US20200131555A1 - Incorporation of unnatural nucleotides and methods thereof - Google Patents
Incorporation of unnatural nucleotides and methods thereof Download PDFInfo
- Publication number
- US20200131555A1 US20200131555A1 US16/629,255 US201816629255A US2020131555A1 US 20200131555 A1 US20200131555 A1 US 20200131555A1 US 201816629255 A US201816629255 A US 201816629255A US 2020131555 A1 US2020131555 A1 US 2020131555A1
- Authority
- US
- United States
- Prior art keywords
- unnatural
- sfgfp
- polymerase
- trna
- nucleic acid
- 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.)
- Abandoned
Links
- 238000000034 method Methods 0.000 title abstract description 23
- 125000003729 nucleotide group Chemical group 0.000 title description 68
- 239000002773 nucleotide Substances 0.000 title description 62
- 238000010348 incorporation Methods 0.000 title description 19
- 108020004705 Codon Proteins 0.000 claims description 77
- -1 nucleoside triphosphate Chemical class 0.000 claims description 63
- 241000588724 Escherichia coli Species 0.000 claims description 38
- 108020004999 messenger RNA Proteins 0.000 claims description 30
- 108091034117 Oligonucleotide Proteins 0.000 claims description 25
- 239000002777 nucleoside Substances 0.000 claims description 14
- 239000001226 triphosphate Substances 0.000 claims description 14
- 235000011178 triphosphate Nutrition 0.000 claims description 14
- 102000052866 Amino Acyl-tRNA Synthetases Human genes 0.000 claims description 7
- 108700028939 Amino Acyl-tRNA Synthetases Proteins 0.000 claims description 7
- 241000203407 Methanocaldococcus jannaschii Species 0.000 claims description 4
- 241000205275 Methanosarcina barkeri Species 0.000 claims description 4
- 241000206744 Phaeodactylum tricornutum Species 0.000 claims description 3
- 108020004566 Transfer RNA Proteins 0.000 abstract description 83
- 108090000623 proteins and genes Proteins 0.000 abstract description 30
- 102000004169 proteins and genes Human genes 0.000 abstract description 24
- 150000001413 amino acids Chemical class 0.000 abstract description 22
- 230000015572 biosynthetic process Effects 0.000 abstract description 9
- 239000000203 mixture Substances 0.000 abstract description 7
- 238000003786 synthesis reaction Methods 0.000 abstract description 4
- 108020004707 nucleic acids Proteins 0.000 description 163
- 102000039446 nucleic acids Human genes 0.000 description 163
- 150000007523 nucleic acids Chemical class 0.000 description 158
- 108091005946 superfolder green fluorescent proteins Proteins 0.000 description 137
- 102000016928 DNA-directed DNA polymerase Human genes 0.000 description 58
- 108010014303 DNA-directed DNA polymerase Proteins 0.000 description 58
- 210000004027 cell Anatomy 0.000 description 51
- 235000000346 sugar Nutrition 0.000 description 51
- 108020005098 Anticodon Proteins 0.000 description 41
- 230000004048 modification Effects 0.000 description 40
- 238000012986 modification Methods 0.000 description 40
- UYTPUPDQBNUYGX-UHFFFAOYSA-N guanine Chemical compound O=C1NC(N)=NC2=C1N=CN2 UYTPUPDQBNUYGX-UHFFFAOYSA-N 0.000 description 24
- 102100034343 Integrase Human genes 0.000 description 23
- 108010092799 RNA-directed DNA polymerase Proteins 0.000 description 23
- 108020004414 DNA Proteins 0.000 description 22
- 125000000217 alkyl group Chemical group 0.000 description 22
- OPTASPLRGRRNAP-UHFFFAOYSA-N cytosine Chemical compound NC=1C=CNC(=O)N=1 OPTASPLRGRRNAP-UHFFFAOYSA-N 0.000 description 20
- 230000000694 effects Effects 0.000 description 20
- 230000000644 propagated effect Effects 0.000 description 19
- 108091032973 (ribonucleotides)n+m Proteins 0.000 description 18
- 230000001915 proofreading effect Effects 0.000 description 18
- 108060002716 Exonuclease Proteins 0.000 description 16
- 102000013165 exonuclease Human genes 0.000 description 16
- UHDGCWIWMRVCDJ-UHFFFAOYSA-N 1-beta-D-Xylofuranosyl-NH-Cytosine Natural products O=C1N=C(N)C=CN1C1C(O)C(O)C(CO)O1 UHDGCWIWMRVCDJ-UHFFFAOYSA-N 0.000 description 15
- UHDGCWIWMRVCDJ-PSQAKQOGSA-N Cytidine Natural products O=C1N=C(N)C=CN1[C@@H]1[C@@H](O)[C@@H](O)[C@H](CO)O1 UHDGCWIWMRVCDJ-PSQAKQOGSA-N 0.000 description 15
- UHDGCWIWMRVCDJ-ZAKLUEHWSA-N cytidine Chemical compound O=C1N=C(N)C=CN1[C@H]1[C@H](O)[C@@H](O)[C@H](CO)O1 UHDGCWIWMRVCDJ-ZAKLUEHWSA-N 0.000 description 15
- 108040001032 pyrrolysyl-tRNA synthetase activity proteins Proteins 0.000 description 15
- RWQNBRDOKXIBIV-UHFFFAOYSA-N thymine Chemical compound CC1=CNC(=O)NC1=O RWQNBRDOKXIBIV-UHFFFAOYSA-N 0.000 description 15
- 238000001262 western blot Methods 0.000 description 15
- ISAKRJDGNUQOIC-UHFFFAOYSA-N Uracil Chemical compound O=C1C=CNC(=O)N1 ISAKRJDGNUQOIC-UHFFFAOYSA-N 0.000 description 14
- 229960000643 adenine Drugs 0.000 description 14
- 229940035893 uracil Drugs 0.000 description 14
- OVONXEQGWXGFJD-UHFFFAOYSA-N 4-sulfanylidene-1h-pyrimidin-2-one Chemical compound SC=1C=CNC(=O)N=1 OVONXEQGWXGFJD-UHFFFAOYSA-N 0.000 description 13
- 239000013612 plasmid Substances 0.000 description 13
- FZWGECJQACGGTI-UHFFFAOYSA-N 2-amino-7-methyl-1,7-dihydro-6H-purin-6-one Chemical compound NC1=NC(O)=C2N(C)C=NC2=N1 FZWGECJQACGGTI-UHFFFAOYSA-N 0.000 description 12
- LRFVTYWOQMYALW-UHFFFAOYSA-N 9H-xanthine Chemical compound O=C1NC(=O)NC2=C1NC=N2 LRFVTYWOQMYALW-UHFFFAOYSA-N 0.000 description 12
- 229930024421 Adenine Natural products 0.000 description 12
- 0 Cc1ccc(*)cc1* Chemical compound Cc1ccc(*)cc1* 0.000 description 12
- 108020005038 Terminator Codon Proteins 0.000 description 12
- 230000010261 cell growth Effects 0.000 description 12
- FDGQSTZJBFJUBT-UHFFFAOYSA-N hypoxanthine Chemical compound O=C1NC=NC2=C1NC=N2 FDGQSTZJBFJUBT-UHFFFAOYSA-N 0.000 description 12
- 230000006698 induction Effects 0.000 description 12
- 230000014759 maintenance of location Effects 0.000 description 12
- 125000002467 phosphate group Chemical group [H]OP(=O)(O[H])O[*] 0.000 description 12
- 238000013518 transcription Methods 0.000 description 12
- 230000035897 transcription Effects 0.000 description 12
- 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 11
- 230000006870 function Effects 0.000 description 11
- 150000003212 purines Chemical group 0.000 description 11
- PEHVGBZKEYRQSX-UHFFFAOYSA-N 7-deaza-adenine Chemical compound NC1=NC=NC2=C1C=CN2 PEHVGBZKEYRQSX-UHFFFAOYSA-N 0.000 description 10
- MSSXOMSJDRHRMC-UHFFFAOYSA-N 9H-purine-2,6-diamine Chemical compound NC1=NC(N)=C2NC=NC2=N1 MSSXOMSJDRHRMC-UHFFFAOYSA-N 0.000 description 10
- HMFHBZSHGGEWLO-SOOFDHNKSA-N D-ribofuranose Chemical compound OC[C@H]1OC(O)[C@H](O)[C@@H]1O HMFHBZSHGGEWLO-SOOFDHNKSA-N 0.000 description 10
- 229940104302 cytosine Drugs 0.000 description 10
- 125000003835 nucleoside group Chemical group 0.000 description 10
- ZLAQATDNGLKIEV-UHFFFAOYSA-N 5-methyl-2-sulfanylidene-1h-pyrimidin-4-one Chemical compound CC1=CNC(=S)NC1=O ZLAQATDNGLKIEV-UHFFFAOYSA-N 0.000 description 9
- 241000713838 Avian myeloblastosis virus Species 0.000 description 9
- 108010017826 DNA Polymerase I Proteins 0.000 description 9
- 102000004594 DNA Polymerase I Human genes 0.000 description 9
- 125000000623 heterocyclic group Chemical group 0.000 description 9
- RYVNIFSIEDRLSJ-UHFFFAOYSA-N 5-(hydroxymethyl)cytosine Chemical compound NC=1NC(=O)N=CC=1CO RYVNIFSIEDRLSJ-UHFFFAOYSA-N 0.000 description 8
- LQLQRFGHAALLLE-UHFFFAOYSA-N 5-bromouracil Chemical compound BrC1=CNC(=O)NC1=O LQLQRFGHAALLLE-UHFFFAOYSA-N 0.000 description 8
- HCGHYQLFMPXSDU-UHFFFAOYSA-N 7-methyladenine Chemical compound C1=NC(N)=C2N(C)C=NC2=N1 HCGHYQLFMPXSDU-UHFFFAOYSA-N 0.000 description 8
- 108090000626 DNA-directed RNA polymerases Proteins 0.000 description 8
- 102000004163 DNA-directed RNA polymerases Human genes 0.000 description 8
- GHASVSINZRGABV-UHFFFAOYSA-N Fluorouracil Chemical compound FC1=CNC(=O)NC1=O GHASVSINZRGABV-UHFFFAOYSA-N 0.000 description 8
- 241000713869 Moloney murine leukemia virus Species 0.000 description 8
- 229910019142 PO4 Inorganic materials 0.000 description 8
- 101100273253 Rhizopus niveus RNAP gene Proteins 0.000 description 8
- PYMYPHUHKUWMLA-LMVFSUKVSA-N Ribose Natural products OC[C@@H](O)[C@@H](O)[C@@H](O)C=O PYMYPHUHKUWMLA-LMVFSUKVSA-N 0.000 description 8
- 101710137500 T7 RNA polymerase Proteins 0.000 description 8
- HMFHBZSHGGEWLO-UHFFFAOYSA-N alpha-D-Furanose-Ribose Natural products OCC1OC(O)C(O)C1O HMFHBZSHGGEWLO-UHFFFAOYSA-N 0.000 description 8
- 229960002949 fluorouracil Drugs 0.000 description 8
- 239000005090 green fluorescent protein Substances 0.000 description 8
- 125000001475 halogen functional group Chemical group 0.000 description 8
- BPHPUYQFMNQIOC-NXRLNHOXSA-N isopropyl beta-D-thiogalactopyranoside Chemical compound CC(C)S[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O BPHPUYQFMNQIOC-NXRLNHOXSA-N 0.000 description 8
- 125000002496 methyl group Chemical group [H]C([H])([H])* 0.000 description 8
- NBIIXXVUZAFLBC-UHFFFAOYSA-K phosphate Chemical compound [O-]P([O-])([O-])=O NBIIXXVUZAFLBC-UHFFFAOYSA-K 0.000 description 8
- 239000010452 phosphate Substances 0.000 description 8
- 235000021317 phosphate Nutrition 0.000 description 8
- RYYWUUFWQRZTIU-UHFFFAOYSA-K thiophosphate Chemical compound [O-]P([O-])([O-])=S RYYWUUFWQRZTIU-UHFFFAOYSA-K 0.000 description 8
- 229940113082 thymine Drugs 0.000 description 8
- LRSASMSXMSNRBT-UHFFFAOYSA-N 5-methylcytosine Chemical compound CC1=CNC(=O)N=C1N LRSASMSXMSNRBT-UHFFFAOYSA-N 0.000 description 7
- 229960005508 8-azaguanine Drugs 0.000 description 7
- 239000002253 acid Substances 0.000 description 7
- 230000002068 genetic effect Effects 0.000 description 7
- TZMSYXZUNZXBOL-UHFFFAOYSA-N 10H-phenoxazine Chemical compound C1=CC=C2NC3=CC=CC=C3OC2=C1 TZMSYXZUNZXBOL-UHFFFAOYSA-N 0.000 description 6
- ICSNLGPSRYBMBD-UHFFFAOYSA-N 2-aminopyridine Chemical compound NC1=CC=CC=N1 ICSNLGPSRYBMBD-UHFFFAOYSA-N 0.000 description 6
- UJBCLAXPPIDQEE-UHFFFAOYSA-N 5-prop-1-ynyl-1h-pyrimidine-2,4-dione Chemical compound CC#CC1=CNC(=O)NC1=O UJBCLAXPPIDQEE-UHFFFAOYSA-N 0.000 description 6
- DCPSTSVLRXOYGS-UHFFFAOYSA-N 6-amino-1h-pyrimidine-2-thione Chemical compound NC1=CC=NC(S)=N1 DCPSTSVLRXOYGS-UHFFFAOYSA-N 0.000 description 6
- PNWOYKVCNDZOLS-UHFFFAOYSA-N 6-amino-5-chloro-1h-pyrimidin-2-one Chemical compound NC=1NC(=O)N=CC=1Cl PNWOYKVCNDZOLS-UHFFFAOYSA-N 0.000 description 6
- UJOBWOGCFQCDNV-UHFFFAOYSA-N 9H-carbazole Chemical compound C1=CC=C2C3=CC=CC=C3NC2=C1 UJOBWOGCFQCDNV-UHFFFAOYSA-N 0.000 description 6
- UGQMRVRMYYASKQ-UHFFFAOYSA-N Hypoxanthine nucleoside Natural products OC1C(O)C(CO)OC1N1C(NC=NC2=O)=C2N=C1 UGQMRVRMYYASKQ-UHFFFAOYSA-N 0.000 description 6
- GFFGJBXGBJISGV-UHFFFAOYSA-N adenyl group Chemical group N1=CN=C2N=CNC2=C1N GFFGJBXGBJISGV-UHFFFAOYSA-N 0.000 description 6
- 230000027455 binding Effects 0.000 description 6
- 239000012634 fragment Substances 0.000 description 6
- 239000000178 monomer Substances 0.000 description 6
- 108091033319 polynucleotide Proteins 0.000 description 6
- 102000040430 polynucleotide Human genes 0.000 description 6
- 239000002157 polynucleotide Substances 0.000 description 6
- WYWHKKSPHMUBEB-UHFFFAOYSA-N tioguanine Chemical compound N1C(N)=NC(=S)C2=C1N=CN2 WYWHKKSPHMUBEB-UHFFFAOYSA-N 0.000 description 6
- 238000013519 translation Methods 0.000 description 6
- UNXRWKVEANCORM-UHFFFAOYSA-N triphosphoric acid Chemical compound OP(O)(=O)OP(O)(=O)OP(O)(O)=O UNXRWKVEANCORM-UHFFFAOYSA-N 0.000 description 6
- 229940075420 xanthine Drugs 0.000 description 6
- ZFTBZKVVGZNMJR-UHFFFAOYSA-N 5-chlorouracil Chemical compound ClC1=CNC(=O)NC1=O ZFTBZKVVGZNMJR-UHFFFAOYSA-N 0.000 description 5
- KSNXJLQDQOIRIP-UHFFFAOYSA-N 5-iodouracil Chemical compound IC1=CNC(=O)NC1=O KSNXJLQDQOIRIP-UHFFFAOYSA-N 0.000 description 5
- QNNARSZPGNJZIX-UHFFFAOYSA-N 6-amino-5-prop-1-ynyl-1h-pyrimidin-2-one Chemical compound CC#CC1=CNC(=O)N=C1N QNNARSZPGNJZIX-UHFFFAOYSA-N 0.000 description 5
- OLAFFPNXVJANFR-UHFFFAOYSA-N DG Chemical compound N1C(N)=NC(=O)C2=C1NC=C2 OLAFFPNXVJANFR-UHFFFAOYSA-N 0.000 description 5
- KDCGOANMDULRCW-UHFFFAOYSA-N Purine Natural products N1=CNC2=NC=NC2=C1 KDCGOANMDULRCW-UHFFFAOYSA-N 0.000 description 5
- 108010006785 Taq Polymerase Proteins 0.000 description 5
- 241000205180 Thermococcus litoralis Species 0.000 description 5
- 125000000304 alkynyl group Chemical group 0.000 description 5
- 230000021615 conjugation Effects 0.000 description 5
- 125000004093 cyano group Chemical group *C#N 0.000 description 5
- NAGJZTKCGNOGPW-UHFFFAOYSA-K dioxido-sulfanylidene-sulfido-$l^{5}-phosphane Chemical compound [O-]P([O-])([S-])=S NAGJZTKCGNOGPW-UHFFFAOYSA-K 0.000 description 5
- 239000003814 drug Substances 0.000 description 5
- 238000002474 experimental method Methods 0.000 description 5
- 230000002209 hydrophobic effect Effects 0.000 description 5
- 230000008676 import Effects 0.000 description 5
- 238000001727 in vivo Methods 0.000 description 5
- 150000002500 ions Chemical class 0.000 description 5
- 125000000325 methylidene group Chemical group [H]C([H])=* 0.000 description 5
- 230000010076 replication Effects 0.000 description 5
- 238000003860 storage Methods 0.000 description 5
- 150000008163 sugars Chemical class 0.000 description 5
- 230000001629 suppression Effects 0.000 description 5
- 125000002264 triphosphate group Chemical class [H]OP(=O)(O[H])OP(=O)(O[H])OP(=O)(O[H])O* 0.000 description 5
- FYADHXFMURLYQI-UHFFFAOYSA-N 1,2,4-triazine Chemical class C1=CN=NC=N1 FYADHXFMURLYQI-UHFFFAOYSA-N 0.000 description 4
- RFLVMTUMFYRZCB-UHFFFAOYSA-N 1-methylguanine Chemical compound O=C1N(C)C(N)=NC2=C1N=CN2 RFLVMTUMFYRZCB-UHFFFAOYSA-N 0.000 description 4
- UHUHBFMZVCOEOV-UHFFFAOYSA-N 1h-imidazo[4,5-c]pyridin-4-amine Chemical compound NC1=NC=CC2=C1N=CN2 UHUHBFMZVCOEOV-UHFFFAOYSA-N 0.000 description 4
- QSHACTSJHMKXTE-UHFFFAOYSA-N 2-(2-aminopropyl)-7h-purin-6-amine Chemical compound CC(N)CC1=NC(N)=C2NC=NC2=N1 QSHACTSJHMKXTE-UHFFFAOYSA-N 0.000 description 4
- ASJSAQIRZKANQN-CRCLSJGQSA-N 2-deoxy-D-ribose Chemical compound OC[C@@H](O)[C@@H](O)CC=O ASJSAQIRZKANQN-CRCLSJGQSA-N 0.000 description 4
- OIVLITBTBDPEFK-UHFFFAOYSA-N 5,6-dihydrouracil Chemical compound O=C1CCNC(=O)N1 OIVLITBTBDPEFK-UHFFFAOYSA-N 0.000 description 4
- KXBCLNRMQPRVTP-UHFFFAOYSA-N 6-amino-1,5-dihydroimidazo[4,5-c]pyridin-4-one Chemical compound O=C1NC(N)=CC2=C1N=CN2 KXBCLNRMQPRVTP-UHFFFAOYSA-N 0.000 description 4
- HRYKDUPGBWLLHO-UHFFFAOYSA-N 8-azaadenine Chemical compound NC1=NC=NC2=NNN=C12 HRYKDUPGBWLLHO-UHFFFAOYSA-N 0.000 description 4
- LPXQRXLUHJKZIE-UHFFFAOYSA-N 8-azaguanine Chemical compound NC1=NC(O)=C2NN=NC2=N1 LPXQRXLUHJKZIE-UHFFFAOYSA-N 0.000 description 4
- MVNHZTYRZUWXDY-UHFFFAOYSA-N CC(C)(C)N1C=CC2=C(SC=C2)C1=S Chemical compound CC(C)(C)N1C=CC2=C(SC=C2)C1=S MVNHZTYRZUWXDY-UHFFFAOYSA-N 0.000 description 4
- TVCMRWKPTIMPKF-UHFFFAOYSA-N COC1=C(C(C)(C)C)C=C2/C=C\C=C/C2=C1 Chemical compound COC1=C(C(C)(C)C)C=C2/C=C\C=C/C2=C1 TVCMRWKPTIMPKF-UHFFFAOYSA-N 0.000 description 4
- 108010071146 DNA Polymerase III Proteins 0.000 description 4
- 102000007528 DNA Polymerase III Human genes 0.000 description 4
- 102000004190 Enzymes Human genes 0.000 description 4
- 108090000790 Enzymes Proteins 0.000 description 4
- NYHBQMYGNKIUIF-UUOKFMHZSA-N Guanosine Chemical compound C1=NC=2C(=O)NC(N)=NC=2N1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O NYHBQMYGNKIUIF-UUOKFMHZSA-N 0.000 description 4
- 108091093037 Peptide nucleic acid Proteins 0.000 description 4
- CZPWVGJYEJSRLH-UHFFFAOYSA-N Pyrimidine Chemical compound C1=CN=CN=C1 CZPWVGJYEJSRLH-UHFFFAOYSA-N 0.000 description 4
- 108010065868 RNA polymerase SP6 Proteins 0.000 description 4
- DRTQHJPVMGBUCF-XVFCMESISA-N Uridine Chemical compound O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C(=O)NC(=O)C=C1 DRTQHJPVMGBUCF-XVFCMESISA-N 0.000 description 4
- OIRDTQYFTABQOQ-KQYNXXCUSA-N adenosine Chemical compound C1=NC=2C(N)=NC=NC=2N1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O OIRDTQYFTABQOQ-KQYNXXCUSA-N 0.000 description 4
- 125000003342 alkenyl group Chemical group 0.000 description 4
- 150000001408 amides Chemical class 0.000 description 4
- 238000004458 analytical method Methods 0.000 description 4
- 108010058966 bacteriophage T7 induced DNA polymerase Proteins 0.000 description 4
- 239000000539 dimer Substances 0.000 description 4
- 238000010494 dissociation reaction Methods 0.000 description 4
- 230000005593 dissociations Effects 0.000 description 4
- 230000012010 growth Effects 0.000 description 4
- 125000001449 isopropyl group Chemical group [H]C([H])([H])C([H])(*)C([H])([H])[H] 0.000 description 4
- 239000003446 ligand Substances 0.000 description 4
- 238000001294 liquid chromatography-tandem mass spectrometry Methods 0.000 description 4
- 239000006166 lysate Substances 0.000 description 4
- 238000005259 measurement Methods 0.000 description 4
- 125000000956 methoxy group Chemical group [H]C([H])([H])O* 0.000 description 4
- YACKEPLHDIMKIO-UHFFFAOYSA-N methylphosphonic acid Chemical class CP(O)(O)=O YACKEPLHDIMKIO-UHFFFAOYSA-N 0.000 description 4
- 150000004713 phosphodiesters Chemical group 0.000 description 4
- PTMHPRAIXMAOOB-UHFFFAOYSA-L phosphoramidate Chemical compound NP([O-])([O-])=O PTMHPRAIXMAOOB-UHFFFAOYSA-L 0.000 description 4
- 229910052698 phosphorus Inorganic materials 0.000 description 4
- 150000003230 pyrimidines Chemical class 0.000 description 4
- 239000000126 substance Substances 0.000 description 4
- 125000001424 substituent group Chemical group 0.000 description 4
- 125000000876 trifluoromethoxy group Chemical group FC(F)(F)O* 0.000 description 4
- NOLHIMIFXOBLFF-KVQBGUIXSA-N (2r,3s,5r)-5-(2,6-diaminopurin-9-yl)-2-(hydroxymethyl)oxolan-3-ol Chemical compound C12=NC(N)=NC(N)=C2N=CN1[C@H]1C[C@H](O)[C@@H](CO)O1 NOLHIMIFXOBLFF-KVQBGUIXSA-N 0.000 description 3
- UFSCXDAOCAIFOG-UHFFFAOYSA-N 1,10-dihydropyrimido[5,4-b][1,4]benzothiazin-2-one Chemical compound S1C2=CC=CC=C2N=C2C1=CNC(=O)N2 UFSCXDAOCAIFOG-UHFFFAOYSA-N 0.000 description 3
- MXHRCPNRJAMMIM-ULQXZJNLSA-N 1-[(2r,4s,5r)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-tritiopyrimidine-2,4-dione Chemical compound O=C1NC(=O)C([3H])=CN1[C@@H]1O[C@H](CO)[C@@H](O)C1 MXHRCPNRJAMMIM-ULQXZJNLSA-N 0.000 description 3
- VUFVGYBIFMCJPB-UHFFFAOYSA-N 1-iodopyrimidine-2,4-dione Chemical compound IN1C=CC(=O)NC1=O VUFVGYBIFMCJPB-UHFFFAOYSA-N 0.000 description 3
- VSNHCAURESNICA-NJFSPNSNSA-N 1-oxidanylurea Chemical compound N[14C](=O)NO VSNHCAURESNICA-NJFSPNSNSA-N 0.000 description 3
- WJFKNYWRSNBZNX-UHFFFAOYSA-N 10H-phenothiazine Chemical compound C1=CC=C2NC3=CC=CC=C3SC2=C1 WJFKNYWRSNBZNX-UHFFFAOYSA-N 0.000 description 3
- NOLHIMIFXOBLFF-UHFFFAOYSA-N 2-Amino-2'-deoxyadenosine Natural products C12=NC(N)=NC(N)=C2N=CN1C1CC(O)C(CO)O1 NOLHIMIFXOBLFF-UHFFFAOYSA-N 0.000 description 3
- JRYMOPZHXMVHTA-DAGMQNCNSA-N 2-amino-7-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1h-pyrrolo[2,3-d]pyrimidin-4-one Chemical compound C1=CC=2C(=O)NC(N)=NC=2N1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O JRYMOPZHXMVHTA-DAGMQNCNSA-N 0.000 description 3
