WO1995027718A2 - Purification of oligodeoxynucleotide phosphorothioates using anion exchange chromatography - Google Patents
Purification of oligodeoxynucleotide phosphorothioates using anion exchange chromatography Download PDFInfo
- Publication number
- WO1995027718A2 WO1995027718A2 PCT/US1995/004492 US9504492W WO9527718A2 WO 1995027718 A2 WO1995027718 A2 WO 1995027718A2 US 9504492 W US9504492 W US 9504492W WO 9527718 A2 WO9527718 A2 WO 9527718A2
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- buffer
- phosphorothioates
- seq
- oligonucleotide
- column
- Prior art date
Links
- RYYWUUFWQRZTIU-UHFFFAOYSA-N Thiophosphoric acid Chemical class OP(O)(S)=O RYYWUUFWQRZTIU-UHFFFAOYSA-N 0.000 title claims abstract description 51
- 238000005571 anion exchange chromatography Methods 0.000 title claims description 6
- 238000000746 purification Methods 0.000 title description 21
- 229940046166 oligodeoxynucleotide Drugs 0.000 title description 13
- 108091034117 Oligonucleotide Proteins 0.000 claims abstract description 51
- 238000000034 method Methods 0.000 claims abstract description 27
- 239000002773 nucleotide Substances 0.000 claims abstract description 15
- 125000003729 nucleotide group Chemical group 0.000 claims abstract description 15
- 150000003839 salts Chemical class 0.000 claims abstract description 14
- UEEJHVSXFDXPFK-UHFFFAOYSA-N N-dimethylaminoethanol Chemical compound CN(C)CCO UEEJHVSXFDXPFK-UHFFFAOYSA-N 0.000 claims abstract 2
- FBPFZTCFMRRESA-KVTDHHQDSA-N D-Mannitol Chemical compound OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO FBPFZTCFMRRESA-KVTDHHQDSA-N 0.000 claims description 10
- 229930195725 Mannitol Natural products 0.000 claims description 10
- 239000012149 elution buffer Substances 0.000 claims description 10
- 239000000594 mannitol Substances 0.000 claims description 10
- 235000010355 mannitol Nutrition 0.000 claims description 10
- RYYWUUFWQRZTIU-UHFFFAOYSA-K thiophosphate Chemical compound [O-]P([O-])([O-])=S RYYWUUFWQRZTIU-UHFFFAOYSA-K 0.000 claims description 7
- 238000000926 separation method Methods 0.000 abstract description 11
- 238000004255 ion exchange chromatography Methods 0.000 abstract description 6
- 238000013375 chromatographic separation Methods 0.000 abstract 1
- 239000000872 buffer Substances 0.000 description 33
- 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 25
- FAPWRFPIFSIZLT-UHFFFAOYSA-M Sodium chloride Chemical compound [Na+].[Cl-] FAPWRFPIFSIZLT-UHFFFAOYSA-M 0.000 description 21
- 238000005342 ion exchange Methods 0.000 description 14
- 239000002245 particle Substances 0.000 description 14
- 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 description 12
- 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 10
- 239000007853 buffer solution Substances 0.000 description 10
- 238000004587 chromatography analysis Methods 0.000 description 10
- 239000011780 sodium chloride Substances 0.000 description 10
- 230000000694 effects Effects 0.000 description 9
- 108020004707 nucleic acids Proteins 0.000 description 8
- 150000007523 nucleic acids Chemical class 0.000 description 8
- 102000039446 nucleic acids Human genes 0.000 description 8
- 238000010828 elution Methods 0.000 description 6
- 239000012467 final product Substances 0.000 description 6
- 239000000047 product Substances 0.000 description 6
- 238000004458 analytical method Methods 0.000 description 5
- 238000002474 experimental method Methods 0.000 description 5
- 238000001502 gel electrophoresis Methods 0.000 description 5
- 230000014759 maintenance of location Effects 0.000 description 5
- 238000005349 anion exchange Methods 0.000 description 4
- 238000004128 high performance liquid chromatography Methods 0.000 description 4
- 230000003993 interaction Effects 0.000 description 4
- 238000004519 manufacturing process Methods 0.000 description 4
- 229940124276 oligodeoxyribonucleotide Drugs 0.000 description 4
- 239000006174 pH buffer Substances 0.000 description 4
- 238000011084 recovery Methods 0.000 description 4
- WEVYAHXRMPXWCK-UHFFFAOYSA-N Acetonitrile Chemical compound CC#N WEVYAHXRMPXWCK-UHFFFAOYSA-N 0.000 description 3
- 230000033228 biological regulation Effects 0.000 description 3
- 230000015572 biosynthetic process Effects 0.000 description 3
- 150000001875 compounds Chemical class 0.000 description 3
- 238000001962 electrophoresis Methods 0.000 description 3
- 239000000203 mixture Substances 0.000 description 3
- 229920002401 polyacrylamide Polymers 0.000 description 3
