subjecting the oligonucleotide-containing ammonium hydroxide solution to hydrophobic interaction chromatography.
- the HIC comprises passing the oligonculeotide-containing ammonium hydroxide through a phenyl-sepharose fast flow chromatography resin or a phenyl-5PW chromatography resin.
- ion exchange wherein ammonium ions are exchanged for sodium ions
- purification are accomplished with a DEAE-5PW column.
- salt concentrations of the eluant are generally too high for desalting with sephadex-gel, as is traditionally done after standard oliognucleotide ion-exchange is conducted.
- desalting is accomplished by any suitable technique capable of effectively handling high salt concentrations.
- Desalting is preferably conducted by tangential flow filtration (TFF).
- TFF tangential flow filtration
- the invention also encompasses a process for preparing purified mixtures of oligonucleotides.
- This aspect of the invention comprises: (a) HIC to remove ammonium hydroxide and to remove oligos not having DMT protecting groups;
- the methods of the invention may be used to purify crude mixtures containing oligonucleotide phosphorothioates that have just been cleaved from a solid phase synthesis support using ammonium hydroxide or mixtures that have been previously subjected to a purification procedure but that are not of acceptable purity.
- oligonucleotide phosphorothioates can be purified on DEAE-
- 5PW ion-exchange columns, phenyl-5PW and phenyl-sepharose columns using aqueous 5PW results in effective separation of oligonucleotide phosphorothioates from phosphodiesters in high yields.
- the protocols presented herein can be employed in large scale purification of oligonucleotide phosphorothioates to replace the conventional rotoevaporation and C 18 silica gel protocols required during the purification process. This results in fewer steps in the manufacturing process and allows for better purity and recovery of product.
- oligonucleotide phosphoro ⁇ thioates from about 10 to about 35 nucleotides in length can be separated on a DEAE-5PW ion exchange column, a phenyl sepharose column or phenyl-5PW column.
- oligonucleotide phosphorothioates having a length of from about 20 to about 35 and more preferably 25-30, can be separated using the present methods.
- the oligonucleotides separable by the present method may have as few as one and as many as all phosphorothioate internucleotide linkages.
- oligonucleotide phosphorothioate is used to describe such an oligonucleotide.
- Oligonucleotide phosphorodithioates of the same size as the oligonucleotide phosphorothioates described can also be separated by the inventive methods.
- the oligonucleotides are placed on the column and eluted at or near ambient (room) temperature with either a gradient or a non-gradient buffer.
- ammonium acetate is used in equilibration buffers at concentrations ranging from about 0.5 to about 2.0 M, preferably 0.75 M.
- concentrations ranging from about 0.5 to about 2.0 M, preferably 0.75 M.
- addition of ammonium acetate may reduce the pH somewhat, the pH should typically be high to minimize the loss of the trityl group. pH values of 7.5 - 11.0 have been used successfully. A typical value of 10.0 is preferred since this more alkaline pH minimizes loss of the trityl group from the oligonucleotide.
- Elution is most effectively accomplished with water, although other schemes employing buffers may prove useful in particular applications.
- Organic solvents are not required for separation, although their inclusion may be desirable when preparing oligonucleotides by HIC for subsequent RPLC separation. While taller columns can be used (see the height: diameter ratios in the Examples, infra), shorter columns work very well and are preferred for large-scale work.
- Column loads can go as high as 650 OD units/ml packing, depending on elution conditions and column geometry. Preferably the column load is about 200 OD units/ml packing. Linear velocities can range as high as 300 cm/hr, but are preferably about 150 cm/hr.
- a variety of buffers can be used at a pH ranging from about 7.2 to about 8.5.
- Tris-HCl is used at a pH of about 7.5.
- Salts such as sodium chloride must be added to the load and to the equilibration and wash buffers in concentrations ranging from about 1 M to about 3 M, preferably about 3 M.
- Elution is accomplished by either linear or step gradients via salt reduction. Phenyl sepharose columns are preferably loaded at high flow rates. Rates exceeding about 250 cm/hr are found to work exceedingly well. Elution at a rate of about 150-200 cm/hr is desirable.
- buffers such as Tris- HCl (preferably in a concentration of about 10 to about 50 mM) are to be used.
- Salts such as sodium chloride are used for equilibration and elution.
- sodium chloride gradients of 0 to 2 M are used.
- the pH of the oligonucleotide solution that is loaded may be between about 7.0 and about 10.5, preferably about 7.2.
- the pH of equilibration, wash and elution buffers can range from about 7.2 to about 8.5, and is preferably about 7.2.