- WKMPTBDYDNUJLF-UHFFFAOYSA-N 2-fluoroadenine Chemical compound NC1=NC(F)=NC2=C1N=CN2 WKMPTBDYDNUJLF-UHFFFAOYSA-N 0.000 description 3
- WAVYAFBQOXCGSZ-UHFFFAOYSA-N 2-fluoropyrimidine Chemical compound FC1=NC=CC=N1 WAVYAFBQOXCGSZ-UHFFFAOYSA-N 0.000 description 3
- 125000004200 2-methoxyethyl group Chemical group [H]C([H])([H])OC([H])([H])C([H])([H])* 0.000 description 3
- FPOVCZDHZSAAIX-UHFFFAOYSA-N 4-amino-5,6-dihydro-1h-pyrimidin-2-one Chemical compound NC1=NC(=O)NCC1 FPOVCZDHZSAAIX-UHFFFAOYSA-N 0.000 description 3
- MFEFTTYGMZOIKO-UHFFFAOYSA-N 5-azacytosine Chemical compound NC1=NC=NC(=O)N1 MFEFTTYGMZOIKO-UHFFFAOYSA-N 0.000 description 3
- GSPMCUUYNASDHM-UHFFFAOYSA-N 5-methyl-4-sulfanylidene-1h-pyrimidin-2-one Chemical compound CC1=CNC(=O)N=C1S GSPMCUUYNASDHM-UHFFFAOYSA-N 0.000 description 3
- TVICROIWXBFQEL-UHFFFAOYSA-N 6-(ethylamino)-1h-pyrimidin-2-one Chemical compound CCNC1=CC=NC(=O)N1 TVICROIWXBFQEL-UHFFFAOYSA-N 0.000 description 3
- QFVKLKDEXOWFSL-UHFFFAOYSA-N 6-amino-5-bromo-1h-pyrimidin-2-one Chemical compound NC=1NC(=O)N=CC=1Br QFVKLKDEXOWFSL-UHFFFAOYSA-N 0.000 description 3
- NLLCDONDZDHLCI-UHFFFAOYSA-N 6-amino-5-hydroxy-1h-pyrimidin-2-one Chemical compound NC=1NC(=O)N=CC=1O NLLCDONDZDHLCI-UHFFFAOYSA-N 0.000 description 3
- UFVWJVAMULFOMC-UHFFFAOYSA-N 6-amino-5-iodo-1h-pyrimidin-2-one Chemical compound NC=1NC(=O)N=CC=1I UFVWJVAMULFOMC-UHFFFAOYSA-N 0.000 description 3
- SPDBZGFVYQCVIU-UHFFFAOYSA-N 6-amino-5-nitro-1h-pyrimidin-2-one Chemical compound NC=1NC(=O)N=CC=1[N+]([O-])=O SPDBZGFVYQCVIU-UHFFFAOYSA-N 0.000 description 3
- NJBMMMJOXRZENQ-UHFFFAOYSA-N 6H-pyrrolo[2,3-f]quinoline Chemical compound c1cc2ccc3[nH]cccc3c2n1 NJBMMMJOXRZENQ-UHFFFAOYSA-N 0.000 description 3
- 241000894006 Bacteria Species 0.000 description 3
- UHDGCWIWMRVCDJ-CCXZUQQUSA-N Cytarabine Chemical compound O=C1N=C(N)C=CN1[C@H]1[C@@H](O)[C@H](O)[C@@H](CO)O1 UHDGCWIWMRVCDJ-CCXZUQQUSA-N 0.000 description 3
- 108010063113 DNA Polymerase II Proteins 0.000 description 3
- 102000010567 DNA Polymerase II Human genes 0.000 description 3
- JCXJVPUVTGWSNB-UHFFFAOYSA-N Nitrogen dioxide Chemical compound O=[N]=O JCXJVPUVTGWSNB-UHFFFAOYSA-N 0.000 description 3
- 229910004679 ONO2 Inorganic materials 0.000 description 3
- 101150054516 PRD1 gene Proteins 0.000 description 3
- 108010002747 Pfu DNA polymerase Proteins 0.000 description 3
- ABLZXFCXXLZCGV-UHFFFAOYSA-N Phosphorous acid Chemical class OP(O)=O ABLZXFCXXLZCGV-UHFFFAOYSA-N 0.000 description 3
- OAICVXFJPJFONN-UHFFFAOYSA-N Phosphorus Chemical compound [P] OAICVXFJPJFONN-UHFFFAOYSA-N 0.000 description 3
- 101100459905 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) NCP1 gene Proteins 0.000 description 3
- RYYWUUFWQRZTIU-UHFFFAOYSA-N Thiophosphoric acid Chemical class OP(O)(S)=O RYYWUUFWQRZTIU-UHFFFAOYSA-N 0.000 description 3
- 108010018161 UlTma DNA polymerase Proteins 0.000 description 3
- 125000002877 alkyl aryl group Chemical group 0.000 description 3
- 125000005600 alkyl phosphonate group Chemical group 0.000 description 3
- 125000000539 amino acid group Chemical group 0.000 description 3
- 125000005122 aminoalkylamino group Chemical group 0.000 description 3
- PYMYPHUHKUWMLA-UHFFFAOYSA-N arabinose Natural products OCC(O)C(O)C(O)C=O PYMYPHUHKUWMLA-UHFFFAOYSA-N 0.000 description 3
- 125000003710 aryl alkyl group Chemical group 0.000 description 3
- 238000003556 assay Methods 0.000 description 3
- SRBFZHDQGSBBOR-UHFFFAOYSA-N beta-D-Pyranose-Lyxose Natural products OC1COC(O)C(O)C1O SRBFZHDQGSBBOR-UHFFFAOYSA-N 0.000 description 3
- FTDHDKPUHBLBTL-SHYZEUOFSA-N dCDP Chemical compound O=C1N=C(N)C=CN1[C@@H]1O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](O)C1 FTDHDKPUHBLBTL-SHYZEUOFSA-N 0.000 description 3
- 235000011180 diphosphates Nutrition 0.000 description 3
- XRECTZIEBJDKEO-UHFFFAOYSA-N flucytosine Chemical compound NC1=NC(=O)NC=C1F XRECTZIEBJDKEO-UHFFFAOYSA-N 0.000 description 3
- 229960004413 flucytosine Drugs 0.000 description 3
- 125000000592 heterocycloalkyl group Chemical group 0.000 description 3
- 229910052739 hydrogen Inorganic materials 0.000 description 3
- 239000001257 hydrogen Substances 0.000 description 3
- 125000002887 hydroxy group Chemical group [H]O* 0.000 description 3
- 238000000338 in vitro Methods 0.000 description 3
- 230000003993 interaction Effects 0.000 description 3
- 239000000138 intercalating agent Substances 0.000 description 3
- 230000007246 mechanism Effects 0.000 description 3
- 244000005700 microbiome Species 0.000 description 3
- 150000004712 monophosphates Chemical class 0.000 description 3
- 230000035772 mutation Effects 0.000 description 3
- 125000001893 nitrooxy group Chemical group [O-][N+](=O)O* 0.000 description 3
- 150000003833 nucleoside derivatives Chemical class 0.000 description 3
- 125000001181 organosilyl group Chemical group [SiH3]* 0.000 description 3
- 230000003285 pharmacodynamic effect Effects 0.000 description 3
- 229950000688 phenothiazine Drugs 0.000 description 3
- 239000011574 phosphorus Substances 0.000 description 3
- 238000003752 polymerase chain reaction Methods 0.000 description 3
- 238000002360 preparation method Methods 0.000 description 3
- IGFXRKMLLMBKSA-UHFFFAOYSA-N purine Chemical compound N1=C[N]C2=NC=NC2=C1 IGFXRKMLLMBKSA-UHFFFAOYSA-N 0.000 description 3
- UBQKCCHYAOITMY-UHFFFAOYSA-N pyridin-2-ol Chemical compound OC1=CC=CC=N1 UBQKCCHYAOITMY-UHFFFAOYSA-N 0.000 description 3
- RXTQGIIIYVEHBN-UHFFFAOYSA-N pyrimido[4,5-b]indol-2-one Chemical compound C1=CC=CC2=NC3=NC(=O)N=CC3=C21 RXTQGIIIYVEHBN-UHFFFAOYSA-N 0.000 description 3
- SRBUGYKMBLUTIS-UHFFFAOYSA-N pyrrolo[2,3-d]pyrimidin-2-one Chemical compound O=C1N=CC2=CC=NC2=N1 SRBUGYKMBLUTIS-UHFFFAOYSA-N 0.000 description 3
- 125000006853 reporter group Chemical group 0.000 description 3
- 238000011160 research Methods 0.000 description 3
- 238000012163 sequencing technique Methods 0.000 description 3
- 238000006467 substitution reaction Methods 0.000 description 3
- 229910052717 sulfur Inorganic materials 0.000 description 3
- 229960003087 tioguanine Drugs 0.000 description 3
- 125000002023 trifluoromethyl group Chemical group FC(F)(F)* 0.000 description 3
- 229920002554 vinyl polymer Polymers 0.000 description 3
- WJNGQIYEQLPJMN-IOSLPCCCSA-N 1-methylinosine Chemical compound C1=NC=2C(=O)N(C)C=NC=2N1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O WJNGQIYEQLPJMN-IOSLPCCCSA-N 0.000 description 2
- SXUXMRMBWZCMEN-UHFFFAOYSA-N 2'-O-methyl uridine Natural products COC1C(O)C(CO)OC1N1C(=O)NC(=O)C=C1 SXUXMRMBWZCMEN-UHFFFAOYSA-N 0.000 description 2
- NCMVOABPESMRCP-SHYZEUOFSA-N 2'-deoxycytosine 5'-monophosphate Chemical compound O=C1N=C(N)C=CN1[C@@H]1O[C@H](COP(O)(O)=O)[C@@H](O)C1 NCMVOABPESMRCP-SHYZEUOFSA-N 0.000 description 2
- LTFMZDNNPPEQNG-KVQBGUIXSA-N 2'-deoxyguanosine 5'-monophosphate Chemical compound C1=2NC(N)=NC(=O)C=2N=CN1[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1 LTFMZDNNPPEQNG-KVQBGUIXSA-N 0.000 description 2
- HLYBTPMYFWWNJN-UHFFFAOYSA-N 2-(2,4-dioxo-1h-pyrimidin-5-yl)-2-hydroxyacetic acid Chemical compound OC(=O)C(O)C1=CNC(=O)NC1=O HLYBTPMYFWWNJN-UHFFFAOYSA-N 0.000 description 2
- SGAKLDIYNFXTCK-UHFFFAOYSA-N 2-[(2,4-dioxo-1h-pyrimidin-5-yl)methylamino]acetic acid Chemical compound OC(=O)CNCC1=CNC(=O)NC1=O SGAKLDIYNFXTCK-UHFFFAOYSA-N 0.000 description 2
- YSAJFXWTVFGPAX-UHFFFAOYSA-N 2-[(2,4-dioxo-1h-pyrimidin-5-yl)oxy]acetic acid Chemical compound OC(=O)COC1=CNC(=O)NC1=O YSAJFXWTVFGPAX-UHFFFAOYSA-N 0.000 description 2
- NOIRDLRUNWIUMX-UHFFFAOYSA-N 2-amino-3,7-dihydropurin-6-one;6-amino-1h-pyrimidin-2-one Chemical compound NC=1C=CNC(=O)N=1.O=C1NC(N)=NC2=C1NC=N2 NOIRDLRUNWIUMX-UHFFFAOYSA-N 0.000 description 2
- XMSMHKMPBNTBOD-UHFFFAOYSA-N 2-dimethylamino-6-hydroxypurine Chemical compound N1C(N(C)C)=NC(=O)C2=C1N=CN2 XMSMHKMPBNTBOD-UHFFFAOYSA-N 0.000 description 2
- SMADWRYCYBUIKH-UHFFFAOYSA-N 2-methyl-7h-purin-6-amine Chemical compound CC1=NC(N)=C2NC=NC2=N1 SMADWRYCYBUIKH-UHFFFAOYSA-N 0.000 description 2
- KOLPWZCZXAMXKS-UHFFFAOYSA-N 3-methylcytosine Chemical compound CN1C(N)=CC=NC1=O KOLPWZCZXAMXKS-UHFFFAOYSA-N 0.000 description 2
- GJAKJCICANKRFD-UHFFFAOYSA-N 4-acetyl-4-amino-1,3-dihydropyrimidin-2-one Chemical compound CC(=O)C1(N)NC(=O)NC=C1 GJAKJCICANKRFD-UHFFFAOYSA-N 0.000 description 2
- WPYRHVXCOQLYLY-UHFFFAOYSA-N 5-[(methoxyamino)methyl]-2-sulfanylidene-1h-pyrimidin-4-one Chemical compound CONCC1=CNC(=S)NC1=O WPYRHVXCOQLYLY-UHFFFAOYSA-N 0.000 description 2
- VKLFQTYNHLDMDP-PNHWDRBUSA-N 5-carboxymethylaminomethyl-2-thiouridine Chemical compound O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C(=S)NC(=O)C(CNCC(O)=O)=C1 VKLFQTYNHLDMDP-PNHWDRBUSA-N 0.000 description 2
- KELXHQACBIUYSE-UHFFFAOYSA-N 5-methoxy-1h-pyrimidine-2,4-dione Chemical compound COC1=CNC(=O)NC1=O KELXHQACBIUYSE-UHFFFAOYSA-N 0.000 description 2
- 101150067361 Aars1 gene Proteins 0.000 description 2
- ZBCMCENQWFDXHM-UHFFFAOYSA-N C#CC1=CC(OC)=C(C(C)(C)C)C=C1F.CC1=C(C(C)(C)C)C=C2S/C=C\C2=C1.COC1=C(C(C)(C)C)C=C(F)C(C)=C1.COC1=C(C(C)(C)C)C=C(F)C(I)=C1.COC1=C(C(C)(C)C)C=C2/C=C\C=C/C2=C1.COC1=C(C(C)(C)C)C=C2/C=C\SC2=C1.COC1=C(C(C)(C)C)C=CC(C#N)=C1.COC1=C(C(C)(C)C)C=CC(C)=C1.COC1=C(C(C)(C)C)C=CC(Cl)=C1.COC1=CC(OC)=C(C(C)(C)C)C=C1.COC1=CC(OC)=C(C(C)(C)C)C=C1F Chemical compound C#CC1=CC(OC)=C(C(C)(C)C)C=C1F.CC1=C(C(C)(C)C)C=C2S/C=C\C2=C1.COC1=C(C(C)(C)C)C=C(F)C(C)=C1.COC1=C(C(C)(C)C)C=C(F)C(I)=C1.COC1=C(C(C)(C)C)C=C2/C=C\C=C/C2=C1.COC1=C(C(C)(C)C)C=C2/C=C\SC2=C1.COC1=C(C(C)(C)C)C=CC(C#N)=C1.COC1=C(C(C)(C)C)C=CC(C)=C1.COC1=C(C(C)(C)C)C=CC(Cl)=C1.COC1=CC(OC)=C(C(C)(C)C)C=C1.COC1=CC(OC)=C(C(C)(C)C)C=C1F ZBCMCENQWFDXHM-UHFFFAOYSA-N 0.000 description 2
- 239000002126 C01EB10 - Adenosine Substances 0.000 description 2
- 125000006374 C2-C10 alkenyl group Chemical group 0.000 description 2
- 125000005865 C2-C10alkynyl group Chemical group 0.000 description 2
- NNFLYXIYWXGPGD-UHFFFAOYSA-N CC(C)(C)N1C=C(C#CCNC(=O)C(Cl)Cl)C2=C(SC=C2)C1=S.CC(C)(C)N1C=CC2=C(C=CC=C2)C1=O.CC(C)(C)N1C=CC2=C(C=CC=C2)C1=S.CC(C)(C)N1C=CC2=C(C=CC=N2)C1=O.CC(C)(C)N1C=CC2=C(C=CC=N2)C1=S.CC(C)(C)N1C=CC2=C(N=CC=C2)C1=O.CC(C)(C)N1C=CC2=C(SC=C2)C1=S.CC1=CC2=C(C=C1)C(=O)N(C(C)(C)C)C=C2.CC1=CC2=C(C=C1)C(=S)N(C(C)(C)C)C=C2.CC1=CC2=C(C=C1)C=CN(C(C)(C)C)C2=O.CC1=CC2=C(C=C1)C=CN(C(C)(C)C)C2=S.CC1=CC2=C(C=CN(C(C)(C)C)C2=S)O1.CC1=CC2=C(C=CN(C(C)(C)C)C2=S)S1 Chemical compound CC(C)(C)N1C=C(C#CCNC(=O)C(Cl)Cl)C2=C(SC=C2)C1=S.CC(C)(C)N1C=CC2=C(C=CC=C2)C1=O.CC(C)(C)N1C=CC2=C(C=CC=C2)C1=S.CC(C)(C)N1C=CC2=C(C=CC=N2)C1=O.CC(C)(C)N1C=CC2=C(C=CC=N2)C1=S.CC(C)(C)N1C=CC2=C(N=CC=C2)C1=O.CC(C)(C)N1C=CC2=C(SC=C2)C1=S.CC1=CC2=C(C=C1)C(=O)N(C(C)(C)C)C=C2.CC1=CC2=C(C=C1)C(=S)N(C(C)(C)C)C=C2.CC1=CC2=C(C=C1)C=CN(C(C)(C)C)C2=O.CC1=CC2=C(C=C1)C=CN(C(C)(C)C)C2=S.CC1=CC2=C(C=CN(C(C)(C)C)C2=S)O1.CC1=CC2=C(C=CN(C(C)(C)C)C2=S)S1 NNFLYXIYWXGPGD-UHFFFAOYSA-N 0.000 description 2
- PDIOTGRUDWQOAV-UHFFFAOYSA-N CC(C)(C)N1C=CC2=C(C=CS2)C1=O.CC(C)(C)N1C=CC2=C(OC=C2)C1=O.CC(C)(C)N1C=CC2=C(SC=C2)C1=O Chemical compound CC(C)(C)N1C=CC2=C(C=CS2)C1=O.CC(C)(C)N1C=CC2=C(OC=C2)C1=O.CC(C)(C)N1C=CC2=C(SC=C2)C1=O PDIOTGRUDWQOAV-UHFFFAOYSA-N 0.000 description 2
- WCQZSYDSBJWDJS-UHFFFAOYSA-N CC(C)(C)N1C=CC2=C(SC=C2)C1=S.COC1=C(C(C)(C)C)C=C2/C=C\C=C/C2=C1 Chemical compound CC(C)(C)N1C=CC2=C(SC=C2)C1=S.COC1=C(C(C)(C)C)C=C2/C=C\C=C/C2=C1 WCQZSYDSBJWDJS-UHFFFAOYSA-N 0.000 description 2
- MIKUYHXYGGJMLM-GIMIYPNGSA-N Crotonoside Natural products C1=NC2=C(N)NC(=O)N=C2N1[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1O MIKUYHXYGGJMLM-GIMIYPNGSA-N 0.000 description 2
- NYHBQMYGNKIUIF-UHFFFAOYSA-N D-guanosine Natural products C1=2NC(N)=NC(=O)C=2N=CN1C1OC(CO)C(O)C1O NYHBQMYGNKIUIF-UHFFFAOYSA-N 0.000 description 2
- SRBFZHDQGSBBOR-IOVATXLUSA-N D-xylopyranose Chemical compound O[C@@H]1COC(O)[C@H](O)[C@H]1O SRBFZHDQGSBBOR-IOVATXLUSA-N 0.000 description 2
- 230000004544 DNA amplification Effects 0.000 description 2
- 102100022302 DNA polymerase beta Human genes 0.000 description 2
- 230000004543 DNA replication Effects 0.000 description 2
- ZRALSGWEFCBTJO-UHFFFAOYSA-N Guanidine Chemical compound NC(N)=N ZRALSGWEFCBTJO-UHFFFAOYSA-N 0.000 description 2
- 101000902539 Homo sapiens DNA polymerase beta Proteins 0.000 description 2
- UGQMRVRMYYASKQ-KQYNXXCUSA-N Inosine Chemical compound O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C2=NC=NC(O)=C2N=C1 UGQMRVRMYYASKQ-KQYNXXCUSA-N 0.000 description 2
- 229930010555 Inosine Natural products 0.000 description 2
- 102000003960 Ligases Human genes 0.000 description 2
- 108090000364 Ligases Proteins 0.000 description 2
- 239000004472 Lysine Substances 0.000 description 2
- SGSSKEDGVONRGC-UHFFFAOYSA-N N(2)-methylguanine Chemical compound O=C1NC(NC)=NC2=C1N=CN2 SGSSKEDGVONRGC-UHFFFAOYSA-N 0.000 description 2
- HYVABZIGRDEKCD-UHFFFAOYSA-N N(6)-dimethylallyladenine Chemical compound CC(C)=CCNC1=NC=NC2=C1N=CN2 HYVABZIGRDEKCD-UHFFFAOYSA-N 0.000 description 2
- 108010010677 Phosphodiesterase I Proteins 0.000 description 2
- 241000422848 Taxodium mucronatum Species 0.000 description 2
- 241000204666 Thermotoga maritima Species 0.000 description 2
- 108010001244 Tli polymerase Proteins 0.000 description 2
- 150000007513 acids Chemical class 0.000 description 2
- 229960005305 adenosine Drugs 0.000 description 2
- 230000003321 amplification Effects 0.000 description 2
- 125000000129 anionic group Chemical group 0.000 description 2
- 230000000692 anti-sense effect Effects 0.000 description 2
- 238000013459 approach Methods 0.000 description 2
- PYMYPHUHKUWMLA-WDCZJNDASA-N arabinose Chemical compound OC[C@@H](O)[C@@H](O)[C@H](O)C=O PYMYPHUHKUWMLA-WDCZJNDASA-N 0.000 description 2
- 230000008901 benefit Effects 0.000 description 2
- DRTQHJPVMGBUCF-PSQAKQOGSA-N beta-L-uridine Natural products O[C@H]1[C@@H](O)[C@H](CO)O[C@@H]1N1C(=O)NC(=O)C=C1 DRTQHJPVMGBUCF-PSQAKQOGSA-N 0.000 description 2
- 125000002915 carbonyl group Chemical group [*:2]C([*:1])=O 0.000 description 2
- HVYWMOMLDIMFJA-DPAQBDIFSA-N cholesterol Chemical group C1C=C2C[C@@H](O)CC[C@]2(C)[C@@H]2[C@@H]1[C@@H]1CC[C@H]([C@H](C)CCCC(C)C)[C@@]1(C)CC2 HVYWMOMLDIMFJA-DPAQBDIFSA-N 0.000 description 2
- 230000000295 complement effect Effects 0.000 description 2
- 125000000753 cycloalkyl group Chemical group 0.000 description 2
- DAEAPNUQQAICNR-RRKCRQDMSA-K dADP(3-) Chemical compound C1=NC=2C(N)=NC=NC=2N1[C@H]1C[C@H](O)[C@@H](COP([O-])(=O)OP([O-])([O-])=O)O1 DAEAPNUQQAICNR-RRKCRQDMSA-K 0.000 description 2
- SUYVUBYJARFZHO-RRKCRQDMSA-N dATP Chemical compound C1=NC=2C(N)=NC=NC=2N1[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)O1 SUYVUBYJARFZHO-RRKCRQDMSA-N 0.000 description 2
- SUYVUBYJARFZHO-UHFFFAOYSA-N dATP Natural products C1=NC=2C(N)=NC=NC=2N1C1CC(O)C(COP(O)(=O)OP(O)(=O)OP(O)(O)=O)O1 SUYVUBYJARFZHO-UHFFFAOYSA-N 0.000 description 2
- RGWHQCVHVJXOKC-SHYZEUOFSA-J dCTP(4-) Chemical compound O=C1N=C(N)C=CN1[C@@H]1O[C@H](COP([O-])(=O)OP([O-])(=O)OP([O-])([O-])=O)[C@@H](O)C1 RGWHQCVHVJXOKC-SHYZEUOFSA-J 0.000 description 2
- CIKGWCTVFSRMJU-KVQBGUIXSA-N dGDP Chemical compound C1=NC=2C(=O)NC(N)=NC=2N1[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O1 CIKGWCTVFSRMJU-KVQBGUIXSA-N 0.000 description 2
- HAAZLUGHYHWQIW-KVQBGUIXSA-N dGTP Chemical compound C1=NC=2C(=O)NC(N)=NC=2N1[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)O1 HAAZLUGHYHWQIW-KVQBGUIXSA-N 0.000 description 2
- UJLXYODCHAELLY-XLPZGREQSA-N dTDP Chemical compound O=C1NC(=O)C(C)=CN1[C@@H]1O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](O)C1 UJLXYODCHAELLY-XLPZGREQSA-N 0.000 description 2
- GYOZYWVXFNDGLU-XLPZGREQSA-N dTMP Chemical compound O=C1NC(=O)C(C)=CN1[C@@H]1O[C@H](COP(O)(O)=O)[C@@H](O)C1 GYOZYWVXFNDGLU-XLPZGREQSA-N 0.000 description 2
- NHVNXKFIZYSCEB-XLPZGREQSA-N dTTP Chemical compound O=C1NC(=O)C(C)=CN1[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)[C@@H](O)C1 NHVNXKFIZYSCEB-XLPZGREQSA-N 0.000 description 2
- KHWCHTKSEGGWEX-UHFFFAOYSA-N deoxyadenylic acid Natural products C1=NC=2C(N)=NC=NC=2N1C1CC(O)C(COP(O)(O)=O)O1 KHWCHTKSEGGWEX-UHFFFAOYSA-N 0.000 description 2
- LTFMZDNNPPEQNG-UHFFFAOYSA-N deoxyguanylic acid Natural products C1=2NC(N)=NC(=O)C=2N=CN1C1CC(O)C(COP(O)(O)=O)O1 LTFMZDNNPPEQNG-UHFFFAOYSA-N 0.000 description 2
- 239000005549 deoxyribonucleoside Substances 0.000 description 2
- 239000001177 diphosphate Substances 0.000 description 2
- XPPKVPWEQAFLFU-UHFFFAOYSA-J diphosphate(4-) Chemical compound [O-]P([O-])(=O)OP([O-])([O-])=O XPPKVPWEQAFLFU-UHFFFAOYSA-J 0.000 description 2
- 229940029575 guanosine Drugs 0.000 description 2
- 229960003786 inosine Drugs 0.000 description 2
- 230000000670 limiting effect Effects 0.000 description 2
- 125000005647 linker group Chemical group 0.000 description 2
- 150000004702 methyl esters Chemical class 0.000 description 2
- 125000004573 morpholin-4-yl group Chemical group N1(CCOCC1)* 0.000 description 2
- 230000007935 neutral effect Effects 0.000 description 2
- 229910052757 nitrogen Inorganic materials 0.000 description 2
- 238000003199 nucleic acid amplification method Methods 0.000 description 2
- 229910052760 oxygen Inorganic materials 0.000 description 2
- 150000008298 phosphoramidates Chemical class 0.000 description 2
- 239000002243 precursor Substances 0.000 description 2
- 108090000765 processed proteins & peptides Proteins 0.000 description 2
- 102000004196 processed proteins & peptides Human genes 0.000 description 2
- 238000000746 purification Methods 0.000 description 2
- 230000009467 reduction Effects 0.000 description 2
- 230000002829 reductive effect Effects 0.000 description 2
- 239000002342 ribonucleoside Substances 0.000 description 2
- 150000003839 salts Chemical class 0.000 description 2
- 230000009897 systematic effect Effects 0.000 description 2
- DRTQHJPVMGBUCF-UHFFFAOYSA-N uracil arabinoside Natural products OC1C(O)C(CO)OC1N1C(=O)NC(=O)C=C1 DRTQHJPVMGBUCF-UHFFFAOYSA-N 0.000 description 2
- 229940045145 uridine Drugs 0.000 description 2
- WCNMEQDMUYVWMJ-JPZHCBQBSA-N wybutoxosine Chemical compound C1=NC=2C(=O)N3C(CC([C@H](NC(=O)OC)C(=O)OC)OO)=C(C)N=C3N(C)C=2N1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O WCNMEQDMUYVWMJ-JPZHCBQBSA-N 0.000 description 2
- NEMHIKRLROONTL-QMMMGPOBSA-N (2s)-2-azaniumyl-3-(4-azidophenyl)propanoate Chemical compound OC(=O)[C@@H](N)CC1=CC=C(N=[N+]=[N-])C=C1 NEMHIKRLROONTL-QMMMGPOBSA-N 0.000 description 1
- BHQCQFFYRZLCQQ-UHFFFAOYSA-N (3alpha,5alpha,7alpha,12alpha)-3,7,12-trihydroxy-cholan-24-oic acid Natural products OC1CC2CC(O)CCC2(C)C2C1C1CCC(C(CCC(O)=O)C)C1(C)C(O)C2 BHQCQFFYRZLCQQ-UHFFFAOYSA-N 0.000 description 1
- QGVQZRDQPDLHHV-DPAQBDIFSA-N (3s,8s,9s,10r,13r,14s,17r)-10,13-dimethyl-17-[(2r)-6-methylheptan-2-yl]-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1h-cyclopenta[a]phenanthrene-3-thiol Chemical compound C1C=C2C[C@@H](S)CC[C@]2(C)[C@@H]2[C@@H]1[C@@H]1CC[C@H]([C@H](C)CCCC(C)C)[C@@]1(C)CC2 QGVQZRDQPDLHHV-DPAQBDIFSA-N 0.000 description 1