- 230000008569 process Effects 0.000 description 3
- 239000002904 solvent Substances 0.000 description 3
- 238000003786 synthesis reaction Methods 0.000 description 3
- 230000001225 therapeutic effect Effects 0.000 description 3
- 208000030507 AIDS Diseases 0.000 description 2
- 108020000948 Antisense Oligonucleotides Proteins 0.000 description 2
- ZRALSGWEFCBTJO-UHFFFAOYSA-N Guanidine Chemical compound NC(N)=N ZRALSGWEFCBTJO-UHFFFAOYSA-N 0.000 description 2
- 206010028980 Neoplasm Diseases 0.000 description 2
- VYPSYNLAJGMNEJ-UHFFFAOYSA-N Silicium dioxide Chemical compound O=[Si]=O VYPSYNLAJGMNEJ-UHFFFAOYSA-N 0.000 description 2
- 150000001450 anions Chemical class 0.000 description 2
- 239000000074 antisense oligonucleotide Substances 0.000 description 2
- 238000012230 antisense oligonucleotides Methods 0.000 description 2
- 239000007864 aqueous solution Substances 0.000 description 2
- 239000003125 aqueous solvent Substances 0.000 description 2
- 230000008901 benefit Effects 0.000 description 2
- 201000011510 cancer Diseases 0.000 description 2
- 230000001419 dependent effect Effects 0.000 description 2
- -1 dimethylaminopropyl functional group Chemical group 0.000 description 2
- 238000006073 displacement reaction Methods 0.000 description 2
- 230000007717 exclusion Effects 0.000 description 2
- 239000011159 matrix material Substances 0.000 description 2
- 239000000178 monomer Substances 0.000 description 2
- 239000003960 organic solvent Substances 0.000 description 2
- 150000004713 phosphodiesters Chemical class 0.000 description 2
- 108090000623 proteins and genes Proteins 0.000 description 2
- 238000011160 research Methods 0.000 description 2
- 238000012552 review Methods 0.000 description 2
- 238000013341 scale-up Methods 0.000 description 2
- 239000000243 solution Substances 0.000 description 2
- 238000012360 testing method Methods 0.000 description 2
- 102100025230 2-amino-3-ketobutyrate coenzyme A ligase, mitochondrial Human genes 0.000 description 1
- 108010087522 Aeromonas hydrophilia lipase-acyltransferase Proteins 0.000 description 1
- 108020004491 Antisense DNA Proteins 0.000 description 1
- 108020005544 Antisense RNA Proteins 0.000 description 1
- 241000557626 Corvus corax Species 0.000 description 1
- 108020004414 DNA Proteins 0.000 description 1
- 108090000790 Enzymes Proteins 0.000 description 1
- 102000004190 Enzymes Human genes 0.000 description 1
- 206010061598 Immunodeficiency Diseases 0.000 description 1
- 208000029462 Immunodeficiency disease Diseases 0.000 description 1
- 102000000589 Interleukin-1 Human genes 0.000 description 1
- 108010002352 Interleukin-1 Proteins 0.000 description 1
- CHJJGSNFBQVOTG-UHFFFAOYSA-N N-methyl-guanidine Natural products CNC(N)=N CHJJGSNFBQVOTG-UHFFFAOYSA-N 0.000 description 1
- 108700020796 Oncogene Proteins 0.000 description 1
- 108091028664 Ribonucleotide Proteins 0.000 description 1
- 241000700605 Viruses Species 0.000 description 1
- 229920004482 WACKER® Polymers 0.000 description 1
- 238000012382 advanced drug delivery Methods 0.000 description 1
- 230000000692 anti-sense effect Effects 0.000 description 1
- 239000003816 antisense DNA Substances 0.000 description 1
- 238000005251 capillar electrophoresis Methods 0.000 description 1
- 230000008859 change Effects 0.000 description 1
- 238000006243 chemical reaction Methods 0.000 description 1
- 239000003795 chemical substances by application Substances 0.000 description 1
- 239000003184 complementary RNA Substances 0.000 description 1
- SWSQBOPZIKWTGO-UHFFFAOYSA-N dimethylaminoamidine Natural products CN(C)C(N)=N SWSQBOPZIKWTGO-UHFFFAOYSA-N 0.000 description 1
- NAGJZTKCGNOGPW-UHFFFAOYSA-N dithiophosphoric acid Chemical class OP(O)(S)=S NAGJZTKCGNOGPW-UHFFFAOYSA-N 0.000 description 1
- 239000003480 eluent Substances 0.000 description 1
- 239000008241 heterogeneous mixture Substances 0.000 description 1
- 230000005660 hydrophilic surface Effects 0.000 description 1
- 230000007813 immunodeficiency Effects 0.000 description 1
- 230000006872 improvement Effects 0.000 description 1
- 230000005764 inhibitory process Effects 0.000 description 1
- 150000002500 ions Chemical class 0.000 description 1
- 238000004811 liquid chromatography Methods 0.000 description 1
- YACKEPLHDIMKIO-UHFFFAOYSA-N methylphosphonic acid Chemical compound CP(O)(O)=O YACKEPLHDIMKIO-UHFFFAOYSA-N 0.000 description 1
- 239000006259 organic additive Substances 0.000 description 1
- 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