- Chelating agents such as 1 mM EDTA and organic solvents such as acetonitrile or ethanol can be added to the buffers in some applications. While linear gradients can be run, excellent recoveries and purities are obtained using simple step gradients. In many cases, better recoveries can be obtained using step gradients ⁇ linear gradients appear to cause a slow "bleed-off" of bound product from the column that often works against effective separation and high recovery. While taller columns can be used, relatively short columns provide excellent results and are preferable for large-scale work. Column capacity for oligonucleotides is somewhat lower that that seen for the HIC resins, with optimum column loads ranging up to about 200 OD units/ml resin, preferably about 150 OD units/ml packing. Optimum linear velocities range between about 50 and about 150 cm/hr and are preferably about 70 cm/hr.
- the separation method of the present invention is essentially independent of column particle size. Sizes ranging from 25 to 90 ⁇ m can be used successfully. In preferred embodiments, the particle size is 25 ⁇ m - 40 ⁇ m or 45 ⁇ m - 165 ⁇ m.
- a particularly preferred hydrophobic interaction chromatography resin has a particle size of about 90 ⁇ m.
- CTCTCGCACCCATCTCTCTCCTTCT (GEM 91) was purified using a 0.5 1 column of 30 ⁇ m TSK DEAE 5PW (commercially available from TosoHaas). The resin was packed into a Pharmacia 5.0 cm diameter glass column. Purification was monitored using an ISCO UA-5 detector equipped with a 254 run filter and a Rainin rabbit pump. Two sources of GEM 91 were used in this example:
- TFF Filtron tangential flow filtration
- the GEM 91 oligonucleotide was loaded onto the column at 150 A 260 O.D. (optical density) units/ml packing.
- 25 mM Tris-HCl, pH 7.2 room temperature having from 0.85 to 1.0 M NaCl was used as the buffer with, in some experiments, 1 mM EDTA.
- Elution was performed with 25 mM Tris-HCl, pH 7.2 (RT) containing 2 M NaCl and, in certain experiments, 1 mM EDTA.
- the column was washed with 6 column volumes (4 column volumes in run no. 4) of the appropriate equilibration buffer after application of sample. Fractions were collected, O.D. recoveries determined, and aliquots analyzed for purity by ion exchange HPLC (IEX) and, in some cases, by CGE analysis.
- IEX ion exchange HPLC
- This oligonucleotide was purified on Phenyl-sepharose fast flow (high substitution) using an Amicon 2.2 cm glass column, a Waters 650 solvent delivery system, an HP integrator, a Rainin Dynamax UV-C absorbance detector and a Perkin-Elmer spectrophotometer.
- the resin was packed into one of two column configurations: a height: diameter ratio of 2.2: 1 or 2.5: 1.
- the deblock solutions were adjusted to 1.7 M ammonium acetate pH 10.3 before loading onto phenyl sepharose.
- the phenyl sepharose was previously equilibrated with ammonium acetate.
- Elution of the oligonucleotide was accomplished with reverse gradients of ammonium acetate, pH 7.85, followed by water. The following run conditions were used:
- oligonucleotides were purified on Phenyl-sepharose fast flow (high substitution) using Amicon 2.2 cm glass columns, a Waters 650 solvent delivery system, an HP integrator, a Rainin Dynamax UV-C absorbance detector, and a Perkin-Elmer spectrophotometer .
- Ammoniacal solutions of GEM 91 were adjusted to 0.75 M ammonium acetate and loaded at 75 cm/hr onto the column which was previously equilibrated with 0.75 M ammonium acetate, pH 10.2. After loading, the column was washed at 317 cm/hr with
- Oligonucleotide Purification by HIC GEM 91 was purified on TSK-gel phenyl-5PW (TosoHaas) and an agarose based phenyl sepharose fast flow (high substitution) (Pharmacia) using a Biorad glass column (1.5 cm diam.), an ISCO UA-5 detector equipped with a 254 nm filter, a Rainin rabbit pump, and a Perkin-Elmer spectrophotometer.
- the GEM 91 sodium salt form was recovered from desalt column (gel filtration) side fractions from production lots via tangential flow filtration (TFF) on 2,000 MWCO modified polyether sulfone filters (Filtron, Inc.).
- the olieodeoxvnucleotide snlntinns were adjusted to 3M NaCl in 25 mM Tris-HCl, pH 7.4-7.5, prior to application to the columns.
- Phenyl 5PW oligonucleotide loaded in 3M NaCl/25 mM Tris-HCl pH 7.5, oligo eluted using linear gradient of 3M - 0M NaCl.
- Example 5 An ammoniacal solution of GEM 91 having an avarage of 62% DMT-on was purified on phenyl sepharose fast flow (high substitution) using a Waters 650 solvent delivery system, a HP integrator, 1 cm (Biorad) and 2.2 cm (Amicon) diameter glass columns and a Perkin-Elmer spectrophotometer.
- Phenyl-sepharose was packed into one of three column configurations at height: diameter ratios of: 5.4: 1 , 2.2: 1 , and 1 : 1.