- 125000000008 (C1-C10) alkyl group Chemical group 0.000 description 1
- 125000004400 (C1-C12) alkyl group Chemical group 0.000 description 1
- XXJGBENTLXFVFI-UHFFFAOYSA-N 1-amino-methylene Chemical compound N[CH2] XXJGBENTLXFVFI-UHFFFAOYSA-N 0.000 description 1
- APXRHPDHORGIEB-UHFFFAOYSA-N 1H-pyrazolo[4,3-d]pyrimidine Chemical class N1=CN=C2C=NNC2=C1 APXRHPDHORGIEB-UHFFFAOYSA-N 0.000 description 1
- RFCQJGFZUQFYRF-UHFFFAOYSA-N 2'-O-Methylcytidine Natural products COC1C(O)C(CO)OC1N1C(=O)N=C(N)C=C1 RFCQJGFZUQFYRF-UHFFFAOYSA-N 0.000 description 1
- RFCQJGFZUQFYRF-ZOQUXTDFSA-N 2'-O-methylcytidine Chemical compound CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C(=O)N=C(N)C=C1 RFCQJGFZUQFYRF-ZOQUXTDFSA-N 0.000 description 1
- SXUXMRMBWZCMEN-ZOQUXTDFSA-N 2'-O-methyluridine Chemical compound CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C(=O)NC(=O)C=C1 SXUXMRMBWZCMEN-ZOQUXTDFSA-N 0.000 description 1
- MPXDAIBTYWGBSL-UHFFFAOYSA-N 2,4-difluoro-1-methylbenzene Chemical compound CC1=CC=C(F)C=C1F MPXDAIBTYWGBSL-UHFFFAOYSA-N 0.000 description 1
- PIINGYXNCHTJTF-UHFFFAOYSA-N 2-(2-azaniumylethylamino)acetate Chemical compound NCCNCC(O)=O PIINGYXNCHTJTF-UHFFFAOYSA-N 0.000 description 1
- 125000003903 2-propenyl group Chemical group [H]C([*])([H])C([H])=C([H])[H] 0.000 description 1
- MQJSSLBGAQJNER-UHFFFAOYSA-N 5-(methylaminomethyl)-1h-pyrimidine-2,4-dione Chemical compound CNCC1=CNC(=O)NC1=O MQJSSLBGAQJNER-UHFFFAOYSA-N 0.000 description 1
- BYPCVKNBGDKXLB-UHFFFAOYSA-N 6-(aminomethyl)-5-methyl-1h-pyrimidine-2,4-dione Chemical compound CC1=C(CN)NC(=O)NC1=O BYPCVKNBGDKXLB-UHFFFAOYSA-N 0.000 description 1
- SHZGCJCMOBCMKK-UHFFFAOYSA-N 6-methyloxane-2,3,4,5-tetrol Chemical compound CC1OC(O)C(O)C(O)C1O SHZGCJCMOBCMKK-UHFFFAOYSA-N 0.000 description 1
- HBAQYPYDRFILMT-UHFFFAOYSA-N 8-[3-(1-cyclopropylpyrazol-4-yl)-1H-pyrazolo[4,3-d]pyrimidin-5-yl]-3-methyl-3,8-diazabicyclo[3.2.1]octan-2-one Chemical class C1(CC1)N1N=CC(=C1)C1=NNC2=C1N=C(N=C2)N1C2C(N(CC1CC2)C)=O HBAQYPYDRFILMT-UHFFFAOYSA-N 0.000 description 1
- 101100107610 Arabidopsis thaliana ABCF4 gene Proteins 0.000 description 1
- 101100278439 Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16) pol gene Proteins 0.000 description 1
- 101100191004 Bacillus subtilis (strain 168) polX gene Proteins 0.000 description 1
- GGWLPNKBHRHCRU-UHFFFAOYSA-N CC(C)(C)N(C=Cc1c2cc(C)cc1)C2=S Chemical compound CC(C)(C)N(C=Cc1c2cc(C)cc1)C2=S GGWLPNKBHRHCRU-UHFFFAOYSA-N 0.000 description 1
- UEIMAEXYYJSXEV-UHFFFAOYSA-N CC(C)(C)c(c(OC)c1)cc2c1[s]cc2 Chemical compound CC(C)(C)c(c(OC)c1)cc2c1[s]cc2 UEIMAEXYYJSXEV-UHFFFAOYSA-N 0.000 description 1
- HKFIQSIHCBBIIX-UHFFFAOYSA-N CC(C)(c(c(OC)c1)cc(F)c1I)F Chemical compound CC(C)(c(c(OC)c1)cc(F)c1I)F HKFIQSIHCBBIIX-UHFFFAOYSA-N 0.000 description 1
- LSCRLTKJCHALIG-UHFFFAOYSA-N CC(C)C(C)N(C=Cc1c2ccc(C)c1)C2=S Chemical compound CC(C)C(C)N(C=Cc1c2ccc(C)c1)C2=S LSCRLTKJCHALIG-UHFFFAOYSA-N 0.000 description 1
- ZEVLAAANUDAVNM-UHFFFAOYSA-N CC(C)C(C)N(C=Cc1c2cccn1)C2=S Chemical compound CC(C)C(C)N(C=Cc1c2cccn1)C2=S ZEVLAAANUDAVNM-UHFFFAOYSA-N 0.000 description 1
- BLWQYTZLMLQAGX-UHFFFAOYSA-N CC(C)N(C=Cc1c2cccc1)C2=S Chemical compound CC(C)N(C=Cc1c2cccc1)C2=S BLWQYTZLMLQAGX-UHFFFAOYSA-N 0.000 description 1
- FRUYCTREBIUZAQ-UHFFFAOYSA-N CC(C)c1cc(cccc2)c2cc1OC Chemical compound CC(C)c1cc(cccc2)c2cc1OC FRUYCTREBIUZAQ-UHFFFAOYSA-N 0.000 description 1
- 108091033409 CRISPR Proteins 0.000 description 1
- SJZAUIVYZWPNAS-UHFFFAOYSA-N Cc1ccc(C)c(OC)c1 Chemical compound Cc1ccc(C)c(OC)c1 SJZAUIVYZWPNAS-UHFFFAOYSA-N 0.000 description 1
- 239000004380 Cholic acid Substances 0.000 description 1
- 125000000824 D-ribofuranosyl group Chemical group [H]OC([H])([H])[C@@]1([H])OC([H])(*)[C@]([H])(O[H])[C@]1([H])O[H] 0.000 description 1
- 102000053602 DNA Human genes 0.000 description 1
- 108091008102 DNA aptamers Proteins 0.000 description 1
- 102000052510 DNA-Binding Proteins Human genes 0.000 description 1
- 108700020911 DNA-Binding Proteins Proteins 0.000 description 1
- 241000701533 Escherichia virus T4 Species 0.000 description 1
- 108091092584 GDNA Proteins 0.000 description 1
- 241000193385 Geobacillus stearothermophilus Species 0.000 description 1
- WQZGKKKJIJFFOK-GASJEMHNSA-N Glucose Natural products OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O WQZGKKKJIJFFOK-GASJEMHNSA-N 0.000 description 1
- 108010043121 Green Fluorescent Proteins Proteins 0.000 description 1
- 102000004144 Green Fluorescent Proteins Human genes 0.000 description 1
- 206010020460 Human T-cell lymphotropic virus type I infection Diseases 0.000 description 1
- 241000714260 Human T-lymphotropic virus 1 Species 0.000 description 1
- 125000002061 L-isoleucyl group Chemical group [H]N([H])[C@]([H])(C(=O)[*])[C@](C([H])([H])[H])([H])C(C([H])([H])[H])([H])[H] 0.000 description 1
- ZFOMKMMPBOQKMC-KXUCPTDWSA-N L-pyrrolysine Chemical compound C[C@@H]1CC=N[C@H]1C(=O)NCCCC[C@H]([NH3+])C([O-])=O ZFOMKMMPBOQKMC-KXUCPTDWSA-N 0.000 description 1
- 241000205274 Methanosarcina mazei Species 0.000 description 1
- 241000713333 Mouse mammary tumor virus Species 0.000 description 1
- CHJJGSNFBQVOTG-UHFFFAOYSA-N N-methyl-guanidine Natural products CNC(N)=N CHJJGSNFBQVOTG-UHFFFAOYSA-N 0.000 description 1
- 101710163270 Nuclease Proteins 0.000 description 1
- 108091028043 Nucleic acid sequence Proteins 0.000 description 1
- 229910003849 O-Si Inorganic materials 0.000 description 1
- REYJJPSVUYRZGE-UHFFFAOYSA-N Octadecylamine Chemical compound CCCCCCCCCCCCCCCCCCN REYJJPSVUYRZGE-UHFFFAOYSA-N 0.000 description 1
- 229910003872 O—Si Inorganic materials 0.000 description 1
- 239000004698 Polyethylene Substances 0.000 description 1
- 239000002202 Polyethylene glycol Substances 0.000 description 1
- 101710146427 Probable tyrosine-tRNA ligase, cytoplasmic Proteins 0.000 description 1
- 241000205160 Pyrococcus Species 0.000 description 1
- 241000205156 Pyrococcus furiosus Species 0.000 description 1
- 241000205192 Pyrococcus woesei Species 0.000 description 1
- 108091008103 RNA aptamers Proteins 0.000 description 1
- 108091030071 RNAI Proteins 0.000 description 1
- 108091028664 Ribonucleotide Proteins 0.000 description 1
- 240000004808 Saccharomyces cerevisiae Species 0.000 description 1
- 101100068078 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GCN4 gene Proteins 0.000 description 1
- 101100064044 Schizosaccharomyces pombe (strain 972 / ATCC 24843) pol1 gene Proteins 0.000 description 1
- MTCFGRXMJLQNBG-UHFFFAOYSA-N Serine Natural products OCC(N)C(O)=O MTCFGRXMJLQNBG-UHFFFAOYSA-N 0.000 description 1
- XUIMIQQOPSSXEZ-UHFFFAOYSA-N Silicon Chemical compound [Si] XUIMIQQOPSSXEZ-UHFFFAOYSA-N 0.000 description 1
- NINIDFKCEFEMDL-UHFFFAOYSA-N Sulfur Chemical compound [S] NINIDFKCEFEMDL-UHFFFAOYSA-N 0.000 description 1
- UCKMPCXJQFINFW-UHFFFAOYSA-N Sulphide Chemical compound [S-2] UCKMPCXJQFINFW-UHFFFAOYSA-N 0.000 description 1
- 241001237851 Thermococcus gorgonarius Species 0.000 description 1
- 241001235254 Thermococcus kodakarensis Species 0.000 description 1
- 101000865057 Thermococcus litoralis DNA polymerase Proteins 0.000 description 1
- 240000002003 Thermococcus sp. JDF-3 Species 0.000 description 1
- 241000589500 Thermus aquaticus Species 0.000 description 1
- 241000589499 Thermus thermophilus Species 0.000 description 1
- 108010028230 Trp-Ser- His-Pro-Gln-Phe-Glu-Lys Proteins 0.000 description 1
- 102100025336 Tyrosine-tRNA ligase, mitochondrial Human genes 0.000 description 1
- 101710107268 Tyrosine-tRNA ligase, mitochondrial Proteins 0.000 description 1
- RLXCFCYWFYXTON-JTTSDREOSA-N [(3S,8S,9S,10R,13S,14S,17R)-3-hydroxy-10,13-dimethyl-17-[(2R)-6-methylheptan-2-yl]-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-16-yl] N-hexylcarbamate Chemical group C1C=C2C[C@@H](O)CC[C@]2(C)[C@@H]2[C@@H]1[C@@H]1CC(OC(=O)NCCCCCC)[C@H]([C@H](C)CCCC(C)C)[C@@]1(C)CC2 RLXCFCYWFYXTON-JTTSDREOSA-N 0.000 description 1
- XVIYCJDWYLJQBG-UHFFFAOYSA-N acetic acid;adamantane Chemical compound CC(O)=O.C1C(C2)CC3CC1CC2C3 XVIYCJDWYLJQBG-UHFFFAOYSA-N 0.000 description 1
- 230000009471 action Effects 0.000 description 1
- 125000001931 aliphatic group Chemical group 0.000 description 1
- 150000001336 alkenes Chemical class 0.000 description 1
- SRBFZHDQGSBBOR-STGXQOJASA-N alpha-D-lyxopyranose Chemical compound O[C@@H]1CO[C@H](O)[C@@H](O)[C@H]1O SRBFZHDQGSBBOR-STGXQOJASA-N 0.000 description 1
- 230000006229 amino acid addition Effects 0.000 description 1
- 230000000689 aminoacylating effect Effects 0.000 description 1
- 241000617156 archaeon Species 0.000 description 1
- 210000004507 artificial chromosome Anatomy 0.000 description 1
- 210000001106 artificial yeast chromosome Anatomy 0.000 description 1
- 125000004429 atom Chemical group 0.000 description 1
- QVGXLLKOCUKJST-UHFFFAOYSA-N atomic oxygen Chemical compound [O] QVGXLLKOCUKJST-UHFFFAOYSA-N 0.000 description 1
- 125000000852 azido group Chemical group *N=[N+]=[N-] 0.000 description 1
- 230000009286 beneficial effect Effects 0.000 description 1
- WQZGKKKJIJFFOK-VFUOTHLCSA-N beta-D-glucose Chemical compound OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1O WQZGKKKJIJFFOK-VFUOTHLCSA-N 0.000 description 1
- 230000004071 biological effect Effects 0.000 description 1
- 210000004899 c-terminal region Anatomy 0.000 description 1
- 125000001314 canonical amino-acid group Chemical group 0.000 description 1
- 125000002091 cationic group Chemical group 0.000 description 1
- 239000013592 cell lysate Substances 0.000 description 1
- 230000001413 cellular effect Effects 0.000 description 1
- 210000002230 centromere Anatomy 0.000 description 1
- 230000008859 change Effects 0.000 description 1
- 238000007385 chemical modification Methods 0.000 description 1
- 238000006243 chemical reaction Methods 0.000 description 1
- 235000012000 cholesterol Nutrition 0.000 description 1
- 235000019416 cholic acid Nutrition 0.000 description 1
- BHQCQFFYRZLCQQ-OELDTZBJSA-N cholic acid Chemical compound C([C@H]1C[C@H]2O)[C@H](O)CC[C@]1(C)[C@@H]1[C@@H]2[C@@H]2CC[C@H]([C@@H](CCC(O)=O)C)[C@@]2(C)[C@@H](O)C1 BHQCQFFYRZLCQQ-OELDTZBJSA-N 0.000 description 1
- 229960002471 cholic acid Drugs 0.000 description 1
- 238000010367 cloning Methods 0.000 description 1
- 230000000052 comparative effect Effects 0.000 description 1
- 239000002299 complementary DNA Substances 0.000 description 1
- 239000000356 contaminant Substances 0.000 description 1
- 239000013078 crystal Substances 0.000 description 1
- 125000001995 cyclobutyl group Chemical group [H]C1([H])C([H])([H])C([H])(*)C1([H])[H] 0.000 description 1
- 125000001511 cyclopentyl group Chemical group [H]C1([H])C([H])([H])C([H])([H])C([H])(*)C1([H])[H] 0.000 description 1
- 238000000354 decomposition reaction Methods 0.000 description 1
- 230000003247 decreasing effect Effects 0.000 description 1
- 125000002704 decyl group Chemical group [H]C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])* 0.000 description 1
- 230000002950 deficient Effects 0.000 description 1
- KXGVEGMKQFWNSR-UHFFFAOYSA-N deoxycholic acid Natural products C1CC2CC(O)CCC2(C)C2C1C1CCC(C(CCC(O)=O)C)C1(C)C(O)C2 KXGVEGMKQFWNSR-UHFFFAOYSA-N 0.000 description 1
- 239000005547 deoxyribonucleotide Substances 0.000 description 1
- 125000002637 deoxyribonucleotide group Chemical group 0.000 description 1
- 238000001514 detection method Methods 0.000 description 1
- 238000011161 development Methods 0.000 description 1
- SWSQBOPZIKWTGO-UHFFFAOYSA-N dimethylaminoamidine Natural products CN(C)C(N)=N SWSQBOPZIKWTGO-UHFFFAOYSA-N 0.000 description 1
- XPPKVPWEQAFLFU-UHFFFAOYSA-N diphosphoric acid Chemical compound OP(O)(=O)OP(O)(O)=O XPPKVPWEQAFLFU-UHFFFAOYSA-N 0.000 description 1
- KPUWHANPEXNPJT-UHFFFAOYSA-N disiloxane Chemical class [SiH3]O[SiH3] KPUWHANPEXNPJT-UHFFFAOYSA-N 0.000 description 1
- 101150008507 dnaE gene Proteins 0.000 description 1
- 231100000673 dose–response relationship Toxicity 0.000 description 1
- 229940079593 drug Drugs 0.000 description 1
- 238000005516 engineering process Methods 0.000 description 1
- LYCAIKOWRPUZTN-UHFFFAOYSA-N ethylene glycol Substances OCCO LYCAIKOWRPUZTN-UHFFFAOYSA-N 0.000 description 1
- 229940093476 ethylene glycol Drugs 0.000 description 1
- 125000003843 furanosyl group Chemical group 0.000 description 1
- 230000009368 gene silencing by RNA Effects 0.000 description 1
- 239000008103 glucose Substances 0.000 description 1
- 125000003827 glycol group Chemical group 0.000 description 1
- 230000009643 growth defect Effects 0.000 description 1
- 239000001963 growth medium Substances 0.000 description 1
- 230000036541 health Effects 0.000 description 1
- 125000005842 heteroatom Chemical group 0.000 description 1
- 150000002402 hexoses Chemical class 0.000 description 1
- BHEPBYXIRTUNPN-UHFFFAOYSA-N hydridophosphorus(.) (triplet) Chemical class [PH] BHEPBYXIRTUNPN-UHFFFAOYSA-N 0.000 description 1
- 230000002519 immonomodulatory effect Effects 0.000 description 1
- 238000000099 in vitro assay Methods 0.000 description 1
- 230000002401 inhibitory effect Effects 0.000 description 1
- 230000005764 inhibitory process Effects 0.000 description 1
- 238000011901 isothermal amplification Methods 0.000 description 1
- 238000002372 labelling Methods 0.000 description 1
- 150000002632 lipids Chemical group 0.000 description 1
- 238000004519 manufacturing process Methods 0.000 description 1
- 238000004949 mass spectrometry Methods 0.000 description 1
- 230000001404 mediated effect Effects 0.000 description 1
- 230000003278 mimic effect Effects 0.000 description 1
- 238000000302 molecular modelling Methods 0.000 description 1
- 230000017066 negative regulation of growth Effects 0.000 description 1
- 238000001668 nucleic acid synthesis Methods 0.000 description 1
- 239000001301 oxygen Substances 0.000 description 1
- 125000004430 oxygen atom Chemical group O* 0.000 description 1
- 238000012856 packing Methods 0.000 description 1
- 125000000913 palmityl group Chemical group [H]C([*])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H] 0.000 description 1
- ONTNXMBMXUNDBF-UHFFFAOYSA-N pentatriacontane-17,18,19-triol Chemical compound CCCCCCCCCCCCCCCCC(O)C(O)C(O)CCCCCCCCCCCCCCCC ONTNXMBMXUNDBF-UHFFFAOYSA-N 0.000 description 1
- 150000002972 pentoses Chemical class 0.000 description 1
- 150000003904 phospholipids Chemical class 0.000 description 1
- PTMHPRAIXMAOOB-UHFFFAOYSA-N phosphoramidic acid Chemical compound NP(O)(O)=O PTMHPRAIXMAOOB-UHFFFAOYSA-N 0.000 description 1
- 125000004437 phosphorous atom Chemical group 0.000 description 1
- 101150088264 pol gene Proteins 0.000 description 1
- 101150055096 polA gene Proteins 0.000 description 1
- 101150005648 polB gene Proteins 0.000 description 1
- 101150060505 polC gene Proteins 0.000 description 1
- 229920000768 polyamine Polymers 0.000 description 1
- 229920001223 polyethylene glycol Polymers 0.000 description 1
- 229920000642 polymer Polymers 0.000 description 1
- 238000006116 polymerization reaction Methods 0.000 description 1
- 125000002924 primary amino group Chemical group [H]N([H])* 0.000 description 1
- 125000006239 protecting group Chemical group 0.000 description 1
- 125000003132 pyranosyl group Chemical group 0.000 description 1
- 125000004528 pyrimidin-5-yl group Chemical group N1=CN=CC(=C1)* 0.000 description 1
- 150000004944 pyrrolopyrimidines Chemical class 0.000 description 1
- 230000003362 replicative effect Effects 0.000 description 1
- 238000012552 review Methods 0.000 description 1
- 239000002336 ribonucleotide Substances 0.000 description 1
- 125000002652 ribonucleotide group Chemical group 0.000 description 1
- 210000003705 ribosome Anatomy 0.000 description 1
- 125000006413 ring segment Chemical group 0.000 description 1
- 229910052710 silicon Inorganic materials 0.000 description 1
- 239000010703 silicon Substances 0.000 description 1
- 150000003384 small molecules Chemical class 0.000 description 1
- 238000002415 sodium dodecyl sulfate polyacrylamide gel electrophoresis Methods 0.000 description 1
- 108010068698 spleen exonuclease Proteins 0.000 description 1
- 239000000758 substrate Substances 0.000 description 1
- IIACRCGMVDHOTQ-UHFFFAOYSA-N sulfamic acid Chemical group NS(O)(=O)=O IIACRCGMVDHOTQ-UHFFFAOYSA-N 0.000 description 1
- 150000003456 sulfonamides Chemical group 0.000 description 1
- BDHFUVZGWQCTTF-UHFFFAOYSA-M sulfonate Chemical compound [O-]S(=O)=O BDHFUVZGWQCTTF-UHFFFAOYSA-M 0.000 description 1
- 150000003457 sulfones Chemical group 0.000 description 1
- 125000000472 sulfonyl group Chemical group *S(*)(=O)=O 0.000 description 1
- 150000003462 sulfoxides Chemical class 0.000 description 1
- 239000011593 sulfur Substances 0.000 description 1
- 230000002194 synthesizing effect Effects 0.000 description 1
- 230000006231 tRNA aminoacylation Effects 0.000 description 1
- 238000004885 tandem mass spectrometry Methods 0.000 description 1
- 125000000999 tert-butyl group Chemical group [H]C([H])([H])C(*)(C([H])([H])[H])C([H])([H])[H] 0.000 description 1
- OFVLGDICTFRJMM-WESIUVDSSA-N tetracycline Chemical compound C1=CC=C2[C@](O)(C)[C@H]3C[C@H]4[C@H](N(C)C)C(O)=C(C(N)=O)C(=O)[C@@]4(O)C(O)=C3C(=O)C2=C1O OFVLGDICTFRJMM-WESIUVDSSA-N 0.000 description 1
- 229930101283 tetracycline Natural products 0.000 description 1
- 229940124597 therapeutic agent Drugs 0.000 description 1
- 150000003568 thioethers Chemical class 0.000 description 1
- ZMANZCXQSJIPKH-UHFFFAOYSA-O triethylammonium ion Chemical compound CC[NH+](CC)CC ZMANZCXQSJIPKH-UHFFFAOYSA-O 0.000 description 1
- 125000002948 undecyl group Chemical group [H]C([*])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H] 0.000 description 1
- 241001430294 unidentified retrovirus Species 0.000 description 1
Images
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
- C12P21/00—Preparation of peptides or proteins
- C12P21/02—Preparation of peptides or proteins having a known sequence of two or more amino acids, e.g. glutathione
-
- 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
- C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
- C12N9/93—Ligases (6)
-
- 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
- C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
-
- 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
- C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
- C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
-
- 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
- C12N15/87—Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
- C12N15/90—Stable introduction of foreign DNA into chromosome
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Y—ENZYMES
- C12Y601/00—Ligases forming carbon-oxygen bonds (6.1)
- C12Y601/01—Ligases forming aminoacyl-tRNA and related compounds (6.1.1)
- C12Y601/01026—Pyrrolysine-tRNAPyl ligase (6.1.1.26)
Definitions
- oligonucleotides and their applications have revolutionized biotechnology.