- 150000003013 phosphoric acid derivatives Chemical class 0.000 description 1
- 229920000867 polyelectrolyte Polymers 0.000 description 1
- 230000002035 prolonged effect Effects 0.000 description 1
- 239000011347 resin Substances 0.000 description 1
- 229920005989 resin Polymers 0.000 description 1
- 238000004366 reverse phase liquid chromatography Methods 0.000 description 1
- 239000002336 ribonucleotide Substances 0.000 description 1
- 125000002652 ribonucleotide group Chemical group 0.000 description 1
- 239000000377 silicon dioxide Substances 0.000 description 1
- 238000001542 size-exclusion chromatography Methods 0.000 description 1
- 239000007858 starting material Substances 0.000 description 1
- 239000000126 substance Substances 0.000 description 1
- 238000002560 therapeutic procedure Methods 0.000 description 1
- 241000712461 unidentified influenza virus Species 0.000 description 1
- 150000003672 ureas Chemical class 0.000 description 1
Classifications
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
- C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
- C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
- C12N15/1006—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers
- C12N15/101—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers by chromatography, e.g. electrophoresis, ion-exchange, reverse phase
Definitions
- This invention relates to the field of purification of oligodeoxynucleotide phosphorothioates. Description of the Prior Art
- 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 &l.,Proc. Natl. Acad. Sci. USA 86, 7790 (1989); Agrawal et al., in Advanced Drug Delivery Reviews 6,
- oligodeoxyribonucleotide phosphorothioates have been the focus in a wide variety of basic research (e.g., Agrawal et al., Proc. Natl. Acad. Sci. USA 87, 1401 (1990) and Eckstein and Gish, Trends Biochem. Sci. 14, 97 (1989)), enzyme inhibition studies (Mujumdar et al., Biochemistry 28, 1340 (1989)), regulation of oncogene expression
- Oligonucleotides are produced stepwise, with the addition of one monomer at a time to the nascent oligonucleotide chain. 2-3% of the reactions fail, however, during each cycle in which a nucleotide monomer is to be added. Consequently, the resulting products are generally a heterogenous mixture of oligonucleotides of varying length.
- the 20mer product represents only 50-60% of the recovered oligonucleotide product.
- the purity of the compounds is extremely important. Consequently, there has been an interest in developing chromatographic techniques for purifying oligonucleotides. Because of their therapeutic potential, much of the focus has been on purifying oligonucleotide phosphorothioates.
- n-1 peaks were well separated from the parent peak. They also found that 30-mer and 35-mer oligonucleotide phosphorothioates were separable with the same gradient, although better separation could be obtained with a shallower gradient.
- Metelev et al. Ann. N.Y. Acad. Sci. 660, 321-323 (1992), reported the analysis of oligoribonucleotides and chimeric oligoribo-oligodeoxyribonucleotieds using ion- exchange HPLC. They found that the retention time of the oligonucleotides studied depended on the number of ribonucleotide moieties in the oligonucleotide. In addition, the retention time of oligoribonucleotides was found to be length dependent. The authors noted that oligoribonucleotides of length up to 25 nucleotides could be purified and analyzed.
- An object of the present invention is to provide improved methods for purifying oligodeoxynucleotide phosphorothioates.
- an object of the invention is to provide purification techniques suitable for large scale separation of oligonucleotide phosphorothioates.
- Another improvement that we have developed is that the methods of the present invention use an elution buffer having a salt concentration that is significantly lower than has been previously known in the art.
- the principal advantage this discovery confers is to allow for separation of longer oligodeoxynucleotide phosphorothioates in ion exchange columns.
- the methods disclosed herein provide the further advantage of being useful for large scale purification of oligodeoxynucleotide phosphorothioates. These methods can replace the conventional C-18 protocol.
- Figure 1 shows the effects of different solvent system on the elution of GEM
- Figure 2 shows the separation of 15mer, 20mer and 25mer on an ion exchange column (medium particle size 25-40 ⁇ m).