- Phenyl sepharose columns were equilibrated in ammonium acetate pH 8.5.
- the run conditions were as follows: (A) no adjustment to the GEM 91 ammoniacal solution; the column was equilibrated with 2.5 M ammonium acetate, pH 8.5; oligonucleotide was eluted with step gradient of 8% acetonitrile (ACN) in water pH 7.85, followed by water; or (B) the GEM 91 ammoniacal solution was adjusted to 1.7 M ammonium acetate, pH 7.85 before loading; the column was equilibrated with 1.5 M ammonium acetate, pH 7.85; oligonucleotide was eluted with step gradient of 8% ACN in water, followed by water.
- GEM 91 is synthesized using a CPG support and an automated synthesizer.
- the oligonucleotide is cleaved from the support using concentrated ammonium hydroxide.
- the oligonucleotide/ ammonium hydroxide mixture is then chromatographed using hydrophobic interaction chromatography using phenyl-sepharose or phenyl-5PW resins essentially according to the procedures set forth above in Examples 1-6.
- the resulting solutions containing GEM 91 are pooled and optionally chromatographed using preparative reverse- phase liquid chromatography.
- the combined GEM 91 fractions are acidified to remove the dimethoxytrityl (DMT) protecting group.
- DMT dimethoxytrityl
- the detritylated GEM 91 is suspended in water and chromatographed over a DEAE-5PW ion-exchange column essentially as described above in Example 1 to purify it and convert it to the sodium salt form of GEM 91.
- the oligonucleotide is then "desalted” via tangential flow filtration (TFF) to remove salt and any remaining small molecule impurities, and then depyrogenated on a membrane referred to as purified BDS.
- the overall recovery of product after these steps is about 70% with a purity of about 98% .
- HIC and DEAE 5PW chromatographies can be effectively combined to obtain good recovery of high purity oligonculeotides from ammoniacal solutions.
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Abstract
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US27058294A | 1994-07-05 | 1994-07-05 | |
| US270582 | 1994-07-05 | ||
| PCT/US1995/008175 WO1996001268A1 (fr) | 1994-07-05 | 1995-06-30 | Purification de phosphorothioates d'oligodesoxynucleotides a l'aide de la chromatographie echangeuse d'anions deae 5pw et de la chromatographie hydrophobe |
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| EP95925363A Withdrawn EP0765334A1 (fr) | 1994-07-05 | 1995-06-30 | Purification de phosphorothioates d'oligodesoxynucleotides a l'aide de la chromatographie echangeuse d'anions deae 5pw et de la chromatographie hydrophobe |
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| Country | Link |
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| EP (1) | EP0765334A1 (fr) |
| JP (1) | JPH10505577A (fr) |
| AU (1) | AU2952395A (fr) |
| CA (1) | CA2194350A1 (fr) |
| WO (1) | WO1996001268A1 (fr) |
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| US6087491A (en) | 1993-01-08 | 2000-07-11 | Hybridon, Inc. | Extremely high purity oligonucleotides and methods of synthesizing them using dimer blocks |
| SE9500183D0 (sv) * | 1995-01-20 | 1995-01-20 | Pharmacia Biotech Ab | Method for the purifivation of short nucleic acids |
| ES2134157B1 (es) | 1997-11-05 | 2000-03-01 | Cuartero Angel Mejuto | Sistema de tacografo electronico y su equipo fijo. |
| EP0964057B1 (fr) * | 1998-05-11 | 2004-12-22 | Tosoh Corporation | Méthode pour la séparation d'acides nucléiques par chromatographie liquide |
| BR112018075667B1 (pt) | 2016-06-14 | 2024-02-20 | Biogen Ma, Inc | Métodos para separar um oligonucleotídeo alvo de uma mistura contendo o oligonucleotídeo alvo e uma impureza relacionada com o produto |
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| DK0646038T3 (da) * | 1992-06-19 | 2001-02-12 | Life Technologies Inc | Passiverede og stabiliserede porøse bærere og fremgangsmåder til fremstilling og anvendelse deraf |
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1995
- 1995-06-30 EP EP95925363A patent/EP0765334A1/fr not_active Withdrawn
- 1995-06-30 JP JP8503914A patent/JPH10505577A/ja active Pending
- 1995-06-30 CA CA 2194350 patent/CA2194350A1/fr not_active Abandoned
- 1995-06-30 AU AU29523/95A patent/AU2952395A/en not_active Abandoned
- 1995-06-30 WO PCT/US1995/008175 patent/WO1996001268A1/fr not_active Ceased
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| Publication number | Publication date |
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| AU2952395A (en) | 1996-01-25 |
| CA2194350A1 (fr) | 1996-01-18 |
| WO1996001268A1 (fr) | 1996-01-18 |
| JPH10505577A (ja) | 1998-06-02 |
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