- the oligonucleotides including both DNA and RNA each includes only the four natural nucleotides of adenosine (A), guanosine (G), cytosine (C), thymine (T) for DNA, and the four natural nucleotides of adenosine (A), guanosine (G), cytosine (C), and uridine (U) for RNA, and which significantly restricts the potential functions and applications of the oligonucleotides.
- oligonucleotides DNA or RNA
- polymerases for example by PCR or isothermal amplification systems (e.g., transcription with T7 RNA polymerase)
- SELEX Systematic Evolution of Ligands by Exponential Enrichment
- these applications are restricted by the limited chemical/physical diversity present in the natural genetic alphabet (the four natural nucleotides A, C, G, and T in DNA, and the four natural nucleotides A, C, G, and U in RNA).
- Disclosed herein is an additional method of generating nucleic acids that contains an expanded genetic alphabet.
- a protein containing an unnatural amino acid comprising: preparing a mutant tRNA wherein the mutant tRNA comprises a mutant anticodon sequence selected from Table 1 or 2; preparing a mutant mRNA wherein the mutant mRNA comprises a mutant codon sequence selected from Table 1 or 2; and synthesizing the protein containing an unnatural amino acid utilizing the mutant tRNA and the mutant mRNA.
- the protein is synthesized in a cell-free translation system.
- the protein is synthesized in a cell (semi-synthetic organism or SSO).
- the semi-synthetic organism comprises a microorganism.
- the semi-synthetic organism comprises a bacterium. In some instances, the semi-synthetic organism comprises an Escherichia coli . In some instances, the mutant anticodon of the mutant tRNA pairs with a mutant codon selected from Tables 1-3. In some instances, the unnatural amino acid comprises at least one unnatural nucleotide. In some instances, the unnatural nucleotide comprises an unnatural nucleobase.
- the unnatural base of the unnatural nucleotide is selected from the group consisting of 2-aminoadenin-9-yl, 2-aminoadenine, 2-F-adenine, 2-thiouracil, 2-thio-thymine, 2-thiocytosine, 2-propyl and alkyl derivatives of adenine and guanine, 2-amino-adenine, 2-amino-propyl-adenine, 2-aminopyridine, 2-pyridone, 2′-deoxyuridine, 2-amino-2′-deoxyadenosine 3-deazaguanine, 3-deazaadenine, 4-thio-uracil, 4-thio-thymine, uracil-5-yl, hypoxanthin-9-yl (I), 5-methyl-cytosine, 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 5-bromo, and 5-trifiuoromethyl uracils and cytosines; 5-halour
- the unnatural nucleotide is selected from the group consisting of (only nucleobase portion shown, ribose and phosphate backbone omitted for clarity)
- the unnatural nucleotide further comprises an unnatural sugar moiety.
- the unnatural sugar moiety of the unnatural nucleotide is selected from the group consisting of a modification at the 2′ position: OH; substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH 3 , OCN, Cl, Br, CN, CF 3 , OCF 3 , SOCH 3 , SO 2 CH 3 , ONO 2 , NO 2 , N 3 , NH 2 F; O-alkyl, S-alkyl, N-alkyl; O-alkenyl, S-alkenyl, N-alkenyl; O-alkynyl, S-alkynyl, N-alkynyl; O-alkyl-O-alkyl, 2′-F, 2′-OCH 3 , 2′-O(CH 2 ) 2 OCH 3 wherein the alkyl, alkyl, alky
- the mutant anticodon or the mutant codon further comprises an unnatural backbone. In some instances, the mutant anticodon and the mutant codon further comprises an unnatural backbone. In some instances, the unnatural nucleotides are recognized by a DNA polymerase, an RNA polymerase, or a reverse transcriptase. In some instances, an unnatural nucleotide is incorporated by the RNA polymerase into the mRNA during transcription to generate a mutant mRNA containing a mutant codon. In some instances, an unnatural nucleotide is incorporated by the RNA polymerase into the tRNA during transcription to generate a mutant tRNA containing a mutant anticodon.
- an unnatural nucleotide is incorporated by the RNA polymerase into the mRNA during transcription to generate a mutant mRNA. In some instances, an unnatural nucleotide is incorporated by the RNA polymerase into the tRNA during transcription to generate a mutant tRNA. In some instances, the mutant tRNA is charged with an unnatural amino acid residue. In some instances, a protein containing an unnatural amino acid is generated during translation utilizing the mutant tRNA and the mutant mRNA.
- FIG. 1A illustrates the chemical structure of the dNaM-dTPT3 UBP and a natural dA-dT base pair.
- FIG. 1B illustrates the gene cassette used to express sfGFP(AXC) 151 and tRNA(GYT) Ser .
- P T7 and T T7 denote the T7 RNAP promoter and terminator, respectively.
- the sequence following the sfGFP T7 terminator is absent.
- FIG. 1C illustrates a graph of fluorescence of cells expressing sfGFP and tRNA Ser with the indicated position 151-codon and anticodon, respectively.
- Minus sign denotes the absence of serT in the expression cassette.
- AGT natural Ser codon; TAG, amber stop codon; CTA amber suppressor anticodon.
- Data shown as mean ⁇ s.d., n 4 cultures, each propagated from an individual colony.
- FIG. 1D illustrates a graph of growth of cells expressing sfGFP and tRNA Ser with the indicated position 151-codon and anticodon, respectively.
- Minus sign denotes the absence of serT in the expression cassette.
- AGT natural Ser codon; TAG, amber stop codon; CTA amber suppressor anticodon.
- Data shown as mean ⁇ s.d., n 4 cultures, each propagated from an individual colony.
- FIG. 1E illustrates a Western blot of lysates (normalized by OD 600 ) from cells collected at the last time point shown in FIG. 1C and FIG. 1D , probed with an ⁇ -GFP antibody (N-terminal epitope).
- FIG. 2A illustrates a graph of fluorescence of cells expressing sfGFP with the indicated position 151-codon, in the presence (+) or absence ( ⁇ ) of a tRNA Py1 with a cognate anticodon, Py1RS, or 20 mM PrK (N 6 -[(2-propynyloxy)carbonyl]-L-lysine) in the media. Fluorescence was determined at the last time point shown in FIG. 2B . Asterisk denotes the absence of tRNA Py1 in cells expressing sfGFP(TAC) 151 . TAC, natural Tyr codon; TAG, amber stop codon; n.d., not determined. Data shown as mean with individual data points, each propagated from an individual colony.
- FIG. 2B illustrates a timecourse analysis of a subset of the data shown in FIG. 2A .
- Plus and minus signs denote the presence or absence, respectively, of 20 mM PrK in the media.
- Data shown as mean ⁇ s.d., n 4 cultures, each propagated from an individual colony.
- FIG. 2C illustrates Western blots of sfGFP purified from cells expressing sfGFP and tRNA Py1 with the indicated position-151 codon and anticodon, respectively, with or without click conjugation of TAMRA and/or addition of 20 mM PrK to the media.
- tRNA Py1 is absent ( ⁇ ) in cells expressing sfGFP(TAC) 151 .
- sfGFP was purified from cultures collected at the last time point shown in FIG. 2B . Western blots were probed with an ⁇ -GFP antibody and imaged to detect both sfGFP and the conjugated TAMRA.
- FIG. 3A illustrates a graph of fluorescence of cells expressing sfGFP(TAC) 151 or sfGFP and tRNA pAzF with the indicated position-151 codon and a cognate anticodon, respectively, in the presence (+) or absence ( ⁇ ) of 5 mM pAzF in the media.
- TAC natural Tyr codon
- TAG amber stop codon.
- Data shown as mean ⁇ s.d., n 4 cultures, each propagated from an individual colony.
- the fluorescence observed with sfGFP(AXC) 151 in the absence of pAzF is attributed to charging of tRNA pAzF (GYT) with a natural amino acid (likely Tyr).
- FIG. 3B illustrates a Western blot of sfGFP purified from cells expressing sfGFP and tRNA pAzF with the indicated position-151 codon and anticodon, respectively, with or without click conjugation of TAMRA and/or addition of 5 mM pAzF to the media.
- the minus sign denotes the absence of tRNA pAzF in cells expressing sfGFP(TAC) 151 .
- sfGFP was purified from cultures collected at the last time point shown in FIG. 3A . Western blots were probed with an ⁇ -GFP antibody and imaged to detect both sfGFP and the conjugated TAMRA.
- FIG. 4 illustrates fluorescence of cells expressing sfGFP with various codons at position 151.
- FIG. 5A illustrates decoding of the AXC codon with natural near-cognate anticodons, with a graph of fluorescence of cells expressing sfGFP(AXC) 151 with or without tRNA Ser with the indicated anticodon.
- Cells were induced as described in FIG. 1C and FIG. 1D and fluorescence measurements correspond to the last time point shown in FIG. 1C .
- Values for the GYT anticodon and in the absence of tRNA Ser ( ⁇ tRNA) correspond to the same values in FIG. 1 c,d .
- Data shown as mean ⁇ s.d., n 4 cultures, each propagated from an individual colony.
- FIG. 5B illustrates decoding of the AXC codon with natural near-cognate anticodons, with a graph of growth of cells expressing sfGFP(AXC) 151 with or without tRNA Ser with the indicated anticodon.
- Cells were induced as described in FIG. 1C and FIG. 1D and fluorescence measurements correspond to the last time point shown in FIG. 1C .
- Values for the GYT anticodon and in the absence of tRNA Ser ( ⁇ tRNA) correspond to the same values in FIG. 1C and FIG. 1D .
- Data shown as mean ⁇ s.d., n 4 cultures, each propagated from an individual colony.
- FIG. 6A illustrates Western blots and growth of cells decoding AXC and GXC codons with tRNA Py1 .
- Western blot of lysates normalized by OD 600 ) from cells expressing sfGFP with the indicated position 151-codon, in the presence (+) or absence ( ⁇ ) of a tRNA Py1 with a cognate anticodon, Py1RS, or 20 mM PrK in the media. Blots were probed with an ⁇ -GFP antibody (N-terminal epitope). Cells were induced and collected at an equivalent time point as described in FIG. 2B .
- FIG. 6B illustrates growth of cultures analyzed in FIG. 6A .
- Data shown as mean ⁇ s.d., n 4 cultures, each propagated from an individual colony.
- FIG. 7A illustrates decoding AXC and GXC codons with tRNA Py1 and cell growth as a function of added unnatural ribotriphosphates. Fluorescence of purified sfGFP (lower panel) from cells expressing sfGFP and tRNA Py1 with the position 151-codon/anticodon indicated, in the presence (+) or absence ( ⁇ ) of each unnatural ribotriphosphate in the media, and with or without 20 mM PrK. Cells were induced as described in FIG. 2B and fluorescence measurements were taken at the end of induction ( ⁇ 3.5 h), prior to collecting the cells and purifying the sfGFP protein for click conjugation of TAMRA and western blotting.
- FIG. 7B illustrates a gel of decoding AXC and GXC codons with tRNA Py1 as a function of added unnatural ribotriphosphates.
- FIG. 7C illustrates graphs of fluorescence and growth of cells expressing sfGFP(TAC) 151 in the presence (+) or absence ( ⁇ ) of both unnatural deoxyribotriphosphates and each unnatural ribotriphosphate.
- Data shown as mean ⁇ s.d., n 3 cultures, each propagated from an individual colony. At the concentrations used (see Methods), dNaMTP and dTPT3TP do not inhibit cell growth, whereas both unnatural ribotriphosphates, particularly TPT3TP, show some inhibition of growth.
- FIG. 7D illustrates a graph of cell growth corresponding to the cultures with added PrK (20 mM) whose fluorescence is shown in FIG. 2B .
- Cells expressing sfGFP with natural codons were grown without any unnatural triphosphates, whereas cells expressing sfGFP with unnatural codons were grown with both unnatural deoxy- and ribotriphosphates.
- Data shown as mean ⁇ s.d., n 4 cultures, each propagated from an individual colony.
- FIG. 8A illustrates a gel of decoding AXC and GXC codons with tRNA Py1 as a function of PrK concentration in the media.
- sfGFP was induced and purified from cells collected as described in FIG. 2B .
- Western blots were probed with an ⁇ -GFP antibody and imaged to detect both sfGFP and the conjugated TAMRA.
- FIG. 8B illustrates a graph of decoding AXC and GXC codons with tRNA Py1 as a function of PrK concentration in the media.
- Fluorescence of cells (measured at the last time point shown in c) expressing sfGFP and tRNA Py1 with the indicated position-151 codon and anticodon, respectively, as a function of PrK concentration in the media.
- Fluorescence values for 0 and 20 mM PrK are the same as the ( ⁇ ) and (+) PrK values, respectively, shown in FIG. 2B .
- Data shown as mean ⁇ s.d., n 4 cultures, each propagated from an individual colony.
- FIG. 8C illustrates a timecourse analysis of fluorescence. For clarity, only one representative culture is shown for each codon/anticodon pair and PrK concentration. Without being bound by theory, we attribute the low level of sfGFP produced in the absence of PrK to decoding by endogenous tRNAs and loss of UBP retention in sfGFP (Table 5). However, the relative amount of sfGFP that contains PrK ( FIG. 8A ) and absolute amount of sfGFP expressed ( FIG. 8B and FIG.
- FIG. 8D illustrates a timecourse analysis of cell growth at various concentrations of PrK for the experiment shown in FIG. 8C .
- FIG. 9 illustrates cell growth of the cultures whose fluorescence is shown in FIG. 3A .
- Data shown as mean ⁇ s.d., n 4 cultures, each propagated from an individual colony
- ranges and amounts can be expressed as “about” a particular value or range. About also includes the exact amount. Hence “about 5 ⁇ L” means “about 5 ⁇ L” and also “5 ⁇ L.” Generally, the term “about” includes an amount that would be expected to be within experimental error.
- the information of life is encoded by a four letter genetic alphabet, which is made possible by the selective formation of two base pairs: (d)G-(d)C and (d)A-dT/U.
- a third, unnatural base pair (UBP) formed between two synthetic nucleotides expands this system, thereby increasing the potential for information storage, and has profound academic and practical implications.
- UBP unnatural base pair
- UBPs that are replicated, transcribed, and translated into protein in vitro provide insights into the forces underlying the storage and retrieval of natural information, and also enable wide ranging applications in chemical and synthetic biology.
- SSO semi-synthetic organism
- an SSO has revolutionary practical applications, including for human health.
- an SSO revolutionizes the growing field of protein therapeutics.
- protein therapeutics are severely limited in their molecular properties due to the finite chemical diversity available with the twenty natural amino acids.
- the protein is synthesized in a cell-free translation system. In some instances, the protein is synthesized in a cell or semi-synthetic organism (SSO). In some instances, the semi-synthetic organism comprises a microorganism. In some instances, the semi-synthetic organism comprises a bacterium. In some instances, the semi-synthetic organism comprises an Escherichia coli . In some instances, the mutant tRNA contains a mutant anticodon sequence. In some instances, the mutant anticodon sequence is an anticodon sequence illustrated in Table 1. In some instances, the mutant anticodon sequence is an anticodon sequence illustrated in Table 2. In some instances, the mutant anticodon sequence is an anticodon sequence illustrated in Table 3.
- the mutant anticodon of the mutant tRNA pairs with a mutant codon.
- the mutant codon is a mutant codon illustrated in Table 1.
- the mutant codon is a mutant codon illustrated in Table 2.
- the mutant codon is a mutant codon illustrated in Table 3.
- the Y and X illustrated in Table 1, Table 2, and Table 3 represent unnatural bases of the unnatural nucleotide.
- the unnatural base is selected from the group consisting of 2-aminoadenin-9-yl, 2-aminoadenine, 2-F-adenine, 2-thiouracil, 2-thio-thymine, 2-thiocytosine, 2-propyl and alkyl derivatives of adenine and guanine, 2-amino-adenine, 2-amino-propyl-adenine, 2-aminopyridine, 2-pyridone, 2′-deoxyuridine, 2-amino-2′-deoxyadenosine 3-deazaguanine, 3-deazaadenine, 4-thio-uracil, 4-thio-thymine, uracil-5-yl, hypoxanthin-9-yl (I), 5-methyl-cytosine, 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 5-
- the unnatural nucleotide is selected from the group consisting of (only nucleobase portion shown, ribose and phosphate backbone omitted for clarity)
- the unnatural nucleotide is selected from the group consisting of (only nucleobase portion shown, ribose and phosphate backbone omitted for clarity)
- the unnatural nucleotide further comprises an unnatural sugar moiety.
- the unnatural sugar moiety is selected from the group consisting of a modification at the 2′ position: OH; substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH 3 , OCN, Cl, Br, CN, CF 3 , OCF 3 , SOCH 3 , SO 2 CH 3 , ONO 2 , NO 2 , N 3 , NH 2 F; O-alkyl, S-alkyl, N-alkyl; O-alkenyl, S-alkenyl, N-alkenyl; O-alkynyl, S-alkynyl, N-alkynyl; O-alkyl-O-alkyl, 2′-F, 2′-OCH 3 , 2′-O(CH 2 ) 2 OCH 3 wherein the alkyl, alkenyl and alkynyl
- the mutant anticodon or the mutant codon further comprises an unnatural backbone. In some instances, the mutant anticodon further comprises an unnatural backbone. In some instances, the mutant codon further comprises an unnatural backbone. In some instances, the unnatural backbone is selected from the group consisting of a phosphorothioate, chiral phosphorothioate, phosphorodithioate, phosphotriester, aminoalkylphosphotriester, phosphonates, 3′-alkylene phosphonate, chiral phosphonates, phosphinates, phosphoramidates, 3′-amino phosphoramidate, aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates.
- the unnatural nucleotides are recognized by a polymerase.
- the polymerase is a DNA polymerase, an RNA polymerase, or a reverse transcriptase.