- Figure 3 shows separation of 24mer and 25mer oligonucleotides on a DMAE Fractogel EMD column.
- Figure 4 shows purification of GEM-91 (SEQ ID NO 1) on a DMAE Fractogel EMD ion exchange column.
- Figure 5 shows polyacrylamide gel electrophoretic analysis of fractions shown in Figure 4.
- Figure 6 shows capillary gel electrophoretic analysis of fraction D shown in Figure 5.
- Figure 7 shows the purification of GEM-91 (GEM-91 (SEQ ID NO 1)) on an ion exchange column using 2.5 cm internal diameter column and the same buffer system as described in Figure 2.
- Figure 8 shows polyacrylamide gel electrophoretic analysis of fractions shown in Figure 7; electrophoresis conditions were the same as described in Figure 5.
- Figure 9 shows purification of GEM on an ion exchange column with an inner diameter of 5 cm).
- Figure 10 shows purification of GEM 91 on an ion exchange column using high pH buffer system.
- Figure 11 shows purification of HOFF (SEQ ID NO 3) on DMAE Fractogel EMD ion exchange column using high pH buffer system; described above in Figure
- Figure 12 shows comparison of the purification of GEM-91 (GEM-91 (SEQ ID NO 1)) on different particle sizes; (A) particle size was 25-40 ⁇ m, (B) 45-90 ⁇ m.
- Figure 13 shows purification of GEM-91 (GEM-91 (SEQ ID NO 1)) on 2.6 cm ID of DMAE Fractogel EMD (particle size 45-90) column using high pH buffer , system
- Figure 14 shows polyacrylamide gel electrophoretic analysis of the fractions shown in Figure 13.
- Figure 15 A shows capillary gel electrophoretic analysis and Figure 15B shows GEN-FAX ion exchange chromatographic analysis of the pooled fractions (fraction #3-9) shown in Figure 13.
- Figure 16 shows purification of HOFF (SEQ ID NO 3) sample on a 2.6 cm ID DMAE Fractogel ion exchange column; the buffer conditions used here were the same as described in Figure 13.
- Figure 17 shows electrophoretic analysis of fractions shown in Figure 16.
- the present invention comprises methods for separating or purifying oligonucleotide phosphorothioates by ion-exchange chromatography.
- 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.
- the present invention comprises the use of DMAE ion exchange chromatography to separate oligonucleotide phosphorothioates.
- oligodeoxynucleotide phosphorothioates The interaction between oligodeoxynucleotide phosphorothioates and the column medium is complicated. Phosphorothioates not only interact with the ion exchanger resin, but with the matrix also. The phosphorothioates bind to the medium more tightly than do phosphodiesters, and thus need higher salt concentrations to elute.
- oligonucleotide phosphorothioates can be purified on ion-exchange columns using aqueous elution buffers having a higher pH and lower salt concentration than has previously been reported.
- the results presented below demonstrate that the purification techniques described can resolve oligonucleotides differing in length by one nucleotide.
- the protocols presented herein can be employed in large scale purification of oligonucleotide phosphorothioates to replace the conventional C 18 protocol. This results in fewer steps in the manufacturing process and allows for better purity and recovery of product.
- the DMAE Fractogel EMD medium has a pK value about 9.
- the manufacturer of the medium suggests that the pH value of the elution buffer used should not exceed 8. Contrary to this warning, we have found that separations of oligonucleotide phosphorothioates having length of about 10 nucleotides to about 35 nucleotides are best performed with an elution buffer having a pH of greater than 8.
- oligonucleotide phosphorothioates from about 10 to about 35 nucleotides in length can be separated on a DMAE ion exchange column.
- a polyethyleneimide column may also be used.
- oligonucleotide phosphorothioates having a length of from about 25 to about 35 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 phosphorodithioates of the same size as the oligonucleotide phosphorothioates described can also be separated by the same methods.
- the oligonucleotides are placed on the column and eluted at or near ambient (room) temperature with a gradient of a first buffer (buffer A) comprising about 25 mM Tris-HCl and about 20% 50 mM aqueous mannitol and a second buffer
- buffer B comprising buffer A and about 2 M NaCl (or another suitable salt). It is found that oligonucleotide phosphorothioates will elute at salt concentrations of less than about 2 M and often less than about 0.5 M.
- 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 two preferred embodiment, the particle size is 25 ⁇ m - 40 ⁇ m or 45 ⁇ m - 90 ⁇ m.
- oligodeoxynucleotide phosphorothioates purified according to the method of the invention were synthesized on an automated synthesizer (MilliGEN 8700 or 8800 DNA synthesizer) using standard conditions. Their sequences are listed in TABLE 1 below.
- DMAE Fractogel EMD manufactured by E. Merck Separation (Earmstat, Germany) in these experiments.