- the polymerase comprises ⁇ 29, B103, GA-1, PZA, ⁇ 15, BS32, M2Y, Nf, G1, Cp-1, PRD1, PZE, SF5, Cp-5, Cp-7, PR4, PR5, PR722, L17, ThermoSequenase®, 9° NmTM TherminatorTM DNA polymerase, Tne, Tma, TfI, Tth, TIi, Stoffel fragment, VentTM and Deep VentTM DNA polymerase, KOD DNA polymerase, Tgo, JDF-3, Pfu, Taq, T7 DNA polymerase, T7 RNA polymerase, PGB-D, UlTma DNA polymerase, E.
- coli DNA polymerase I E. coli DNA polymerase III, archaeal DP1I/DP2 DNA polymerase II, 9° N DNA Polymerase, Taq DNA polymerase, Phusion® DNA polymerase, Pfu DNA polymerase, SP6 RNA polymerase, RB69 DNA polymerase, Avian Myeloblastosis Virus (AMV) reverse transcriptase, Moloney Murine Leukemia Virus (MMLV) reverse transcriptase, SuperScript® II reverse transcriptase, and SuperScript® III reverse transcriptase.
- AMV Avian Myeloblastosis Virus
- MMLV Moloney Murine Leukemia Virus
- the polymerase is DNA polymerase 1-Klenow fragment, Vent polymerase, Phusion® DNA polymerase, KOD DNA polymerase, Taq polymerase, T7 DNA polymerase, T7 RNA polymerase, TherminatorTM DNA polymerase, POLB polymerase, SP6 RNA polymerase, E. coli DNA polymerase I, E. coli DNA polymerase III, Avian Myeloblastosis Virus (AMV) reverse transcriptase, Moloney Murine Leukemia Virus (MMLV) reverse transcriptase, SuperScript® II reverse transcriptase, or SuperScript® III reverse transcriptase.
- AMV Avian Myeloblastosis Virus
- MMLV Moloney Murine Leukemia Virus
- an unnatural nucleotide is incorporated by the polymerase into the mRNA during transcription to generate a mutant mRNA containing a mutant codon. In some instances, an unnatural nucleotide is incorporated by the polymerase into the mRNA during transcription to generate a mutant mRNA.
- an unnatural nucleotide is incorporated by the polymerase into the tRNA during transcription to generate a mutant tRNA containing a mutant anticodon. In some instances, an unnatural nucleotide is incorporated by the polymerase into the tRNA during transcription to generate a mutant tRNA.
- the mutant tRNA represents an unnatural amino acid residue.
- an unnatural amino acid residue is a non-natural amino acid such as those described in Liu C. C., Schultz, P. G. Annu. Rev. Biochem. 2010, 79, 413.
- a protein containing an unnatural amino acid is generated during translation utilizing the mutant tRNA and the mutant mRNA. In some instances, the protein containing an unnatural amino acid is generated under a cell free translation system. In some instances, the protein is synthesized in a cell or semi-synthetic organism (SSO). In some instances, the semi-synthetic organism comprises a microorganism. In some instances, the semi-synthetic organism comprises a bacterium. In some instances, the semi-synthetic organism comprises an Escherichia coli.
- a nucleic acid (e.g., also referred to herein as target nucleic acid, target nucleotide sequence, nucleic acid sequence of interest or nucleic acid region of interest) can be from any source or composition, such as DNA, cDNA, gDNA (genomic DNA), RNA, siRNA (short inhibitory RNA), RNAi, tRNA or mRNA, for example, and can be in any form (e.g., linear, circular, supercoiled, single-stranded, double-stranded, and the like). Nucleic acids can comprise nucleotides, nucleosides, or polynucleotides. Nucleic acids can comprise natural and unnatural nucleic acids.
- a nucleic acid can also comprise unnatural nucleic acids, such as DNA or RNA analogs (e.g., containing base analogs, sugar analogs and/or a non-native backbone and the like). It is understood that the term “nucleic acid” does not refer to or infer a specific length of the polynucleotide chain, thus polynucleotides and oligonucleotides are also included in the definition.
- Exemplary natural nucleotides include, without limitation, ATP, UTP, CTP, GTP, ADP, UDP, CDP, GDP, AMP, UMP, CMP, GMP, dATP, dTTP, dCTP, dGTP, dADP, dTDP, dCDP, dGDP, dAMP, dTMP, dCMP, and dGMP.
- Exemplary natural deoxyribonucleotides include dATP, dTTP, dCTP, dGTP, dADP, dTDP, dCDP, dGDP, dAMP, dTMP, dCMP, and dGMP.
- Exemplary natural ribonucleotides include ATP, UTP, CTP, GTP, ADP, UDP, CDP, GDP, AMP, UMP, CMP, and GMP.
- the uracil base is uridine.
- a nucleic acid sometimes is a vector, plasmid, phage, autonomously replicating sequence (ARS), centromere, artificial chromosome, yeast artificial chromosome (e.g., YAC) or other nucleic acid able to replicate or be replicated.
- An unnatural nucleic acid can be a nucleic acid analogue.
- a nucleotide analog, or unnatural nucleotide comprises a nucleotide which contains some type of modification to either the base, sugar, or phosphate moieties.
- a modification can comprise a chemical modification. Modifications may be, for example, of the 3′OH or 5′OH group, of the backbone, of the sugar component, or of the nucleotide base. Modifications may include addition of non-naturally occurring linker molecules and/or of interstrand or intrastrand cross links.
- the modified nucleic acid comprises modification of one or more of the 3′OH or 5′OH group, the backbone, the sugar component, or the nucleotide base, and/or addition of non-naturally occurring linker molecules.
- a modified backbone comprises a backbone other than a phosphodiester backbone.
- a modified sugar comprises a sugar other than deoxyribose (in modified DNA) or other than ribose (modified RNA).
- a modified base comprises a base other than adenine, guanine, cytosine or thymine (in modified DNA) or a base other than adenine, guanine, cytosine or uracil (in modified RNA).
- the nucleic acid may comprise at least one modified base. Modifications to the base moiety would include natural and synthetic modifications of A, C, G, and T/U as well as different purine or pyrimidine bases. In some embodiments, a modification is to a modified form of adenine, guanine cytosine or thymine (in modified DNA) or a modified form of adenine, guanine cytosine or uracil (modified RNA).
- a modified base of a unnatural nucleic acid includes but is not limited to uracil-5-yl, hypoxanthin-9-yl (I), 2-aminoadenin-9-yl, 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted
- Certain unnatural nucleic acids such as 5-substituted pyrimidines, 6-azapyrimidines and N-2 substituted purines, N-6 substituted purines, 0-6 substituted purines, 2-aminopropyladenine, 5-propynyluracil, 5-propynylcytosine, 5-methylcytosine, those that increase the stability of duplex formation, universal nucleic acids, hydrophobic nucleic acids, promiscuous nucleic acids, size-expanded nucleic acids, fluorinated nucleic acids, 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine.
- 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl, other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil, 5-halocytosine, 5-propynyl (—C ⁇ C—CI1 ⁇ 4) uracil, 5-propynyl cytosine, other alkynyl derivatives of pyrimidine nucleic acids, 6-azo uracil, 6-azo cytosine, 6-azo thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-
- nucleic acids comprising various heterocyclic bases and various sugar moieties (and sugar analogs) are available in the art, and the nucleic acid can include one or several heterocyclic bases other than the principal five base components of naturally-occurring nucleic acids.
- the heterocyclic base may include uracil-5-yl, cytosin-5-yl, adenin-7-yl, adenin-8-yl, guanin-7-yl, guanin-8-yl, 4-aminopyrrolo [2.3-d] pyrimidin-5-yl, 2-amino-4-oxopyrolo [2,3-d] pyrimidin-5-yl, 2-amino-4-oxopyrrolo [2.3-d] pyrimidin-3-yl groups, where the purines are attached to the sugar moiety of the nucleic acid via the 9-position, the pyrimidines via the 1-position, the pyrrolopyrimidines via the 7-position and the pyrazolopyrimidines via the 1-position.
- Nucleotide analogs can also be modified at the phosphate moiety.
- Modified phosphate moieties include but are not limited to those that can be modified so that the linkage between two nucleotides contains a phosphorothioate, chiral phosphorothioate, phosphorodithioate, phosphotriester, aminoalkylphosphotriester, methyl and other alkyl phosphonates including 3′-alkylene phosphonate and chiral phosphonates, phosphinates, phosphoramidates including 3′-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates.
- these phosphate or modified phosphate linkage between two nucleotides can be through a 3′-5′ linkage or a 2′-5′ linkage, and the linkage can contain inverted polarity such as 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′.
- Various salts, mixed salts and free acid forms are also included. Numerous United States patents teach how to make and use nucleotides containing modified phosphates and include but are not limited to, U.S. Pat. Nos.
- Unnatural nucleic acids can include 2′,3′-dideoxy-2′,3′-didehydro-nucleosides (PCT/US2002/006460), 5′-substituted DNA and RNA derivatives (PCT/US2011/033961; Saha et al, J.
- Unnatural nucleic acids can include modifications at the 5′-position and the 2′-position of the sugar ring (PCT/US94/02993), such as 5′-CH 2 substituted 2′-O-protected nucleosides (Wu et al., Helvetica Chimica Acta, 2000, 83, 1127-1143 and Wu et al. Bioconjugate Chem. 1999, 10, 921-924).
- Unnatural nucleic acids can include amide linked nucleoside dimers have been prepared for incorporation into oligonucleotides wherein the 3′ linked nucleoside in the dimer (5′ to 3′) comprises a 2′-OCH 3 and a 5′-(S)—CH 3 (Mesmaeker et al, Synlett, 1997, 1287-1290).
- Unnatural nucleic acids can include 2′-substituted 5′-CH 2 (or O) modified nucleosides (PCT/US92/01020).
- Unnatural nucleic acids can include 5′methylenephosphonate DNA and RNA monomers, and dimers (Bohringer et al, Tet.
- Unnatural nucleic acids can include 5′-phosphonate monomers having a 2′-substitution (US 2006/0074035) and other modified 5′-phosphonate monomers (WO 97/35869).
- Unnatural nucleic acids can include 5′-modified methylenephosphonate monomers (EP614907 and EP629633).
- Unnatural nucleic acids can include analogs of 5′ or 6′-phosphonate ribonucleosides comprising a hydroxyl group at the 5′ and or 6′ position (Chen et al, Phosphorus, Sulfur and Silicon, 2002, 777, 1783-1786; Jung et al, Bioorg. Med. Chem., 2000, 8, 2501-2509, Gallier et al, Eur. J. Org. Chem., 2007, 925-933 and Hampton et al, J. Med. Chem., 1976, 19(8), 1029-1033).
- Unnatural nucleic acids can include 5′-phosphonate deoxyribonucleoside monomers and dimers having a 5′-phosphate group (Nawrot et al, Oligonucleotides, 2006, 16(1), 68-82).
- Unnatural nucleic acids can include nucleosides having a 6′-phosphonate group wherein the 5′ or/and 6′-position is unsubstituted or substituted with a thio-tert-butyl group (SC(CH 3 ) 3 ) (and analogs thereof); a methyleneamino group (CH 2 NH 2 ) (and analogs thereof) or a cyano group (CN) (and analogs thereof) (Fairhurst et al, Synlett, 2001, 4, 467-472; Kappler et al, J.
- Unnatural nucleic acids can also include modifications of the sugar moiety.
- Nucleic acids of the invention can optionally contain one or more nucleosides wherein the sugar group has been modified. Such sugar modified nucleosides may impart enhanced nuclease stability, increased binding affinity, or some other beneficial biological property.
- nucleic acids comprise a chemically modified ribofuranose ring moiety.
- Examples of chemically modified ribofuranose rings include, without limitation, addition of substitutent groups (including 5′ and/or 2′ substituent groups; bridging of two ring atoms to form bicyclic nucleic acids (BNA); replacement of the ribosyl ring oxygen atom with S, N(R), or C(R 1 )(R 2 ) (R ⁇ H, C 1 -C 12 alkyl or a protecting group); and combinations thereof.
- Examples of chemically modified sugars can be found in WO 2008/101157, US 2005/0130923, and WO 2007/134181.
- a modified nucleic acid may comprise modified sugars or sugar analogs.
- the sugar moiety can be pentose, deoxypentose, hexose, deoxyhexose, glucose, arabinose, xylose, lyxose, and a sugar “analog” cyclopentyl group.
- the sugar can be in pyranosyl or in a furanosyl form.
- the sugar moiety may be the furanoside of ribose, deoxyribose, arabinose or 2′-O-alkylribose, and the sugar can be attached to the respective heterocyclic bases either in [alpha] or [beta] anomeric configuration.
- Sugar modifications include, but are not limited to, 2′-alkoxy-RNA analogs, 2′-amino-RNA analogs, 2′-fluoro-DNA, and 2′-alkoxy- or amino-RNA/DNA chimeras.
- a sugar modification may include, 2′-O-methyl-uridine and 2′-O-methyl-cytidine.
- Sugar modifications include 2′-O-alkyl-substituted deoxyribonucleosides and 2′-O-ethyleneglycol like ribonucleosides.
- the preparation of these sugars or sugar analogs and the respective “nucleosides” wherein such sugars or analogs are attached to a heterocyclic base (nucleic acid base) is known.
- Sugar modifications may also be made and combined with other modifications.
- Modifications to the sugar moiety include natural modifications of the ribose and deoxy ribose as well as unnatural modifications.
- Sugar modifications include but are not limited to the following modifications at the 2′ position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl may be substituted or unsubstituted C 1 to C 10 , alkyl or C 2 to C 10 alkenyl and alkynyl.
- 2′ sugar modifications also include but are not limited to —O[(CH 2 ) n O] m CH 3 , —O(CH 2 ) n OCH 3 , —O(CH 2 ) n NH 2 , —O(CH 2 ) n CH 3 , —O(CH 2 ) n —ONH 2 , and —O(CH 2 ) n ON[(CH 2 )n CH 3 )J 2 , where n and m are from 1 to about 10.
- modifications at the 2′ position include but are not limited to: C 1 to C 10 lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH 3 , OCN, Cl, Br, CN, CF 3 , OCF 3 , SOCH 3 , SO 2 CH 3 , ONO 2 , NO 2 , N 3 , NH 2 , heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide, and other substituents having similar properties.
- Similar modifications may also be made at other positions on the sugar, particularly the 3′ position of the sugar on the 3′ terminal nucleotide or in 2′-5′ linked oligonucleotides and the 5′ position of 5′ terminal nucleotide.
- Modified sugars would also include those that contain modifications at the bridging ring oxygen, such as CH 2 and S.
- Nucleotide sugar analogs may also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar.
- nucleic acids having modified sugar moieties include, without limitation, nucleic acids comprising 5′-vinyl, 5′-methyl (R or S), 4′-S, 2′-F, 2′-OCH 3 , and 2′-O(CH 2 ) 2 OCH 3 substituent groups.
- the substituent at the 2′ position can also be selected from allyl, amino, azido, thio, O-allyl, O—C C 10 alkyl, OCF 3 , O(CH 2 ) 2 SCH 3 , O(CH 2 ) 2 —O—N(R m )(R n ), and O—CH 2 —C( ⁇ O)—N(R m )(R n ), where each R m and R n is, independently, H or substituted or unsubstituted C 1 -C 10 alkyl.
- nucleic acids of the present invention include one or more bicyclic nucleic acids.
- the bicyclic nucleic acid comprises a bridge between the 4′ and the 2′ ribosyl ring atoms.
- nucleic acids provided herein include one or more bicyclic nucleic acids wherein the bridge comprises a 4′ to 2′ bicyclic nucleic acid.
- 4′ to 2′ bicyclic nucleic acids include, but are not limited to, one of the formulae: 4′-(CH 2 )—O-2′ (LNA); 4′-(CH 2 )—S-2′; 4′-(CH 2 ) 2 —O-2′ (ENA); 4′-CH(CH 3 )—O-2′ and 4′-CH(CH 2 OCH 3 )—O-2′, and analogs thereof (see, U.S. Pat. No. 7,399,845, issued on Jul. 15, 2008); 4′-C(CH 3 )(CH 3 )—O-2′ and analogs thereof, (see WO2009/006478, WO2008/150729, US2004/0171570, U.S. Pat. No.
- PCT/US2008/064591 PCT US2008/066154, and PCT US2008/068922, PCT/DK98/00393; and U.S. Pat. Nos. 4,849,513; 5,015,733; 5,118,800; and 5,118,802.
- nucleic acids can comprise linked nucleic acids.
- Nucleic acids can be linked together using any inter nucleic acid linkage.
- the two main classes of inter nucleic acid linking groups are defined by the presence or absence of a phosphorus atom.
- Non-phosphorus containing inter nucleic acid linking groups include, but are not limited to, methylenemethylimino (—CH 2 —N(CH 3 )—O—CH 2 —), thiodiester (—O—C(O)—S—), thionocarbamate (—O— C(O)(NH)—S—); siloxane (—O—Si(H)2-O—); and N,N*-dimethylhydrazine (—CH 2 —N(CH 3 )—N(CH 3 )—).
- inter nucleic acids linkages having a chiral atom can be prepared a racemic mixture, as separate enantiomers, e.g., alkylphosphonates and phosphorothioates.
- Unnatural nucleic acids can contain a single modification.
- Unnatural nucleic acids can contain multiple modifications within one of the moieties or between different moieties.
- Backbone phosphate modifications to nucleic acid include, but are not limited to, methyl phosphonate, phosphorothioate, phosphoramidate (bridging or non-bridging), phosphotriester, phosphorodithioate, phosphodithioate, and boranophosphate, and may be used in any combination. Other non-phosphate linkages may also be used.
- backbone modifications e.g., methylphosphonate, phosphorothioate, phosphoroamidate and phosphorodithioate internucleotide linkages
- backbone modifications can confer immunomodulatory activity on the modified nucleic acid and/or enhance their stability in vivo.
- a phosphorous derivative can be attached to the sugar or sugar analog moiety in and can be a monophosphate, diphosphate, triphosphate, alkylphosphonate, phosphorothioate, phosphorodithioate, phosphoramidate or the like.
- Exemplary polynucleotides containing modified phosphate linkages or non-phosphate linkages can be found in Peyrottes et al. (1996) Nucleic Acids Res. 24: 1841-1848; Chaturvedi et al. (1996) Nucleic Acids Res. 24:2318-2323; and Schultz et al. (1996) Nucleic Acids Res.
- Backbone modification may comprise replacing the phosphodiester linkage with an alternative moiety such as an anionic, neutral or cationic group.
- modifications include: anionic internucleoside linkage; N3′ to P5′ phosphoramidate modification; boranophosphate DNA; prooligonucleotides; neutral internucleoside linkages such as methylphosphonates; amide linked DNA; methylene(methylimino) linkages; formacetal and thioformacetal linkages; backbones containing sulfonyl groups; morpholino oligos; peptide nucleic acids (PNA); and positively charged deoxyribonucleic guanidine (DNG) oligos, Micklefield, J.
- anionic internucleoside linkage N3′ to P5′ phosphoramidate modification
- boranophosphate DNA prooligonucleotides
- neutral internucleoside linkages such as methylphosphonates
- amide linked DNA methylene(methyli
- a modified nucleic acid may comprise a chimeric or mixed backbone comprising one or more modifications, e.g. a combination of phosphate linkages such as a combination of phosphodiester and phosphorothioate linkages.
- Substitutes for the phosphate can be for example, short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages.
- morpholino linkages formed in part from the sugar portion of a nucleoside
- siloxane backbones sulfide, sulfoxide and sulfone backbones
- formacetyl and thioformacetyl backbones methylene formacetyl and thioformacetyl backbones
- alkene containing backbones sulfamate backbones
- sulfonate and sulfonamide backbones amide backbones; and others having mixed N, O, S and CH 2 component parts.
- nucleotide substitute that both the sugar and the phosphate moieties of the nucleotide can be replaced, by for example an amide type linkage (aminoethylglycine) (PNA).
- PNA aminoethylglycine
- U.S. Pat. Nos. 5,539,082; 5,714,331; and 5,719,262 teach how to make and use PNA molecules, each of which is herein incorporated by reference. (See also Nielsen et al., Science, 1991, 254, 1497-1500).
- Conjugates can be chemically linked to the nucleotide or nucleotide analogs. Such conjugates include but are not limited to lipid moieties such as a cholesterol moiety (Letsinger et al., Proc.
- Acids Res., 1990, 18, 3777-3783 a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides & Nucleotides, 1995, 14, 969-973), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654), a palmityl moiety (Mishra et al., Biochem. Biophys. Acta, 1995, 1264, 229-237), or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp.
- a particularly useful function of a polymerase is to catalyze the polymerization of a nucleic acid strand using an existing nucleic acid as a template. Other functions that are useful are described elsewhere herein. Examples of useful polymerases include DNA polymerases and RNA polymerases.
- the ability to improve specificity, processivity, or other features of polymerases unnatural nucleic acids would be highly desirable in a variety of contexts where, e.g., unnatural nucleic acid incorporation is desired, including amplification, sequencing, labeling, detection, cloning, and many others.
- the present invention provides polymerases with modified properties for unnatural nucleic acids, methods of making such polymerases, methods of using such polymerases, and many other features that will become apparent upon a complete review of the following.
- polymerases that incorporate unnatural nucleic acids into a growing template copy, e.g., during DNA amplification.
- polymerases can be modified such that the active site of the polymerase is modified to reduce steric entry inhibition of the unnatural nucleic acid into the active site.
- polymerases can be modified to provide complementarity with one or more unnatural features of the unnatural nucleic acids. Accordingly, the invention includes compositions that include a heterologous or recombinant polymerase and methods of use thereof.
- Polymerases can be modified using methods pertaining to protein engineering. For example, molecular modeling can be carried out based on crystal structures to identify the locations of the polymerases where mutations can be made to modify a target activity. A residue identified as a target for replacement can be replaced with a residue selected using energy minimization modeling, homology modeling, and/or conservative amino acid substitutions, such as described in Bordo, et al. J Mol Biol 217: 721-729 (1991) and Hayes, et al. Proc Natl Acad Sci, USA 99: 15926-15931 (2002).
- polymerases can be used in a method or composition set forth herein including, for example, protein-based enzymes isolated from biological systems and functional variants thereof. Reference to a particular polymerase, such as those exemplified below, will be understood to include functional variants thereof unless indicated otherwise.
- a polymerase is a wild type polymerase. In some embodiments, a polymerase is a modified, or mutant, polymerase.
- a modified polymerase has a modified nucleotide binding site.
- a modified polymerase has a specificity for an unnatural nucleic acid that is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, 99.5%, 99.99% the specificity of the wild type polymerase toward the unnatural nucleic acid.
- a modified or wild type polymerase has a specificity for an unnatural nucleic acid comprising a modified sugar that is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, 99.5%, 99.99% the specificity of the wild type polymerase toward a natural nucleic acid and/or the unnatural nucleic acid without the modified sugar.
- a modified or wild type polymerase has a specificity for an unnatural nucleic acid comprising a modified base that is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, 99.5%, 99.99% the specificity of the wild type polymerase toward a natural nucleic acid and/or the unnatural nucleic acid without the modified base.
- a modified or wild type polymerase has a specificity for an unnatural nucleic acid comprising a triphosphate that is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, 99.5%, 99.99% the specificity of the wild type polymerase toward a nucleic acid comprising a triphosphate and/or the unnatural nucleic acid without the triphosphate.
- a modified or wild type polymerase can have a specificity for an unnatural nucleic acid comprising a triphosphate that is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, 99.5%, 99.99% the specificity of the wild type polymerase toward the unnatural nucleic acid with a diphosphate or monophosphate, or no phosphate, or a combination thereof.
- a modified or wild type polymerase has a relaxed specificity for an unnatural nucleic acid. In some embodiments, a modified or wild type polymerase has a specificity for an unnatural nucleic acid and a specificity to a natural nucleic acid that is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, 99.5%, 99.99% the specificity of the wild type polymerase toward the natural nucleic acid.
- a modified or wild type polymerase has a specificity for an unnatural nucleic acid comprising a modified sugar and a specificity to a natural nucleic acid that is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, 99.5%, 99.99% the specificity of the wild type polymerase toward the natural nucleic acid.
- a modified or wild type polymerase has a specificity for an unnatural nucleic acid comprising a modified base and a specificity to a natural nucleic acid that is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, 99.5%, 99.99% the specificity of the wild type polymerase toward the natural nucleic acid.
- Absence of exonuclease activity can be a wild type characteristic or a characteristic imparted by a variant or engineered polymerase.