- the Fractogel matrix, copolymerized from oligoethyleneglycol, glycidlmethacrylate, and pentaerythroldimethacrylate combines a hydrophilic surface with mechanical stability and chemical resistance at extreme pH values.
- the tentacle ion exchange moieties are exclusively on linear polyelectrolyte chains grafted on the support.
- a Tris-HCl plus mannitol buffer was chosen here for the purification of GEM-91 (SEQ ID NO 1). Mannitol may act as a displacement factor.
- GEM-91 (SEQ ID NO 1) (trityl-off), purified on C 18 reverse phase chromatography with trityl-on and then detritylated, was loaded on a DMAE (dimethylaminoethyl) Fractogel EMD (particle size 25-40 ⁇ m) ion exchange column having inner diameter of 1.5 cm and a flow rate of 5 ml/min.
- DMAE dimethylaminoethyl
- Fractogel EMD particle size 25-40 ⁇ m
- Buffer A 25 mM Tris-HCl (pH 8.0) containing 20% acetonitrile; Buffer B — Buffer A + 2M NaCl.
- Buffer A 25 mM Tris-HCl (pH 8.0) containing 20% 50 mM aqueous solution of mannitol;
- Buffer B Buffer A + 2 M NaCl.
- Table 2 presents the elution gradient used.
- Figure 1A shows the elution profile when buffer system 1 was used
- Figure IB shows the elution profile when buffer system 2 was used. The results show that
- GEM-91 (SEQ ID NO 1) eluted at a salt concentration of about 1.1 M NaCl in buffer system 1, while in buffer system 2 it eluted at a lower salt concentration, about 1 M
- Tris-HCl/mannitol solution because an aqueous system is more suitable than organic-aqueous solvent in pharmaceutical manufacturing.
- the effect of mannitol on the elution of GEM-91 (SEQ ID NO 1) is unknown, except that mannitol may act as a displacement factor.
- Buffer A 25 mM Tris-HCL (pH 8.0) containing 20% 50 mM aqueous solution of mannitol; Buffer B - Buffer A + 2 M NaCl. Table 3 presents the gradient used.
- GEM-91 Purification of GEM-91 (SEQ ID NO 1)
- SEQ ID NO 1 Crude sample of GEM 91 (SEQ ID NO 1) (60 A 260 units), which contained 50% produt using the same methods described in Example 2.
- Fractions containing GEM-91 (SEQ ID NO 1) were collected ( Figure 4) and analyzed with PAGE gel (20% of gel, run under constant current of 15 mA, Figure 5) and capillary gel ( Figure 6) electrophoresis.
- the purity of the final product was 88% based on CE analysis.
- the amount of final product was about 30% of the crude sample.
- GEM-91 SEQ ID NO 1
- Table 4 presents the gradient used.
- Figure 7 presents the results.
- the final product had a purity of about 85%; the recovery was about 30%.
- PAGE analysis showed that the rear fractions contained more h-1 failure sequence than front fractions (Figure 8), possibly resulting from the linear flow rate.
- the linear flow rate employed in the column (2.04 cm/min) was lower than . in the small column (1.5 cm diameter), which had a flow rate 10 ml/min.
- the tentacle moiety of the column medium causes the column to behave as a size exclusion chromatography column, causing late elution of n-1 failure sequence.
- Figure 9 presents the results.
- the purity of the final product was about the same as on 2.5 cm diameter column, but the recovery was only 25%.
- the rear fractions also contained more n-1 failure sequence.
- More salts were needed to elute GEM-91 (SEQ ID NO 1) (about 1.3 M NaCL instead of 0. 8 M) .
- the linear flow rate employed in this column was lowered to 1.02 cm/min due to the limitation of back pressure.
- the insufficient volume of eluent caused by low linear flow rate required high concentration of NaCl to elute GEM-91 (SEQ ID NO 1).
- HOFF SEQ ID NO 3 (24mer) samples rich in guanidine could not be eluted with Tris-HCl, mannitol at 2 M NaCl, even when the solution contained saturated urea.
- Buffer A 50 mM Tris-HCl, pH 9
- Buffer B buffer A + 2 M NaCl. Table 6 presents the gradient used.
- Buffer A 50 mM Tris-HCl, pH 9.0
- Buffer B buffer A + 1 M NaCl.
- Table 7 presents gradient used with a flow rate of 35 ml/min:
- the main peak of the GEM-91 (SEQ ID NO 1) sample was fractionated into 9 different fractions ( Figure 13). Each fraction and the latest peak were analyzed by PAGE. Less failure sequences were observed in fraction #4-#9. No n-1 failure sequences were present in later fractions ( Figure 14). This suggests that the higher linear flow rate (6.6 cm/min) may prevent the size exclusion effect of the tentacle moiety.