- an exo minus Klenow fragment is a mutated version of Klenow fragment that lacks 3′ to 5′ proofreading exonuclease activity.
- the method of the invention may be used to expand the substrate range of any DNA polymerase which lacks an intrinsic 3 to 5′ exonuclease proofreading activity or where a 3 to 5′ exonuclease proofreading activity has been disabled, e.g. through mutation.
- DNA polymerases include polA, polB (see e.g. Parrel & Loeb, Nature Struc Biol 2001) polC, polD, polY, polX and reverse transcriptases (RT) but preferably are processive, high-fidelity polymerases (PCT/GB2004/004643).
- a modified or wild type polymerase substantially lacks 3′ to 5′ proofreading exonuclease activity.
- a modified or wild type polymerase substantially lacks 3′ to 5′ proofreading exonuclease activity for an unnatural nucleic acid. In some embodiments, a modified or wild type polymerase has a 3′ to 5′ proofreading exonuclease activity. In some embodiments, a modified or wild type polymerase has a 3′ to 5′ proofreading exonuclease activity for a natural nucleic acid and substantially lacks 3′ to 5′ proofreading exonuclease activity for an unnatural nucleic acid.
- a modified polymerase has a 3′ to 5′ proofreading exonuclease activity that is at least about 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, 99.5%, 99.99% the proofreading exonuclease activity of the wild type polymerase.
- a modified polymerase has a 3′ to 5′ proofreading exonuclease activity for an unnatural nucleic acid that is at least about 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, 99.5%, 99.99% the proofreading exonuclease activity of the wild type polymerase to a natural nucleic acid.
- a modified polymerase has a 3′ to 5′ proofreading exonuclease activity for an unnatural nucleic acid and a 3′ to 5′ proofreading exonuclease activity for a natural nucleic acid that is at least about 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, 99.5%, 99.99% the proofreading exonuclease activity of the wild type polymerase to a natural nucleic acid.
- a modified polymerase has a 3′ to 5′ proofreading exonuclease activity for a natural nucleic acid that is at least about 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, 99.5%, 99.99% the proofreading exonuclease activity of the wild type polymerase to the natural nucleic acid.
- the invention provides methods of making a modified polymerase that include structurally modeling a parental polymerase, e.g., a DNA polymerase, identifying one or more complex stability or nucleotide interaction feature affecting complex stability or nucleotide access or binding in the active site or a complementarity feature for a nucleotide analog at the active site, and mutating the parental polymerase to include or remove these features.
- a parental polymerase e.g., a DNA polymerase
- identifying one or more complex stability or nucleotide interaction feature affecting complex stability or nucleotide access or binding in the active site or a complementarity feature for a nucleotide analog at the active site mutating the parental polymerase to include or remove these features.
- the polymerase can be mutated to improve steric access of the unnatural nucleotide to the active site or to improve charge-charge or hydrophobic interactions between the unnatural nucleotide and the polymerase.
- Polymerases can be characterized according to their rate of dissociation from nucleic acids.
- a polymerase has a relatively low dissociation rate for one or more natural and unnatural nucleic acids.
- a polymerase has a relatively high dissociation rate for one or more natural and unnatural nucleic acids.
- the dissociation rate is an activity of a polymerase that can be adjusted to tune reaction rates in methods set forth herein.
- Polymerases can be characterized according to their fidelity when used with a particular natural and/or unnatural nucleic acid or collections of natural and/or unnatural nucleic acid. Fidelity generally refers to the accuracy with which a polymerase incorporates correct nucleic acids into a growing nucleic acid chain when making a copy of a nucleic acid template. DNA polymerase fidelity can be measured as the ratio of correct to incorrect natural and unnatural nucleic acid incorporations when the natural and unnatural nucleic acid are present, e.g., at equal concentrations, to compete for strand synthesis at the same site in the polymerase-strand-template nucleic acid binary complex.
- DNA polymerase fidelity can be calculated as the ratio of (k cat /K m ) for the natural and unnatural nucleic acid and (kc at /K m ) for the incorrect natural and unnatural nucleic acid; where k cat and K m are Michaelis-Menten parameters in steady state enzyme kinetics (Fersht, A. R. (1985) Enzyme Structure and Mechanism, 2nd ed., p 350, W. H. Freeman & Co., New York., incorporated herein by reference).
- a polymerase has a fidelity value of at least about 100, 1000, 10,000, 100,000, or 1 ⁇ 10 6 , with or without a proofreading activity.
- Polymerases from native sources or variants thereof can be screened using an assay that detects incorporation of an unnatural nucleic acid having a particular structure.
- polymerases can be screened for the ability to incorporate an unnatural nucleic acid or UBP; e.g., d5SICSTP, dNaMTP, or d5SICSTP-dNaMTP UBP.
- a polymerase e.g., a heterologous polymerase, can be used that displays a modified property for the unnatural nucleic acid as compared to the wild-type polymerase.
- the modified property can be, e.g., K m , k cat , V max , polymerase processivity in the presence of an unnatural nucleic acid (or of a naturally occurring nucleotide), average template read-length by the polymerase in the presence of an unnatural nucleic acid, specificity of the polymerase for an unnatural nucleic acid, rate of binding of an unnatural nucleic acid, rate of product (pyrophosphate, triphosphate, etc.) release, branching rate, or any combination thereof.
- the modified property is a reduced K m for an unnatural nucleic acid and/or an increased k cat /K m or V max /K m for an unnatural nucleic acid.
- the polymerase optionally has an increased rate of binding of an unnatural nucleic acid, an increased rate of product release, and/or a decreased branching rate, as compared to a wild-type polymerase.
- a polymerase can incorporate natural nucleic acids, e.g., A, C, G, and T, into a growing nucleic acid copy.
- a polymerase optionally displays a specific activity for a natural nucleic acid that is at least about 5% as high (e.g., 5%, 10%, 25%, 50%, 75%, 100% or higher), as a corresponding wild-type polymerase and a processivity with natural nucleic acids in the presence of a template that is at least 5% as high (e.g., 5%, 10%, 25%, 50%, 75%, 100% or higher) as the wild-type polymerase in the presence of the natural nucleic acid.
- the polymerase displays a k cat /K m or V max /K m for a naturally occurring nucleotide that is at least about 5% as high (e.g., about 5%, 10%, 25%, 50%, 75% or 100% or higher) as the wild-type polymerase.
- Polymerases used herein that can have the ability to incorporate an unnatural nucleic acid of a particular structure can also be produced using a directed evolution approach.
- a nucleic acid synthesis assay can be used to screen for polymerase variants having specificity for any of a variety of unnatural nucleic acids.
- polymerase variants can be screened for the ability to incorporate an unnatural nucleic acid or UBP; e.g., dTPT3, dNaM analog, or dTPT3-dNaM UBP into nucleic acids.
- such an assay is an in vitro assay, e.g., using a recombinant polymerase variant.
- Such directed evolution techniques can be used to screen variants of any suitable polymerase for activity toward any of the unnatural nucleic acids set forth herein.
- Modified polymerases of the compositions described can optionally be a modified and/or recombinant ⁇ 29-type DNA polymerase.
- the polymerase can be a modified and/or recombinant ⁇ 29, B103, GA-1, PZA, ⁇ 15, BS32, M2Y, Nf, G1, Cp-1, PRD1, PZE, SF5, Cp-5, Cp-7, PR4, PR5, PR722, or L17 polymerase.
- Nucleic acid polymerases generally useful in the invention include DNA polymerases, RNA polymerases, reverse transcriptases, and mutant or altered forms thereof. DNA polymerases and their properties are described in detail in, among other places, DNA Replication 2 nd edition, Kornberg and Baker, W. H. Freeman, New York, N. Y. (1991).
- Known conventional DNA polymerases useful in the invention include, but are not limited to, Pyrococcus furiosus (Pfu) DNA polymerase (Lundberg et al., 1991, Gene, 108: 1, Stratagene), Pyrococcus woesei (Pwo) DNA polymerase (Hinnisdaels et al., 1996, Biotechniques, 20:186-8, Boehringer Mannheim), Thermus thermophilus (Tth) DNA polymerase (Myers and Gelfand 1991, Biochemistry 30:7661), Bacillus stearothermophilus DNA polymerase (Stenesh and McGowan, 1977, Biochim Biophys Acta 475:32), Thermococcus litoralis (TIi) DNA polymerase (also referred to as VentTM DNA polymerase, Cariello et al, 1991, Polynucleotides Res, 19: 4193, New England Biolabs), 9° NmTM DNA polymerase (New England Biolabs), Stoffe
- thermococcus sp Thermus aquaticus (Taq) DNA polymerase (Chien et al, 1976, J. Bacteoriol, 127: 1550), DNA polymerase, Pyrococcus kodakaraensis KOD DNA polymerase (Takagi et al., 1997, Appl. Environ. Microbiol. 63:4504), JDF-3 DNA polymerase (from thermococcus sp.
- Thermophilic DNA polymerases include, but are not limited to, ThermoSequenase®, 9° NmTM, TherminatorTM, Taq, Tne, Tma, Pfu, TfI, Tth, TIi, Stoffel fragment, VentTM and Deep VentTM DNA polymerase, KOD DNA polymerase, Tgo, JDF-3, and mutants, variants and derivatives thereof.
- a polymerase that is a 3 exonuclease-deficient mutant is also contemplated.
- Reverse transcriptases useful in the invention include, but are not limited to, reverse transcriptases from HIV, HTLV-I, HTLV-1I, FeLV, FIV, SIV, AMV, MMTV, MoMuLV and other retroviruses (see Levin, Cell 88:5-8 (1997); Verma, Biochim Biophys Acta. 473:1-38 (1977); Wu et al, CRC Crit Rev Biochem. 3:289-347(1975)).
- Further examples of polymerases include, but are not limited to 9° N DNA Polymerase, Taq DNA polymerase, Phusion® DNA polymerase, Pfu DNA polymerase, RB69 DNA polymerase, KOD DNA polymerase, and VentR® DNA polymerase Gardner et al.
- Polymerases isolated from non-thermophilic organisms can be heat inactivatable. Examples are DNA polymerases from phage. It will be understood that polymerases from any of a variety of sources can be modified to increase or decrease their tolerance to high temperature conditions.
- a polymerase can be thermophilic.
- a thermophilic polymerase can be heat inactivatable. Thermophilic polymerases are typically useful for high temperature conditions or in thermocycling conditions such as those employed for polymerase chain reaction (PCR) techniques.
- the polymerase comprises 129, B103, GA-1, PZA, ⁇ 15, BS32, M2Y, Nf, G1, Cp-1, PRD1, PZE, SF5, Cp-5, Cp-7, PR4, PR5, PR722, L17, ThermoSequenase®, 9° NmTM, TherminatorTM DNA polymerase, Tne, Tma, TfI, Tth, TIi, Stoffel fragment, VentTM and Deep VentTM DNA polymerase, KOD DNA polymerase, Tgo, JDF-3, Pfu, Taq, T7 DNA polymerase, T7 RNA polymerase, PGB-D, UlTma DNA polymerase, E.
- coli DNA polymerase I E. coli DNA polymerase III, archaeal DP1I/DP2 DNA polymerase II, 9° N DNA Polymerase, Taq DNA polymerase, Phusion® DNA polymerase, Pfu DNA polymerase, SP6 RNA polymerase, RB69 DNA polymerase, Avian Myeloblastosis Virus (AMV) reverse transcriptase, Moloney Murine Leukemia Virus (MMLV) reverse transcriptase, SuperScript® II reverse transcriptase, and SuperScript® III reverse transcriptase.
- AMV Avian Myeloblastosis Virus
- MMLV Moloney Murine Leukemia Virus
- the polymerase is DNA polymerase 1-Klenow fragment, Vent polymerase, Phusion® DNA polymerase, KOD DNA polymerase, Taq polymerase, T7 DNA polymerase, T7 RNA polymerase, TherminatorTM DNA polymerase, POLB polymerase, SP6 RNA polymerase, E. coli DNA polymerase I, E. coli DNA polymerase III, Avian Myeloblastosis Virus (AMV) reverse transcriptase, Moloney Murine Leukemia Virus (MMLV) reverse transcriptase, SuperScript® II reverse transcriptase, or SuperScript® III reverse transcriptase.
- AMV Avian Myeloblastosis Virus
- MMLV Moloney Murine Leukemia Virus
- such polymerases can be used for DNA amplification and/or sequencing applications, including real-time applications, e.g., in the context of amplification or sequencing that include incorporation of unnatural nucleic acid residues into DNA by the polymerase.
- the unnatural nucleic acid that is incorporated can be the same as a natural residue, e.g., where a label or other moiety of the unnatural nucleic acid is removed by action of the polymerase during incorporation, or the unnatural nucleic acid can have one or more feature that distinguishes it from a natural nucleic acid.
- Green fluorescent protein and variants such as sfGFP have served as model systems for the study of ncAA incorporation using the amber suppression system, including at position Y151, which has been shown to tolerate a variety of natural and ncAAs ( FIG. 4 ).
- Ser at position 151 of sfGFP we first focused on the incorporation of Ser at position 151 of sfGFP, as E. coli serine aminoacyl-tRNA synthetase (SerRS) does not rely on anticodon recognition for tRNA aminoacylation, thus eliminating the potential complications of inefficient charging.
- SSO strain YZ3 was transformed with a plasmid encoding sfGFP and an E.
- Transformants were grown in media supplemented with dNaMTP and dTPT3TP, then supplemented further with NaMTP and TPT3TP, as well as isopropyl- ⁇ -D-thiogalactoside (IPTG) to induce expression of T7 RNA polymerase (T7 RNAP) and tRNA Ser (GYT). After a brief period of tRNA induction, anhydrotetracycline (aTc) was added to induce expression of sfGFP(AXC) 151 .
- TAC sfGFP codon 151
- X Na
- Lysates of these cells were subjected to western blotting with an anti-GFP antibody, which revealed a significant reduction in sfGFP expression and the presence of sfGFP truncated at the position of the unnatural codon ( FIG. 1E ).
- cells transformed with the plasmid encoding both sfGFP(AXC) 151 and tRNA Ser (GYT) exhibited fluorescence that was nearly equal to that of control cells expressing sfGFP(AGT) 151 ( FIG. 1C ), cell growth did not plateau upon induction of sfGFP(AXC) 151 ( FIG.
- FIGS. 5A and 5B western blots of lysates from these cells revealed only full-length sfGFP protein.
- tRNA Ser GNT
- N G, C, A, or T
- tRNA Py1 can be selectively charged by the Methanosarcina barkeri pyrrolysine aminoacyl tRNA synthetase (Py1RS) with the ncAA N 6 -[(2-propynyloxy)carbonyl]-L-lysine (PrK).
- Py1RS Methanosarcina barkeri pyrrolysine aminoacyl tRNA synthetase
- PrK Methanosarcina barkeri pyrrolysine aminoacyl tRNA synthetase
- GYC Methanosarcina barkeri pyrrolysine aminoacyl tRNA synthetase
- the SSO carrying a separate plasmid encoding an IPTG-inducible Py1RS, was transformed with the required plasmids and grown with or without added PrK.
- the cognate unnatural tRNA Py1 , or PrK we observed only low cellular fluorescence ( FIG. 2A ), truncation of sfGFP ( FIGS. 6A and 6B ), and a plateau in cell growth ( FIG. 6B ).
- sfGFP was affinity purified from cell lysates using a C-terminal Strep-tag II and subjected to copper-catalyzed click chemistry to attach a carboxytetramethylrhodamine (TAMRA) dye (TAMRA-PEG 4 -N 3 ), which was found to shift the electrophoretic mobility of sfGFP during SDS-PAGE, thus allowing us to assess the fidelity of PrK incorporation by western blotting ( FIG. 2C ).
- TAMRA carboxytetramethylrhodamine
- DBCO dibenzocyclooctyl
- the UBP is unlikely to be limited to these, and when combined with a recently reported Cas9 editing system that reinforces UBP retention, it will likely make available more codons than can ever be used.
- the reported SSO may be just the first of a new form of semi-synthetic life that is able to access a broad range of forms and functions not available to natural organisms.
Landscapes
- Life Sciences & Earth Sciences (AREA)
- Health & Medical Sciences (AREA)
- Genetics & Genomics (AREA)
- Engineering & Computer Science (AREA)
- Chemical & Material Sciences (AREA)
- Organic Chemistry (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
- Biomedical Technology (AREA)
- Biotechnology (AREA)
- Molecular Biology (AREA)
- Biochemistry (AREA)
- General Health & Medical Sciences (AREA)
- Microbiology (AREA)
- Physics & Mathematics (AREA)
- Plant Pathology (AREA)
- Biophysics (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Chemical Kinetics & Catalysis (AREA)
- General Chemical & Material Sciences (AREA)
- Medicinal Chemistry (AREA)
- Mycology (AREA)
- Preparation Of Compounds By Using Micro-Organisms (AREA)
- Peptides Or Proteins (AREA)
- Saccharide Compounds (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Priority Applications (1)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US16/629,255 US20200131555A1 (en) | 2017-07-11 | 2018-07-10 | Incorporation of unnatural nucleotides and methods thereof |
Applications Claiming Priority (3)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US201762531325P | 2017-07-11 | 2017-07-11 | |
PCT/US2018/041509 WO2019014267A1 (en) | 2017-07-11 | 2018-07-10 | INCORPORATION OF NON-NATURAL NUCLEOTIDES AND ASSOCIATED METHODS |
US16/629,255 US20200131555A1 (en) | 2017-07-11 | 2018-07-10 | Incorporation of unnatural nucleotides and methods thereof |
Related Parent Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
PCT/US2018/041509 A-371-Of-International WO2019014267A1 (en) | 2017-07-11 | 2018-07-10 | INCORPORATION OF NON-NATURAL NUCLEOTIDES AND ASSOCIATED METHODS |
Related Child Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
US17/196,151 Continuation US11834689B2 (en) | 2017-07-11 | 2021-03-09 | Incorporation of unnatural nucleotides and methods thereof |
Publications (1)
Publication Number | Publication Date |
---|---|
US20200131555A1 true US20200131555A1 (en) | 2020-04-30 |
Family
ID=65002471
Family Applications (4)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
US16/629,255 Abandoned US20200131555A1 (en) | 2017-07-11 | 2018-07-10 | Incorporation of unnatural nucleotides and methods thereof |
US16/530,742 Abandoned US20190376054A1 (en) | 2017-07-11 | 2019-08-02 | Incorporation of unnatural nucleotides and methods thereof |
US17/196,151 Active 2039-01-08 US11834689B2 (en) | 2017-07-11 | 2021-03-09 | Incorporation of unnatural nucleotides and methods thereof |
US18/481,086 Pending US20240043823A1 (en) | 2017-07-11 | 2023-10-04 | Incorporation of unnatural nucleotides and methods thereof |
Family Applications After (3)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
US16/530,742 Abandoned US20190376054A1 (en) | 2017-07-11 | 2019-08-02 | Incorporation of unnatural nucleotides and methods thereof |
US17/196,151 Active 2039-01-08 US11834689B2 (en) | 2017-07-11 | 2021-03-09 | Incorporation of unnatural nucleotides and methods thereof |
US18/481,086 Pending US20240043823A1 (en) | 2017-07-11 | 2023-10-04 | Incorporation of unnatural nucleotides and methods thereof |
Country Status (15)
Country | Link |
---|---|
US (4) | US20200131555A1 (es) |
EP (1) | EP3652316A4 (es) |
JP (2) | JP7325341B2 (es) |
KR (2) | KR102649135B1 (es) |
CN (1) | CN111051512A (es) |
AR (1) | AR112756A1 (es) |
AU (1) | AU2018300069A1 (es) |
CA (1) | CA3069321A1 (es) |
EA (1) | EA202090090A1 (es) |
IL (1) | IL271903A (es) |
MA (1) | MA49578A (es) |
NZ (1) | NZ761479A (es) |
SG (1) | SG11202000167SA (es) |
TW (1) | TWI821192B (es) |
WO (1) | WO2019014267A1 (es) |
Cited By (6)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US11466279B2 (en) | 2014-04-09 | 2022-10-11 | The Scripps Research Institute | Import of unnatural or modified nucleoside triphosphates into cells via nucleic acid triphosphate transporters |
US11634451B2 (en) | 2013-08-08 | 2023-04-25 | The Scripps Research Institute | Method for the site-specific enzymatic labelling of nucleic acids in vitro by incorporation of unnatural nucleotides |
US11761007B2 (en) | 2015-12-18 | 2023-09-19 | The Scripps Research Institute | Production of unnatural nucleotides using a CRISPR/Cas9 system |
US11834479B2 (en) | 2016-06-24 | 2023-12-05 | The Scripps Research Institute | Nucleoside triphosphate transporter and uses thereof |
US11834689B2 (en) | 2017-07-11 | 2023-12-05 | The Scripps Research Institute | Incorporation of unnatural nucleotides and methods thereof |
US11879145B2 (en) | 2019-06-14 | 2024-01-23 | The Scripps Research Institute | Reagents and methods for replication, transcription, and translation in semi-synthetic organisms |
Families Citing this family (29)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP3651774A4 (en) * | 2017-07-11 | 2021-07-07 | The Scripps Research Institute | INTEGRATION OF INNATURAL NUCLEOTIDES AND APPLICATION METHODS IN VIVO |