- the data also show that the latest peak contains mostly n+x sequence, which may be caused in the synthesis and can not be separated using a C18 reverse phase column ( Figure 14).
- Fractions #3-#9 were pooled and analyzed on a GENFAX anion exchange column (Figure 15 A) and by capillary electrophoresis (Figure 15B). The purity of the final product was higher than 90% and the recovery was 50% of the starting material.
- SEQ ID 3 (24mer) can be purified from the crude sample using the same column gradient (Figure 16). However, the three main peaks contained main products ( Figures 16 and 17), indicating that base stacking may occur during separation.
- Buffer A 50 mM Tris-HCl, pH 9.0
- Buffer B buffer A + 1 M NaCl, with a flow rate of 5 ml/min. Table 8 presents the gradient used. TABLE 8
Landscapes
- Chemical & Material Sciences (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Life Sciences & Earth Sciences (AREA)
- Genetics & Genomics (AREA)
- Organic Chemistry (AREA)
- Molecular Biology (AREA)
- Biotechnology (AREA)
- Biomedical Technology (AREA)
- Biochemistry (AREA)
- General Health & Medical Sciences (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Analytical Chemistry (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- General Engineering & Computer Science (AREA)
- Crystallography & Structural Chemistry (AREA)
- Plant Pathology (AREA)
- Microbiology (AREA)
- Biophysics (AREA)
- Physics & Mathematics (AREA)
- Saccharide Compounds (AREA)
- Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Abstract
Description
Claims
Priority Applications (3)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
EP95916332A EP0755400A1 (en) | 1994-04-08 | 1995-04-07 | Purification of oligodeoxynucleotide phosphorothioates using anion exchange chromatography |
JP7526519A JPH10502052A (en) | 1994-04-08 | 1995-04-07 | Purification of oligodeoxynucleotide phosphorothieoate using anion exchange chromatography |
AU22867/95A AU2286795A (en) | 1994-04-08 | 1995-04-07 | Purification of oligodeoxynucleotide phosphorothioates using anion exchange chromatography |
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US22547594A | 1994-04-08 | 1994-04-08 | |
US08/225,475 | 1994-04-08 |
Publications (2)
Publication Number | Publication Date |
---|---|
WO1995027718A2 true WO1995027718A2 (en) | 1995-10-19 |
WO1995027718A3 WO1995027718A3 (en) | 1995-11-02 |
Family
ID=22845023
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
PCT/US1995/004492 WO1995027718A2 (en) | 1994-04-08 | 1995-04-07 | Purification of oligodeoxynucleotide phosphorothioates using anion exchange chromatography |
Country Status (6)
Country | Link |
---|---|
EP (1) | EP0755400A1 (en) |
JP (1) | JPH10502052A (en) |
CN (1) | CN1150431A (en) |
AU (1) | AU2286795A (en) |
CA (1) | CA2187338A1 (en) |
WO (1) | WO1995027718A2 (en) |
Cited By (8)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO1996022299A1 (en) * | 1995-01-20 | 1996-07-25 | Pharmacia Biotech Ab | Method for the purification of short nucleic acids |
WO1999029703A2 (en) * | 1997-12-06 | 1999-06-17 | Dna Research Instruments Limited | Isolation of nucleic acids |
US6087491A (en) * | 1993-01-08 | 2000-07-11 | Hybridon, Inc. | Extremely high purity oligonucleotides and methods of synthesizing them using dimer blocks |
WO2003080834A2 (en) * | 2002-03-21 | 2003-10-02 | Avecia Biotechnology Inc. | Purification methods for oligonucleotides and their analogs |
US6914137B2 (en) | 1997-12-06 | 2005-07-05 | Dna Research Innovations Limited | Isolation of nucleic acids |
US9663779B2 (en) | 2008-12-23 | 2017-05-30 | Qiagen Gmbh | Nucleic acid purification method |
US10190172B2 (en) | 2014-02-28 | 2019-01-29 | National Cancer Center | Method for determining prognosis of renal cell carcinoma |
WO2020055922A1 (en) * | 2018-09-11 | 2020-03-19 | Amgen Inc. | Purification methods for guanine-rich oligonucleotides |
Families Citing this family (5)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
GB9425138D0 (en) | 1994-12-12 | 1995-02-08 | Dynal As | Isolation of nucleic acid |
US6706162B1 (en) * | 2000-09-25 | 2004-03-16 | Applera Corporation | High speed, high resolution compositions, methods, and kits for capillary electrophoresis |