AU2018309166B2 (en) | 2017-08-03 | 2022-12-08 | Synthorx, Inc. | Cytokine conjugates for the treatment of proliferative and infectious diseases |
SG11202107354WA (en) | 2019-02-06 | 2021-08-30 | Synthorx Inc | Il-2 conjugates and methods of use thereof |
AU2020328597A1 (en) | 2019-08-15 | 2022-03-03 | Synthorx, Inc. | Immuno oncology combination therapies with IL-2 conjugates |
TW202122401A (zh) | 2019-08-23 | 2021-06-16 | 美商欣爍克斯公司 | 新穎之il-15接合物及其用途 |
US20210070827A1 (en) | 2019-09-10 | 2021-03-11 | Synthorx, Inc. | Il-2 conjugates and methods of use to treat autoimmune diseases |
MX2022003825A (es) * | 2019-09-30 | 2022-05-11 | Scripps Research Inst | Organismos semisinteticos eucariotas. |
TW202128996A (zh) * | 2019-10-10 | 2021-08-01 | 美商史基普研究協會 | 用於活體內合成非天然多肽的組合物及方法 |
CN115175704A (zh) | 2019-11-04 | 2022-10-11 | 新索思股份有限公司 | 白介素10缀合物及其用途 |
JP2023504314A (ja) | 2019-12-02 | 2023-02-02 | シェイプ セラピューティクス インコーポレイテッド | 治療的編集 |
TW202203973A (zh) | 2020-04-22 | 2022-02-01 | 美商默沙東藥廠 | 對介白素-2受體βγc二聚體具偏性且結合至非肽、水溶性聚合物之人類介白素-2結合物 |
KR20230027235A (ko) | 2020-06-25 | 2023-02-27 | 신톡스, 인크. | Il-2 콘쥬게이트 및 항-egfr 항체를 사용한 면역 종양학 병용 요법 |
WO2022076853A1 (en) | 2020-10-09 | 2022-04-14 | Synthorx, Inc. | Immuno oncology combination therapy with il-2 conjugates and pembrolizumab |
IL301612A (en) | 2020-10-09 | 2023-05-01 | Synthorx Inc | Immuno-oncological treatments with IL-2 couples |
WO2022098160A1 (ko) * | 2020-11-06 | 2022-05-12 | 한국과학기술원 | 비천연 아미노산이 위치-특이적으로 도입된 유전자 편집 단백질 및 이를 이용한 유전자 편집 방법 |
CN114807154B (zh) * | 2020-12-10 | 2024-05-28 | 深圳瑞吉生物科技有限公司 | 一种修饰的核酸及其应用 |
EP4291243A1 (en) | 2021-02-12 | 2023-12-20 | Synthorx, Inc. | Lung cancer combination therapy with il-2 conjugates and an anti-pd-1 antibody or antigen-binding fragment thereof |
WO2022174101A1 (en) | 2021-02-12 | 2022-08-18 | Synthorx, Inc. | Skin cancer combination therapy with il-2 conjugates and cemiplimab |
WO2022200525A1 (en) | 2021-03-26 | 2022-09-29 | Innate Pharma | Multispecific proteins comprising an nkp46-binding site, a cancer antgienge binding site fused to a cytokine for nk cell engaging |
WO2022256538A1 (en) | 2021-06-03 | 2022-12-08 | Synthorx, Inc. | Head and neck cancer combination therapy comprising an il-2 conjugate and cetuximab |
WO2022258678A1 (en) | 2021-06-09 | 2022-12-15 | Innate Pharma | Multispecific proteins binding to nkp30, a cytokine receptor, a tumour antigen and cd16a |
WO2022258691A1 (en) | 2021-06-09 | 2022-12-15 | Innate Pharma | Multispecific proteins binding to nkg2d, a cytokine receptor, a tumour antigen and cd16a |
CN117529504A (zh) | 2021-06-09 | 2024-02-06 | 先天制药公司 | 结合至cd20、nkp46、cd16并缀合至il-2的多特异性抗体 |
JP2024521405A (ja) | 2021-06-09 | 2024-05-31 | イナート・ファルマ・ソシエテ・アノニム | Nkp46、サイトカイン受容体、腫瘍抗原およびcd16aに結合する多特異性タンパク質 |
WO2023288111A2 (en) | 2021-07-16 | 2023-01-19 | Aptah Bio, Inc. | Polynucleotide compositions and methods for gene expression regulation |
CN114196714B (zh) * | 2021-11-04 | 2023-09-29 | 华南理工大学 | 利用末端脱氧核糖核苷酸转移酶无模板合成含非天然碱基寡核苷酸链的方法及其应用 |
WO2023122573A1 (en) | 2021-12-20 | 2023-06-29 | Synthorx, Inc. | Head and neck cancer combination therapy comprising an il-2 conjugate and pembrolizumab |
WO2023122750A1 (en) | 2021-12-23 | 2023-06-29 | Synthorx, Inc. | Cancer combination therapy with il-2 conjugates and cetuximab |
WO2024136899A1 (en) | 2022-12-21 | 2024-06-27 | Synthorx, Inc. | Cancer therapy with il-2 conjugates and chimeric antigen receptor therapies |
Family Cites Families (295)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US3687808A (en) | 1969-08-14 | 1972-08-29 | Univ Leland Stanford Junior | Synthetic polynucleotides |
US4469863A (en) | 1980-11-12 | 1984-09-04 | Ts O Paul O P | Nonionic nucleic acid alkyl and aryl phosphonates and processes for manufacture and use thereof |
US5023243A (en) | 1981-10-23 | 1991-06-11 | Molecular Biosystems, Inc. | Oligonucleotide therapeutic agent and method of making same |
US4476301A (en) | 1982-04-29 | 1984-10-09 | Centre National De La Recherche Scientifique | Oligonucleotides, a process for preparing the same and their application as mediators of the action of interferon |
JPS5927900A (ja) | 1982-08-09 | 1984-02-14 | Wakunaga Seiyaku Kk | 固定化オリゴヌクレオチド |
FR2540122B1 (fr) | 1983-01-27 | 1985-11-29 | Centre Nat Rech Scient | Nouveaux composes comportant une sequence d'oligonucleotide liee a un agent d'intercalation, leur procede de synthese et leur application |
US4605735A (en) | 1983-02-14 | 1986-08-12 | Wakunaga Seiyaku Kabushiki Kaisha | Oligonucleotide derivatives |
US4948882A (en) | 1983-02-22 | 1990-08-14 | Syngene, Inc. | Single-stranded labelled oligonucleotides, reactive monomers and methods of synthesis |
US4824941A (en) | 1983-03-10 | 1989-04-25 | Julian Gordon | Specific antibody to the native form of 2'5'-oligonucleotides, the method of preparation and the use as reagents in immunoassays or for binding 2'5'-oligonucleotides in biological systems |
US4587044A (en) | 1983-09-01 | 1986-05-06 | The Johns Hopkins University | Linkage of proteins to nucleic acids |
US4849513A (en) | 1983-12-20 | 1989-07-18 | California Institute Of Technology | Deoxyribonucleoside phosphoramidites in which an aliphatic amino group is attached to the sugar ring and their use for the preparation of oligonucleotides containing aliphatic amino groups |
US5118802A (en) | 1983-12-20 | 1992-06-02 | California Institute Of Technology | DNA-reporter conjugates linked via the 2' or 5'-primary amino group of the 5'-terminal nucleoside |
US5015733A (en) | 1983-12-20 | 1991-05-14 | California Institute Of Technology | Nucleosides possessing blocked aliphatic amino groups |
US5118800A (en) | 1983-12-20 | 1992-06-02 | California Institute Of Technology | Oligonucleotides possessing a primary amino group in the terminal nucleotide |
EP0154316B1 (en) | 1984-03-06 | 1989-09-13 | Takeda Chemical Industries, Ltd. | Chemically modified lymphokine and production thereof |
US4569790A (en) | 1984-03-28 | 1986-02-11 | Cetus Corporation | Process for recovering microbially produced interleukin-2 and purified recombinant interleukin-2 compositions |
US5550111A (en) | 1984-07-11 | 1996-08-27 | Temple University-Of The Commonwealth System Of Higher Education | Dual action 2',5'-oligoadenylate antiviral derivatives and uses thereof |
FR2567892B1 (fr) | 1984-07-19 | 1989-02-17 | Centre Nat Rech Scient | Nouveaux oligonucleotides, leur procede de preparation et leurs applications comme mediateurs dans le developpement des effets des interferons |
US5258506A (en) | 1984-10-16 | 1993-11-02 | Chiron Corporation | Photolabile reagents for incorporation into oligonucleotide chains |
US5367066A (en) | 1984-10-16 | 1994-11-22 | Chiron Corporation | Oligonucleotides with selectably cleavable and/or abasic sites |
US5430136A (en) | 1984-10-16 | 1995-07-04 | Chiron Corporation | Oligonucleotides having selectably cleavable and/or abasic sites |
US4828979A (en) | 1984-11-08 | 1989-05-09 | Life Technologies, Inc. | Nucleotide analogs for nucleic acid labeling and detection |
FR2575751B1 (fr) | 1985-01-08 | 1987-04-03 | Pasteur Institut | Nouveaux nucleosides de derives de l'adenosine, leur preparation et leurs applications biologiques |
US5166315A (en) | 1989-12-20 | 1992-11-24 | Anti-Gene Development Group | Sequence-specific binding polymers for duplex nucleic acids |
US5235033A (en) | 1985-03-15 | 1993-08-10 | Anti-Gene Development Group | Alpha-morpholino ribonucleoside derivatives and polymers thereof |
US5405938A (en) | 1989-12-20 | 1995-04-11 | Anti-Gene Development Group | Sequence-specific binding polymers for duplex nucleic acids |
US5185444A (en) | 1985-03-15 | 1993-02-09 | Anti-Gene Deveopment Group | Uncharged morpolino-based polymers having phosphorous containing chiral intersubunit linkages |
US5034506A (en) | 1985-03-15 | 1991-07-23 | Anti-Gene Development Group | Uncharged morpholino-based polymers having achiral intersubunit linkages |
US4965188A (en) | 1986-08-22 | 1990-10-23 | Cetus Corporation | Process for amplifying, detecting, and/or cloning nucleic acid sequences using a thermostable enzyme |
US5656493A (en) | 1985-03-28 | 1997-08-12 | The Perkin-Elmer Corporation | System for automated performance of the polymerase chain reaction |
US4683202A (en) | 1985-03-28 | 1987-07-28 | Cetus Corporation | Process for amplifying nucleic acid sequences |
US4683195A (en) | 1986-01-30 | 1987-07-28 | Cetus Corporation | Process for amplifying, detecting, and/or-cloning nucleic acid sequences |
US4762779A (en) | 1985-06-13 | 1988-08-09 | Amgen Inc. | Compositions and methods for functionalizing nucleic acids |
US4766106A (en) | 1985-06-26 | 1988-08-23 | Cetus Corporation | Solubilization of proteins for pharmaceutical compositions using polymer conjugation |
US5206344A (en) | 1985-06-26 | 1993-04-27 | Cetus Oncology Corporation | Interleukin-2 muteins and polymer conjugation thereof |
US5576195A (en) | 1985-11-01 | 1996-11-19 | Xoma Corporation | Vectors with pectate lyase signal sequence |
US4910300A (en) | 1985-12-11 | 1990-03-20 | Chiron Corporation | Method for making nucleic acid probes |
US5093232A (en) | 1985-12-11 | 1992-03-03 | Chiron Corporation | Nucleic acid probes |
US5317098A (en) | 1986-03-17 | 1994-05-31 | Hiroaki Shizuya | Non-radioisotope tagging of fragments |
JPS638396A (ja) | 1986-06-30 | 1988-01-14 | Wakunaga Pharmaceut Co Ltd | ポリ標識化オリゴヌクレオチド誘導体 |
US4931544A (en) | 1986-09-04 | 1990-06-05 | Cetus Corporation | Succinylated interleukin-2 for pharmaceutical compositions |
US5264423A (en) | 1987-03-25 | 1993-11-23 | The United States Of America As Represented By The Department Of Health And Human Services | Inhibitors for replication of retroviruses and for the expression of oncogene products |
US5276019A (en) | 1987-03-25 | 1994-01-04 | The United States Of America As Represented By The Department Of Health And Human Services | Inhibitors for replication of retroviruses and for the expression of oncogene products |
US4904582A (en) | 1987-06-11 | 1990-02-27 | Synthetic Genetics | Novel amphiphilic nucleic acid conjugates |
AU598946B2 (en) | 1987-06-24 | 1990-07-05 | Howard Florey Institute Of Experimental Physiology And Medicine | Nucleoside derivatives |
US5585481A (en) | 1987-09-21 | 1996-12-17 | Gen-Probe Incorporated | Linking reagents for nucleotide probes |
US5188897A (en) | 1987-10-22 | 1993-02-23 | Temple University Of The Commonwealth System Of Higher Education | Encapsulated 2',5'-phosphorothioate oligoadenylates |
US4924624A (en) | 1987-10-22 | 1990-05-15 | Temple University-Of The Commonwealth System Of Higher Education | 2,',5'-phosphorothioate oligoadenylates and plant antiviral uses thereof |
US5525465A (en) | 1987-10-28 | 1996-06-11 | Howard Florey Institute Of Experimental Physiology And Medicine | Oligonucleotide-polyamide conjugates and methods of production and applications of the same |
DE3738460A1 (de) | 1987-11-12 | 1989-05-24 | Max Planck Gesellschaft | Modifizierte oligonukleotide |
US5082830A (en) | 1988-02-26 | 1992-01-21 | Enzo Biochem, Inc. | End labeled nucleotide probe |
EP0406309A4 (en) | 1988-03-25 | 1992-08-19 | The University Of Virginia Alumni Patents Foundation | Oligonucleotide n-alkylphosphoramidates |
US5278302A (en) | 1988-05-26 | 1994-01-11 | University Patents, Inc. | Polynucleotide phosphorodithioates |
US5109124A (en) | 1988-06-01 | 1992-04-28 | Biogen, Inc. | Nucleic acid probe linked to a label having a terminal cysteine |
US5216141A (en) | 1988-06-06 | 1993-06-01 | Benner Steven A | Oligonucleotide analogs containing sulfur linkages |
US5175273A (en) | 1988-07-01 | 1992-12-29 | Genentech, Inc. | Nucleic acid intercalating agents |
US5262536A (en) | 1988-09-15 | 1993-11-16 | E. I. Du Pont De Nemours And Company | Reagents for the preparation of 5'-tagged oligonucleotides |
US5512439A (en) | 1988-11-21 | 1996-04-30 | Dynal As | Oligonucleotide-linked magnetic particles and uses thereof |
EP0379369B1 (en) | 1989-01-19 | 1996-09-04 | BEHRINGWERKE Aktiengesellschaft | Nucleic acid amplification using single primer |
US4902502A (en) | 1989-01-23 | 1990-02-20 | Cetus Corporation | Preparation of a polymer/interleukin-2 conjugate |
US5089261A (en) | 1989-01-23 | 1992-02-18 | Cetus Corporation | Preparation of a polymer/interleukin-2 conjugate |
US5599923A (en) | 1989-03-06 | 1997-02-04 | Board Of Regents, University Of Tx | Texaphyrin metal complexes having improved functionalization |
US5457183A (en) | 1989-03-06 | 1995-10-10 | Board Of Regents, The University Of Texas System | Hydroxylated texaphyrins |
US5391723A (en) | 1989-05-31 | 1995-02-21 | Neorx Corporation | Oligonucleotide conjugates |
US4958013A (en) | 1989-06-06 | 1990-09-18 | Northwestern University | Cholesteryl modified oligonucleotides |
US5451463A (en) | 1989-08-28 | 1995-09-19 | Clontech Laboratories, Inc. | Non-nucleoside 1,3-diol reagents for labeling synthetic oligonucleotides |
US5134066A (en) | 1989-08-29 | 1992-07-28 | Monsanto Company | Improved probes using nucleosides containing 3-dezauracil analogs |
US5254469A (en) | 1989-09-12 | 1993-10-19 | Eastman Kodak Company | Oligonucleotide-enzyme conjugate that can be used as a probe in hybridization assays and polymerase chain reaction procedures |
US5591722A (en) | 1989-09-15 | 1997-01-07 | Southern Research Institute | 2'-deoxy-4'-thioribonucleosides and their antiviral activity |
US5399676A (en) | 1989-10-23 | 1995-03-21 | Gilead Sciences | Oligonucleotides with inverted polarity |
US5264564A (en) | 1989-10-24 | 1993-11-23 | Gilead Sciences | Oligonucleotide analogs with novel linkages |
US5264562A (en) | 1989-10-24 | 1993-11-23 | Gilead Sciences, Inc. | Oligonucleotide analogs with novel linkages |
DE69034150T2 (de) | 1989-10-24 | 2005-08-25 | Isis Pharmaceuticals, Inc., Carlsbad | 2'-Modifizierte Oligonukleotide |
US5292873A (en) | 1989-11-29 | 1994-03-08 | The Research Foundation Of State University Of New York | Nucleic acids labeled with naphthoquinone probe |
US5177198A (en) | 1989-11-30 | 1993-01-05 | University Of N.C. At Chapel Hill | Process for preparing oligoribonucleoside and oligodeoxyribonucleoside boranophosphates |
US5130302A (en) | 1989-12-20 | 1992-07-14 | Boron Bilogicals, Inc. | Boronated nucleoside, nucleotide and oligonucleotide compounds, compositions and methods for using same |
US5486603A (en) | 1990-01-08 | 1996-01-23 | Gilead Sciences, Inc. | Oligonucleotide having enhanced binding affinity |
US5578718A (en) | 1990-01-11 | 1996-11-26 | Isis Pharmaceuticals, Inc. | Thiol-derivatized nucleosides |
US5681941A (en) | 1990-01-11 | 1997-10-28 | Isis Pharmaceuticals, Inc. | Substituted purines and oligonucleotide cross-linking |
US5587361A (en) | 1991-10-15 | 1996-12-24 | Isis Pharmaceuticals, Inc. | Oligonucleotides having phosphorothioate linkages of high chiral purity |
US5646265A (en) | 1990-01-11 | 1997-07-08 | Isis Pharmceuticals, Inc. | Process for the preparation of 2'-O-alkyl purine phosphoramidites |
US5670633A (en) | 1990-01-11 | 1997-09-23 | Isis Pharmaceuticals, Inc. | Sugar modified oligonucleotides that detect and modulate gene expression |
US5587470A (en) | 1990-01-11 | 1996-12-24 | Isis Pharmaceuticals, Inc. | 3-deazapurines |
US5459255A (en) | 1990-01-11 | 1995-10-17 | Isis Pharmaceuticals, Inc. | N-2 substituted purines |
US5214136A (en) | 1990-02-20 | 1993-05-25 | Gilead Sciences, Inc. | Anthraquinone-derivatives oligonucleotides |
AU7579991A (en) | 1990-02-20 | 1991-09-18 | Gilead Sciences, Inc. | Pseudonucleosides and pseudonucleotides and their polymers |
US5321131A (en) | 1990-03-08 | 1994-06-14 | Hybridon, Inc. | Site-specific functionalization of oligodeoxynucleotides for non-radioactive labelling |
WO1991014781A1 (en) | 1990-03-19 | 1991-10-03 | Henkel Research Corporation | METHOD FOR INCREASING THE OMEGA-HYDROXYLASE ACTIVITY IN $i(CANDIDA TROPICALIS) |
US5470967A (en) | 1990-04-10 | 1995-11-28 | The Dupont Merck Pharmaceutical Company | Oligonucleotide analogs with sulfamate linkages |
GB9009980D0 (en) | 1990-05-03 | 1990-06-27 | Amersham Int Plc | Phosphoramidite derivatives,their preparation and the use thereof in the incorporation of reporter groups on synthetic oligonucleotides |
EP0455905B1 (en) | 1990-05-11 | 1998-06-17 | Microprobe Corporation | Dipsticks for nucleic acid hybridization assays and methods for covalently immobilizing oligonucleotides |
JPH04126084A (ja) | 1990-05-11 | 1992-04-27 | Hoechst Japan Ltd | 蛋白質の製造法 |
US5618704A (en) | 1990-07-27 | 1997-04-08 | Isis Pharmacueticals, Inc. | Backbone-modified oligonucleotide analogs and preparation thereof through radical coupling |
US5623070A (en) | 1990-07-27 | 1997-04-22 | Isis Pharmaceuticals, Inc. | Heteroatomic oligonucleoside linkages |
US5610289A (en) | 1990-07-27 | 1997-03-11 | Isis Pharmaceuticals, Inc. | Backbone modified oligonucleotide analogues |
US5608046A (en) | 1990-07-27 | 1997-03-04 | Isis Pharmaceuticals, Inc. | Conjugated 4'-desmethyl nucleoside analog compounds |
US5602240A (en) | 1990-07-27 | 1997-02-11 | Ciba Geigy Ag. | Backbone modified oligonucleotide analogs |
US5677437A (en) | 1990-07-27 | 1997-10-14 | Isis Pharmaceuticals, Inc. | Heteroatomic oligonucleoside linkages |
US5688941A (en) | 1990-07-27 | 1997-11-18 | Isis Pharmaceuticals, Inc. | Methods of making conjugated 4' desmethyl nucleoside analog compounds |
US5218105A (en) | 1990-07-27 | 1993-06-08 | Isis Pharmaceuticals | Polyamine conjugated oligonucleotides |
US5138045A (en) | 1990-07-27 | 1992-08-11 | Isis Pharmaceuticals | Polyamine conjugated oligonucleotides |
BR9106702A (pt) | 1990-07-27 | 1993-06-08 | Isis Pharmaceuticals Inc | Analogo de oligonucleotideos e processos para modular a producao de uma proteina por um organismo e para tratar um organismo |
US5489677A (en) | 1990-07-27 | 1996-02-06 | Isis Pharmaceuticals, Inc. | Oligonucleoside linkages containing adjacent oxygen and nitrogen atoms |
US5541307A (en) | 1990-07-27 | 1996-07-30 | Isis Pharmaceuticals, Inc. | Backbone modified oligonucleotide analogs and solid phase synthesis thereof |
DE69115702T2 (de) | 1990-08-03 | 1996-06-13 | Sterling Winthrop Inc | Verbindungen und verfahren zur unterdrückung der genexpression |
US5245022A (en) | 1990-08-03 | 1993-09-14 | Sterling Drug, Inc. | Exonuclease resistant terminally substituted oligonucleotides |
US5177196A (en) | 1990-08-16 | 1993-01-05 | Microprobe Corporation | Oligo (α-arabinofuranosyl nucleotides) and α-arabinofuranosyl precursors thereof |
US5512667A (en) | 1990-08-28 | 1996-04-30 | Reed; Michael W. | Trifunctional intermediates for preparing 3'-tailed oligonucleotides |
US5214134A (en) | 1990-09-12 | 1993-05-25 | Sterling Winthrop Inc. | Process of linking nucleosides with a siloxane bridge |
US5561225A (en) | 1990-09-19 | 1996-10-01 | Southern Research Institute | Polynucleotide analogs containing sulfonate and sulfonamide internucleoside linkages |
JPH06505704A (ja) | 1990-09-20 | 1994-06-30 | ギリアド サイエンシズ,インコーポレイテッド | 改変ヌクレオシド間結合 |
NZ239893A (en) | 1990-09-25 | 1993-11-25 | Hoechst Japan | A method for introducing a foreign dna into a cell |
US5432272A (en) | 1990-10-09 | 1995-07-11 | Benner; Steven A. | Method for incorporating into a DNA or RNA oligonucleotide using nucleotides bearing heterocyclic bases |
KR930702373A (ko) | 1990-11-08 | 1993-09-08 | 안토니 제이. 페이네 | 합성 올리고누클레오티드에 대한 다중 리포터(Reporter)그룹의 첨합 |
US5268273A (en) | 1990-12-14 | 1993-12-07 | Phillips Petroleum Company | Pichia pastoris acid phosphatase gene, gene regions, signal sequence and expression vectors comprising same |
US5672697A (en) | 1991-02-08 | 1997-09-30 | Gilead Sciences, Inc. | Nucleoside 5'-methylene phosphonates |
US5595732A (en) | 1991-03-25 | 1997-01-21 | Hoffmann-La Roche Inc. | Polyethylene-protein conjugates |
US5539082A (en) | 1993-04-26 | 1996-07-23 | Nielsen; Peter E. | Peptide nucleic acids |
US5714331A (en) | 1991-05-24 | 1998-02-03 | Buchardt, Deceased; Ole | Peptide nucleic acids having enhanced binding affinity, sequence specificity and solubility |
US5719262A (en) | 1993-11-22 | 1998-02-17 | Buchardt, Deceased; Ole | Peptide nucleic acids having amino acid side chains |
US5389529A (en) | 1991-06-12 | 1995-02-14 | Regeneron Pharmaceuticals, Inc. | Modified lamβ signal sequence and processes for producing recombinant neurotrophins |
US5371241A (en) | 1991-07-19 | 1994-12-06 | Pharmacia P-L Biochemicals Inc. | Fluorescein labelled phosphoramidites |
US5571799A (en) | 1991-08-12 | 1996-11-05 | Basco, Ltd. | (2'-5') oligoadenylate analogues useful as inhibitors of host-v5.-graft response |
US5612199A (en) | 1991-10-11 | 1997-03-18 | Behringwerke Ag | Method for producing a polynucleotide for use in single primer amplification |
ES2103918T3 (es) | 1991-10-17 | 1997-10-01 | Ciba Geigy Ag | Nucleosidos biciclicos, oligonucleotidos, procedimiento para su obtencion y productos intermedios. |