DE102008063001A1 (en) * | 2008-12-23 | 2010-06-24 | Qiagen Gmbh | Nucleic acid purification method |
CN103570774B (en) * | 2012-08-07 | 2017-08-25 | 博瑞生物医药(苏州)股份有限公司 | A kind of purification process of pentose compound |
CN103833797A (en) * | 2012-11-26 | 2014-06-04 | 福建金山生物制药股份有限公司 | Industrial method for purifying phosphorothioate oligodeoxynucleotide |
Citations (1)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US5183885A (en) * | 1991-10-18 | 1993-02-02 | Applied Biosystems, Inc. | Method for chromatographic separation of synthetic phosphorothioate oligonucleotides |
-
1995
- 1995-04-07 CN CN 95193486 patent/CN1150431A/en active Pending
- 1995-04-07 AU AU22867/95A patent/AU2286795A/en not_active Abandoned
- 1995-04-07 CA CA 2187338 patent/CA2187338A1/en not_active Abandoned
- 1995-04-07 EP EP95916332A patent/EP0755400A1/en not_active Withdrawn
- 1995-04-07 WO PCT/US1995/004492 patent/WO1995027718A2/en not_active Application Discontinuation
- 1995-04-07 JP JP7526519A patent/JPH10502052A/en active Pending
Patent Citations (1)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US5183885A (en) * | 1991-10-18 | 1993-02-02 | Applied Biosystems, Inc. | Method for chromatographic separation of synthetic phosphorothioate oligonucleotides |
Non-Patent Citations (5)
Title |
---|
BIOSEPARATION , vol. 2, no. 4, 1991 pages 207-215, LLOYD, L. L. ET AL 'Oligonucleotide analysis by anion exchange HPLC' * |
JOURNAL OF CHROMATOGRAPHY, BIOMEDICAL APPLICATIONS, vol. 617, no. 1, 1993 AMSTERDAM NL, pages 43-49, BOURQUE, A. J. ET AL 'Quantitative analysis of phosphorothioate oligonucleotides in biological fluids using fast anion-exchange chromatography' * |
JOURNAL OF CHROMATOGRAPHY, vol. 599, no. 1-2, 1992 AMSTERDAM NL, pages 35-42, BERGOT, B. JOHN ET AL 'Separation of synthetic phosphorothioate oligodeoxynucloetides from their oxygenated (phosphodiester) defect species by strong-anion-exchange high-performance liquid chromatography' * |
JOURNAL OF CHROMATOGRAPHY, vol. 638, no. 2, 1993 AMSTERDAM NL, pages 293-301, COHEN, AHARON S. ET AL 'High-performance liquid chromatography and capillary gel electrophoresis as applied to antisense DNA' * |
See also references of EP0755400A1 * |
Cited By (15)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US6087491A (en) * | 1993-01-08 | 2000-07-11 | Hybridon, Inc. | Extremely high purity oligonucleotides and methods of synthesizing them using dimer blocks |
US6310198B1 (en) | 1993-01-08 | 2001-10-30 | Avecia Biotechnology Inc. | Extremely high purity oligonucleotides and methods of synthesizing them using dimer blocks |
US5801237A (en) * | 1995-01-20 | 1998-09-01 | Pharmacia Biotech Ab | Method for the purification of short nucleic acids |
WO1996022299A1 (en) * | 1995-01-20 | 1996-07-25 | Pharmacia Biotech Ab | Method for the purification of short nucleic acids |
EP1234832A2 (en) * | 1997-12-06 | 2002-08-28 | DNA Research Innovations Limited | Isolation of nucleic acids |
WO1999029703A3 (en) * | 1997-12-06 | 1999-08-26 | Dna Research Instr Limited | Isolation of nucleic acids |
WO1999029703A2 (en) * | 1997-12-06 | 1999-06-17 | Dna Research Instruments Limited | Isolation of nucleic acids |
EP1234832A3 (en) * | 1997-12-06 | 2003-08-13 | DNA Research Innovations Limited | Isolation of nucleic acids |
US6914137B2 (en) | 1997-12-06 | 2005-07-05 | Dna Research Innovations Limited | Isolation of nucleic acids |
WO2003080834A2 (en) * | 2002-03-21 | 2003-10-02 | Avecia Biotechnology Inc. | Purification methods for oligonucleotides and their analogs |
WO2003080834A3 (en) * | 2002-03-21 | 2003-12-31 | Avecia Biotechnology Inc | Purification methods for oligonucleotides and their analogs |
US9663779B2 (en) | 2008-12-23 | 2017-05-30 | Qiagen Gmbh | Nucleic acid purification method |
US10190172B2 (en) | 2014-02-28 | 2019-01-29 | National Cancer Center | Method for determining prognosis of renal cell carcinoma |
WO2020055922A1 (en) * | 2018-09-11 | 2020-03-19 | Amgen Inc. | Purification methods for guanine-rich oligonucleotides |
US12049620B2 (en) | 2018-09-11 | 2024-07-30 | Amgen Inc. | Purification methods for guanine-rich oligonucleotides |
Also Published As
Publication number | Publication date |
---|---|
CA2187338A1 (en) | 1995-10-19 |
EP0755400A1 (en) | 1997-01-29 |
JPH10502052A (en) | 1998-02-24 |
WO1995027718A3 (en) | 1995-11-02 |
CN1150431A (en) | 1997-05-21 |
AU2286795A (en) | 1995-10-30 |
Similar Documents
Publication | Publication Date | Title |
---|---|---|
US20060035224A1 (en) | Purification methods for oligonucleotides and their analogs | |
El Zahar et al. | Chromatographic approaches for the characterization and quality control of therapeutic oligonucleotide impurities | |
WO1995027718A2 (en) | Purification of oligodeoxynucleotide phosphorothioates using anion exchange chromatography | |
US5183885A (en) | Method for chromatographic separation of synthetic phosphorothioate oligonucleotides | |
JP2005520547A (en) | Purification method for oligonucleotides and analogs thereof | |
CA3110524A1 (en) | Purification methods for guanine-rich oligonucleotides | |
CA3143047A1 (en) | Purification methods for carbohydrate-linked oligonucleotides | |
Metelev et al. | Ion-exchange high-performance liquid chromatography analysis of oligodeoxyribonucleotide phosphorothioates | |
EP2751283B1 (en) | Process for separation of oligonucleotide of interest from a mixture | |
Yang et al. | Separation of synthetic oligonucleotide dithioates from monothiophosphate impurities by anion-exchange chromatography on a mono-q column | |
EP0729510B1 (en) | Method for detecting charged oligonucleotides in biological fluids | |
EP0458876B1 (en) | Method of separating oligonucleotides from a mixture | |
Deshmukh et al. | Purification of antisense oligonucleotides | |
Ravikumar et al. | Large-scale synthesis of oligodeoxyribonucleotide phosphorothioate using controlled-pore glass as support | |
AU2952395A (en) | Purification of oligodeoxynucleotide phosphorothioates using deae 5pw anion ion-exchange chromatography and hydrophobic interaction chromatography | |
Pon et al. | Tandem oligonucleotide synthesis using linker phosphoramidites | |
EP1578968B1 (en) | Isolation of antisense oligonucleotides | |
US5808042A (en) | Detritylation of DMT-oligonucleotides using cationic ion-exchange resin | |
WO1998027425A1 (en) | Large-scale purification of full length oligonucleotides by solid-liquid affinity extraction | |
Deshmukh et al. | Large-scale chromatographic purification of ougonucleotides | |
WO1997025444A1 (en) | Method of monitoring pharmacokinetics of oligonucleotide pharmaceuticals |
Legal Events
Date | Code | Title | Description |
---|---|---|---|
WWE | Wipo information: entry into national phase |
Ref document number: 95193486.4 Country of ref document: CN |
|
AK | Designated states |
Kind code of ref document: A2 Designated state(s): AM AT AU BB BG BR BY CA CH CN CZ DE DK EE ES FI GB GE HU IS JP KE KG KP KR KZ LK LR LT LU LV MD MG MN MW MX NO NZ PL PT RO RU SD SE SG SI SK TJ TM TT UA US UZ VN |
|
AL | Designated countries for regional patents |
Kind code of ref document: A2 Designated state(s): KE MW SD SZ UG AT BE CH DE DK ES FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN ML MR NE SN TD TG |
|
AK | Designated states |
Kind code of ref document: A3 Designated state(s): AM AT AU BB BG BR BY CA CH CN CZ DE DK EE ES FI GB GE HU IS JP KE KG KP KR KZ LK LR LT LU LV MD MG MN MW MX NO NZ PL PT RO RU SD SE SG SI SK TJ TM TT UA US UZ VN |
|
AL | Designated countries for regional patents |
Kind code of ref document: A3 Designated state(s): KE MW SD SZ UG AT BE CH DE DK ES FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN ML MR NE SN TD TG |
|
121 | Ep: the epo has been informed by wipo that ep was designated in this application | ||
DFPE | Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101) | ||
WWE | Wipo information: entry into national phase |
Ref document number: 284293 Country of ref document: NZ |
|
WWE | Wipo information: entry into national phase |
Ref document number: 1995916332 Country of ref document: EP |
|
WWP | Wipo information: published in national office |
Ref document number: 1995916332 Country of ref document: EP |
|
REG | Reference to national code |
Ref country code: DE Ref legal event code: 8642 |
|
WWW | Wipo information: withdrawn in national office |
Ref document number: 1995916332 Country of ref document: EP |
|
NENP | Non-entry into the national phase in: |
Ref country code: CA |