US5594121A (en) | 1991-11-07 | 1997-01-14 | Gilead Sciences, Inc. | Enhanced triple-helix and double-helix formation with oligomers containing modified purines |
TW393513B (en) | 1991-11-26 | 2000-06-11 | Isis Pharmaceuticals Inc | Enhanced triple-helix and double-helix formation with oligomers containing modified pyrimidines |
US5484908A (en) | 1991-11-26 | 1996-01-16 | Gilead Sciences, Inc. | Oligonucleotides containing 5-propynyl pyrimidines |
AU3222793A (en) | 1991-11-26 | 1993-06-28 | Gilead Sciences, Inc. | Enhanced triple-helix and double-helix formation with oligomers containing modified pyrimidines |
US5359044A (en) | 1991-12-13 | 1994-10-25 | Isis Pharmaceuticals | Cyclobutyl oligonucleotide surrogates |
DE9115660U1 (de) | 1991-12-18 | 1992-07-30 | Aventis Research & Technologies GmbH & Co KG, 65929 Frankfurt | L-Phenylalanyl-tRNA-Synthetase mit erweiterter Substratselektivität aus Mikroorganismen |
US5595726A (en) | 1992-01-21 | 1997-01-21 | Pharmacyclics, Inc. | Chromophore probe for detection of nucleic acid |
US5565552A (en) | 1992-01-21 | 1996-10-15 | Pharmacyclics, Inc. | Method of expanded porphyrin-oligonucleotide conjugate synthesis |
FR2687679B1 (fr) | 1992-02-05 | 1994-10-28 | Centre Nat Rech Scient | Oligothionucleotides. |
US5633360A (en) | 1992-04-14 | 1997-05-27 | Gilead Sciences, Inc. | Oligonucleotide analogs capable of passive cell membrane permeation |
US5229109A (en) | 1992-04-14 | 1993-07-20 | Board Of Regents, The University Of Texas System | Low toxicity interleukin-2 analogues for use in immunotherapy |
US5434257A (en) | 1992-06-01 | 1995-07-18 | Gilead Sciences, Inc. | Binding compentent oligomers containing unsaturated 3',5' and 2',5' linkages |
EP0577558A2 (de) | 1992-07-01 | 1994-01-05 | Ciba-Geigy Ag | Carbocyclische Nukleoside mit bicyclischen Ringen, Oligonukleotide daraus, Verfahren zu deren Herstellung, deren Verwendung und Zwischenproduckte |
US5272250A (en) | 1992-07-10 | 1993-12-21 | Spielvogel Bernard F | Boronated phosphoramidate compounds |
TW263437B (es) | 1992-09-24 | 1995-11-21 | Takeda Pharm Industry Co Ltd | |
US6288302B1 (en) | 1992-11-04 | 2001-09-11 | National Science Council Of R.O.C. | Application of α-amylase gene promoter and signal sequence in the production of recombinant proteins in transgenic plants and transgenic plant seeds |
US5574142A (en) | 1992-12-15 | 1996-11-12 | Microprobe Corporation | Peptide linkers for improved oligonucleotide delivery |
US5476925A (en) | 1993-02-01 | 1995-12-19 | Northwestern University | Oligodeoxyribonucleotides including 3'-aminonucleoside-phosphoramidate linkages and terminal 3'-amino groups |
GB9304618D0 (en) | 1993-03-06 | 1993-04-21 | Ciba Geigy Ag | Chemical compounds |
CA2159631A1 (en) | 1993-03-30 | 1994-10-13 | Sanofi | Acyclic nucleoside analogs and oligonucleotide sequences containing them |
WO1994022891A1 (en) | 1993-03-31 | 1994-10-13 | Sterling Winthrop Inc. | Oligonucleotides with amide linkages replacing phosphodiester linkages |
CA2159632A1 (en) | 1993-03-31 | 1994-10-13 | Ashis Kumar Saha | Novel 5'-substituted nucleosides and oligomers produced therefrom |
DE4311944A1 (de) | 1993-04-10 | 1994-10-13 | Degussa | Umhüllte Natriumpercarbonatpartikel, Verfahren zu deren Herstellung und sie enthaltende Wasch-, Reinigungs- und Bleichmittelzusammensetzungen |
US6294323B1 (en) | 1993-04-14 | 2001-09-25 | Behringwerke Ag | Self initiating single primer amplification of nucleic acids |
GB9311682D0 (en) | 1993-06-05 | 1993-07-21 | Ciba Geigy Ag | Chemical compounds |
US5502177A (en) | 1993-09-17 | 1996-03-26 | Gilead Sciences, Inc. | Pyrimidine derivatives for labeled binding partners |
US5457187A (en) | 1993-12-08 | 1995-10-10 | Board Of Regents University Of Nebraska | Oligonucleotides containing 5-fluorouracil |
US5446137B1 (en) | 1993-12-09 | 1998-10-06 | Behringwerke Ag | Oligonucleotides containing 4'-substituted nucleotides |
US5519134A (en) | 1994-01-11 | 1996-05-21 | Isis Pharmaceuticals, Inc. | Pyrrolidine-containing monomers and oligomers |
US5596091A (en) | 1994-03-18 | 1997-01-21 | The Regents Of The University Of California | Antisense oligonucleotides comprising 5-aminoalkyl pyrimidine nucleotides |
US5470719A (en) | 1994-03-18 | 1995-11-28 | Meng; Shi-Yuan | Modified OmpA signal sequence for enhanced secretion of polypeptides |
US5627053A (en) | 1994-03-29 | 1997-05-06 | Ribozyme Pharmaceuticals, Inc. | 2'deoxy-2'-alkylnucleotide containing nucleic acid |
US5625050A (en) | 1994-03-31 | 1997-04-29 | Amgen Inc. | Modified oligonucleotides and intermediates useful in nucleic acid therapeutics |
US5525711A (en) | 1994-05-18 | 1996-06-11 | The United States Of America As Represented By The Secretary Of The Department Of Health And Human Services | Pteridine nucleotide analogs as fluorescent DNA probes |
US5597696A (en) | 1994-07-18 | 1997-01-28 | Becton Dickinson And Company | Covalent cyanine dye oligonucleotide conjugates |
US5597909A (en) | 1994-08-25 | 1997-01-28 | Chiron Corporation | Polynucleotide reagents containing modified deoxyribose moieties, and associated methods of synthesis and use |
US5580731A (en) | 1994-08-25 | 1996-12-03 | Chiron Corporation | N-4 modified pyrimidine deoxynucleotides and oligonucleotide probes synthesized therewith |
JPH0889278A (ja) | 1994-09-29 | 1996-04-09 | Ajinomoto Co Inc | 遺伝子導入用修飾蛋白質及びその製法 |
US6010871A (en) | 1994-09-29 | 2000-01-04 | Ajinomoto Co., Inc. | Modification of peptide and protein |
US5712114A (en) | 1995-06-06 | 1998-01-27 | Basf Aktiengesellschaft | Compositions for expression of proteins in host cells using a preprocollagen signal sequence |
ATE222289T1 (de) | 1995-06-07 | 2002-08-15 | Invitrogen Corp | Rekombinatorische klonierung in vitro unter verwendung genmanipulierter rekombinationsorte |
US6720140B1 (en) | 1995-06-07 | 2004-04-13 | Invitrogen Corporation | Recombinational cloning using engineered recombination sites |
US6143557A (en) | 1995-06-07 | 2000-11-07 | Life Technologies, Inc. | Recombination cloning using engineered recombination sites |
US6261797B1 (en) | 1996-01-29 | 2001-07-17 | Stratagene | Primer-mediated polynucleotide synthesis and manipulation techniques |
GB9606158D0 (en) | 1996-03-23 | 1996-05-29 | Ciba Geigy Ag | Chemical compounds |
JPH09324000A (ja) | 1996-06-05 | 1997-12-16 | Suntory Ltd | インターロイキン−2受容体を特異的に認識する因子とリボヌクレアーゼとの接合体 |
US6770748B2 (en) | 1997-03-07 | 2004-08-03 | Takeshi Imanishi | Bicyclonucleoside and oligonucleotide analogue |
JP3756313B2 (ja) | 1997-03-07 | 2006-03-15 | 武 今西 | 新規ビシクロヌクレオシド及びオリゴヌクレオチド類縁体 |
US6794499B2 (en) | 1997-09-12 | 2004-09-21 | Exiqon A/S | Oligonucleotide analogues |
JP4236812B2 (ja) | 1997-09-12 | 2009-03-11 | エクシコン エ/エス | オリゴヌクレオチド類似体 |
US6054271A (en) | 1997-10-21 | 2000-04-25 | The Regents Of The University Of California | Methods of using synthetic molecules and target sequences |
US6008378A (en) | 1997-10-21 | 1999-12-28 | The Regents Of The University Of California | Synthetic molecules that specifically react with target sequences |
US5932474A (en) | 1997-10-21 | 1999-08-03 | The Regents Of The University Of California | Target sequences for synthetic molecules |
EP1684073A3 (en) | 1997-10-21 | 2007-09-26 | The Regents of the University of California | Target sequences for synthetic molecules and methods of using same |
IL135776A0 (en) | 1997-10-24 | 2001-05-20 | Life Technologies Inc | Recombinational cloning using nucleic acids having recombination sites |
DE19813317A1 (de) | 1998-03-26 | 1999-09-30 | Roche Diagnostics Gmbh | Verbessertes Verfahren zur Primer Extension Präamplifikations-PCR |
US6955807B1 (en) | 1998-05-15 | 2005-10-18 | Bayer Pharmaceuticals Corporation | IL-2 selective agonists and antagonists |
US6391544B1 (en) | 1998-05-15 | 2002-05-21 | Abbott Laboratories | Method for using unequal primer concentrations for generating nucleic acid amplification products |
US6562798B1 (en) | 1998-06-05 | 2003-05-13 | Dynavax Technologies Corp. | Immunostimulatory oligonucleotides with modified bases and methods of use thereof |
WO2000011028A2 (en) | 1998-08-21 | 2000-03-02 | Yeda Research And Development Co. Ltd. | Anti-inflammatory peptides derived from il-2 and analogues thereof |
US6175001B1 (en) | 1998-10-16 | 2001-01-16 | The Scripps Research Institute | Functionalized pyrimidine nucleosides and nucleotides and DNA's incorporating same |
NZ514569A (en) | 1999-03-02 | 2004-02-27 | Invitrogen Corp | Compositions and methods for use in recombinational cloning of nucleic acids |
AU776362B2 (en) | 1999-05-04 | 2004-09-09 | Roche Innovation Center Copenhagen A/S | L-ribo-LNA analogues |
US6525191B1 (en) | 1999-05-11 | 2003-02-25 | Kanda S. Ramasamy | Conformationally constrained L-nucleosides |
JP2003501402A (ja) | 1999-06-03 | 2003-01-14 | バイオイノベイション・リミテッド | 遺伝子治療用生成物 |
DE60045238D1 (de) | 1999-07-15 | 2010-12-30 | Japan Science & Tech Agency | Nukleinsäurebasenpaar |
DE60027040T2 (de) | 1999-10-29 | 2006-11-23 | Stratagene California, La Jolla | Zusammensetzungen und methoden zur verwendung von dna polymerasen |
EP2210948A3 (en) | 1999-12-10 | 2010-10-06 | Life Technologies Corporation | Use of multiple recombination sites with unique specificity in recombinational cloning |
WO2003070918A2 (en) | 2002-02-20 | 2003-08-28 | Ribozyme Pharmaceuticals, Incorporated | Rna interference by modified short interfering nucleic acid |
US20020001804A1 (en) | 2000-02-25 | 2002-01-03 | Wayne Mitchell | Genomic analysis of tRNA gene sets |
AU2002212108A1 (en) | 2000-11-02 | 2002-05-15 | Maxygen Aps | Single-chain multimeric polypeptides |
EP1368366A1 (en) | 2001-02-07 | 2003-12-10 | Celltech R & D Limited | Non-natural nucleotides and dinucleotides |
IL157478A0 (en) | 2001-03-01 | 2004-03-28 | Pharmasset Ltd | Method for the synthesis of 2', 3'-didehydronucleosides |
DK2128246T3 (da) * | 2001-04-19 | 2014-05-12 | Univ California | Fremgangsmåder og sammensætninger til fremstilling af ortogonale tRNA-aminoacyl-tRNA-syntetasepar. |
DK1578771T3 (da) | 2001-10-10 | 2013-06-10 | Novo Nordisk As | Remodellering og glycokonjugering af peptider |
KR100948532B1 (ko) | 2001-11-07 | 2010-03-23 | 넥타르 테라퓨틱스 | 분지형 중합체 및 그의 공액체 |
AUPR975201A0 (en) | 2001-12-24 | 2002-01-24 | Unisearch Limited | Enzymatic redox labelling of nucleic acids |
US20060074035A1 (en) | 2002-04-17 | 2006-04-06 | Zhi Hong | Dinucleotide inhibitors of de novo RNA polymerases for treatment or prevention of viral infections |
US7745417B2 (en) | 2002-07-17 | 2010-06-29 | Riken | Nucleosides or nucleotides having novel unnatural bases and use thereof |
US7977049B2 (en) | 2002-08-09 | 2011-07-12 | President And Fellows Of Harvard College | Methods and compositions for extending the life span and increasing the stress resistance of cells and organisms |
AU2003291755A1 (en) | 2002-11-05 | 2004-06-07 | Isis Pharmaceuticals, Inc. | Oligomers comprising modified bases for binding cytosine and uracil or thymine and their use |
EP1562971B1 (en) | 2002-11-05 | 2014-02-12 | Isis Pharmaceuticals, Inc. | Polycyclic sugar surrogate-containing oligomeric compounds and compositions for use in gene modulation |
CA2507189C (en) | 2002-11-27 | 2018-06-12 | Sequenom, Inc. | Fragmentation-based methods and systems for sequence variation detection and discovery |
TWI364295B (en) | 2002-12-26 | 2012-05-21 | Mountain View Pharmaceuticals | Polymer conjugates of cytokines, chemokines, growth factors, polypeptide hormones and antagonists thereof with preserved receptor-binding activity |
JP2006523211A (ja) | 2003-03-14 | 2006-10-12 | ネオス テクノロジーズ インコーポレイテッド | 分岐水溶性ポリマーとその複合物 |
EP2338333B1 (en) | 2003-04-09 | 2017-09-06 | ratiopharm GmbH | Glycopegylation methods and proteins/peptides produced by the methods |
KR101171397B1 (ko) | 2003-04-17 | 2012-08-07 | 더 스크립스 리서치 인스티튜트 | 진핵 유전자 코드의 확장 |
WO2004106356A1 (en) | 2003-05-27 | 2004-12-09 | Syddansk Universitet | Functionalized nucleotide derivatives |
WO2005007121A2 (en) | 2003-07-18 | 2005-01-27 | Massachusetts Institute Of Technology | Mutant interleukin-2(il-2) polypeptides |
ES2382807T3 (es) | 2003-08-28 | 2012-06-13 | Takeshi Imanishi | Nuevos ácidos nucleicos artificiales del tipo de enlace N-O con reticulación |
WO2005026187A1 (ja) | 2003-09-10 | 2005-03-24 | Riken | 非天然型塩基を有するヌクレオシド又はヌクレオチド及びその利用 |
SI1675622T1 (sl) | 2003-09-17 | 2017-09-29 | Nektar Therapeutics | Večkraka polimerna predzdravila |
AU2004274021B2 (en) | 2003-09-18 | 2009-08-13 | Isis Pharmaceuticals, Inc. | 4'-thionucleosides and oligomeric compounds |
US7348146B2 (en) | 2003-10-02 | 2008-03-25 | Epoch Biosciences, Inc. | Single nucleotide polymorphism analysis of highly polymorphic target sequences |
EP1685246A2 (en) | 2003-11-03 | 2006-08-02 | Medical Research Council | Polymerase |
JP2007519422A (ja) | 2004-02-02 | 2007-07-19 | アンブレツクス・インコーポレイテツド | 修飾されたヒト四螺旋バンドルポリペプチド及びそれらの使用 |
CN101659704A (zh) | 2004-03-11 | 2010-03-03 | 弗雷泽纽斯卡比德国有限公司 | 通过还原氨基化制备的羟烷基淀粉和蛋白质的偶联物 |
WO2006019876A2 (en) | 2004-07-14 | 2006-02-23 | Invitrogen Corporation | Production of fusion proteins by cell-free protein synthesis |
AU2005328382C1 (en) | 2004-07-21 | 2013-01-24 | Alnylam Pharmaceuticals, Inc. | Oligonucleotides comprising a modified or non-natural nucleobase |
WO2006049297A1 (ja) | 2004-11-08 | 2006-05-11 | Riken | 新規なヌクレオシド若しくはヌクレオチド誘導体及びその利用 |
ES2432141T3 (es) | 2005-01-27 | 2013-11-29 | Novartis Vaccines And Diagnostics, Inc. | Procedimientos para tratar carcinoma de células renales |
TWI376234B (en) | 2005-02-01 | 2012-11-11 | Msd Oss Bv | Conjugates of a polypeptide and an oligosaccharide |
JP5649018B2 (ja) | 2005-08-04 | 2015-01-07 | タグシクス・バイオ株式会社 | 新規人工塩基対及びその利用 |
JP5146957B2 (ja) | 2005-12-09 | 2013-02-20 | 独立行政法人理化学研究所 | 核酸の複製の方法及び新規人工塩基対 |
CA2640171C (en) | 2006-01-27 | 2014-10-28 | Isis Pharmaceuticals, Inc. | 6-modified bicyclic nucleic acid analogs |
CA2638837A1 (en) | 2006-01-27 | 2007-08-02 | Santaris Pharma A/S | Lna modified phosphorothiolated oligonucleotides |
WO2007093599A1 (en) | 2006-02-14 | 2007-08-23 | Basf Se | Pyridin-4 -ylmethylamides for combating pests |
CA2648009A1 (en) | 2006-02-22 | 2007-09-07 | Riken | Method for synthesis of suppressor trna, dna construct, and production of protein having non-natural amino acid integrated therein by using the dna construct |
US20140314864A1 (en) | 2006-03-31 | 2014-10-23 | Massachusetts Institute Of Technology | System for Targeted Delivery of Therapeutic Agents |
WO2007130453A2 (en) | 2006-05-02 | 2007-11-15 | Allozyne, Inc. | Non-natural amino acid substituted polypeptides |
DK2066684T3 (da) | 2006-05-11 | 2012-10-22 | Isis Pharmaceuticals Inc | 5´-Modificerede bicycliske nukleinsyreanaloge |
EP2289564A3 (en) | 2006-09-08 | 2012-11-14 | Piramal Imaging SA | Derivatives of aniline as precursors for F18-labeling |
US8420792B2 (en) | 2006-09-08 | 2013-04-16 | Ambrx, Inc. | Suppressor tRNA transcription in vertebrate cells |
EP2120998B1 (en) | 2006-11-28 | 2013-08-07 | HanAll Biopharma Co., Ltd. | Modified erythropoietin polypeptides and uses thereof for treatment |
WO2008067825A1 (en) | 2006-12-06 | 2008-06-12 | Erik Bjerregaard Pedersen | Hoogsteen-type triplex formation of pyrene labelled probes for nucleic acid detection in fluorescence assay |
EP2125852B1 (en) | 2007-02-15 | 2016-04-06 | Ionis Pharmaceuticals, Inc. | 5'-substituted-2'-f modified nucleosides and oligomeric compounds prepared therefrom |
KR101508617B1 (ko) | 2007-02-28 | 2015-04-06 | 세리나 쎄라퓨틱스, 인코포레이티드 | 활성화된 폴리옥사졸린 및 이를 포함하는 조성물 |
JP4761086B2 (ja) | 2007-03-09 | 2011-08-31 | 独立行政法人理化学研究所 | 核酸、標識物質、核酸検出方法およびキット |
EP2170917B1 (en) | 2007-05-30 | 2012-06-27 | Isis Pharmaceuticals, Inc. | N-substituted-aminomethylene bridged bicyclic nucleic acid analogs |
EP2173760B2 (en) | 2007-06-08 | 2015-11-04 | Isis Pharmaceuticals, Inc. | Carbocyclic bicyclic nucleic acid analogs |
CA2692579C (en) | 2007-07-05 | 2016-05-03 | Isis Pharmaceuticals, Inc. | 6-disubstituted bicyclic nucleic acid analogs |
CA2707840A1 (en) | 2007-08-20 | 2009-02-26 | Allozyne, Inc. | Amino acid substituted molecules |
CA2706889C (en) * | 2007-09-20 | 2018-08-28 | Riken | Mutant pyrrolysyl-trna synthetase, and method for production of protein having non-natural amino acid integrated therein by using the same |
WO2009067647A1 (en) | 2007-11-21 | 2009-05-28 | Isis Pharmaceuticals, Inc. | Carbocyclic alpha-l-bicyclic nucleic acid analogs |
EP2246428A4 (en) | 2008-02-07 | 2011-04-13 | Univ Tokyo | MODIFIED TRNA WITH NON-NATURAL NUCLEOTIDE AND USE THEREOF |
JP5424414B2 (ja) | 2008-03-31 | 2014-02-26 | 独立行政法人理化学研究所 | 高選択・高効率でpcr増幅が可能な新規dna |
WO2009134339A2 (en) | 2008-04-29 | 2009-11-05 | Monsanto Technology, Llc | Genes and uses for plant enhancement |
US20100112660A1 (en) | 2008-05-30 | 2010-05-06 | Barofold, Inc. | Method for Derivatization of Proteins Using Hydrostatic Pressure |
US20110150820A1 (en) | 2008-08-28 | 2011-06-23 | Insight Biopharmaceuticals Ltd. | Methods for covalently attaching a polymer to a methionine residue in proteins and peptides |
US8501805B2 (en) | 2008-09-24 | 2013-08-06 | Isis Pharmaceuticals, Inc. | Substituted alpha-L-bicyclic nucleosides |
EP2370473B1 (en) | 2008-12-10 | 2016-05-11 | The Scripps Research Institute | Production of carrier-peptide conjugates using chemically reactive unnatural amino acids |
WO2010085495A1 (en) | 2009-01-21 | 2010-07-29 | Amgen Inc. | Compositions and methods of treating inflammatory and autoimmune diseases |
CN102741266A (zh) | 2009-10-06 | 2012-10-17 | 塔古西库斯生物株式会社 | 形成特异碱基对的人工碱基对 |
WO2011053065A2 (ko) | 2009-10-29 | 2011-05-05 | 한국과학기술원 | 카테콜 폴리에틸렌글리콜 유도체와 단백질 또는 펩타이드의 접합체 및 이의 제조방법 |
US9127033B2 (en) | 2010-04-28 | 2015-09-08 | Isis Pharmaceuticals, Inc. | 5′ modified nucleosides and oligomeric compounds prepared therefrom |
WO2012038706A1 (en) * | 2010-09-24 | 2012-03-29 | Medical Research Council | Methods for incorporating unnatural amino acids in eukaryotic cells |
HUE054318T2 (hu) | 2010-11-12 | 2021-08-30 | Nektar Therapeutics | IL-2 molekularész konjugátumai és polimer |
EP3075745B1 (en) | 2011-02-10 | 2018-09-05 | Roche Glycart AG | Mutant interleukin-2 polypeptides |
US8343752B2 (en) | 2011-05-03 | 2013-01-01 | Verdezyne, Inc. | Biological methods for preparing adipic acid |
DK3401400T3 (da) | 2012-05-25 | 2019-06-03 | Univ California | Fremgangsmåder og sammensætninger til rna-styret mål-dna-modifikation og til rna-styret transskriptionsmodulering |
EP3584255B1 (en) | 2012-08-31 | 2022-02-16 | Sutro Biopharma, Inc. | Modified amino acids comprising an azido group |
US9650621B2 (en) | 2012-10-12 | 2017-05-16 | Sutro Biopharma, Inc. | Proteolytic inactivation of select proteins in bacterial extracts for improved expression |
AU2013364065B2 (en) | 2012-12-21 | 2018-10-04 | Altrubio Inc. | Hydrophilic self-immolative linkers and conjugates thereof |
CA2905049A1 (en) | 2013-03-13 | 2014-10-02 | Trustees Of Boston University | Tunable control of protein degradation in synthetic and endogenous bacterial systems |
US9234213B2 (en) | 2013-03-15 | 2016-01-12 | System Biosciences, Llc | Compositions and methods directed to CRISPR/Cas genomic engineering systems |
US10190145B2 (en) | 2013-04-19 | 2019-01-29 | Sutro Biopharma, Inc. | Expression of biologically active proteins in a bacterial cell-free synthesis system using bacterial cells transformed to exhibit elevated levels of chaperone expression |
PT3041854T (pt) | 2013-08-08 | 2020-03-05 | Scripps Research Inst | Um método para a identificação enzimática específica ao local de ácidos nucleicos in vitro pela incorporação de nucleótidos não-naturais |
WO2015038426A1 (en) | 2013-09-13 | 2015-03-19 | Asana Biosciences, Llc | Self-immolative linkers containing mandelic acid derivatives, drug-ligand conjugates for targeted therapies and uses thereof |
WO2015054590A2 (en) | 2013-10-11 | 2015-04-16 | Sutro Biopharma, Inc. | NON-NATURAL AMINO ACID tRNA SYNTHETASES FOR PYRIDYL TETRAZINE |
HUE042421T2 (hu) | 2013-10-11 | 2019-07-29 | Sutro Biopharma Inc | Nem természetes aminosav tRNS szintetázok a para-metilazid-L-fenilalaninhoz |
US9840493B2 (en) | 2013-10-11 | 2017-12-12 | Sutro Biopharma, Inc. | Modified amino acids comprising tetrazine functional groups, methods of preparation, and methods of their use |
CA2933134A1 (en) | 2013-12-13 | 2015-06-18 | Cellectis | Cas9 nuclease platform for microalgae genome engineering |
DK3129493T3 (da) | 2014-04-09 | 2021-09-27 | Scripps Research Inst | Import af unaturlige eller modificerede nukleosidtriphosphater ind i celler via nukleinsyre-triphosphat-transportører |
WO2015164815A1 (en) | 2014-04-24 | 2015-10-29 | The Board Of Trustees Of The Leland Stanford Junior University | Superagonists, partial agonists and antagonists of interleukin-2 |
WO2016025385A1 (en) | 2014-08-11 | 2016-02-18 | Delinia, Inc. | Modified il-2 variants that selectively activate regulatory t cells for the treatment of autoimmune diseases |
CN107406838A (zh) | 2014-11-06 | 2017-11-28 | 纳幕尔杜邦公司 | Rna引导的内切核酸酶向细胞中的肽介导的递送 |
WO2016094867A1 (en) | 2014-12-12 | 2016-06-16 | The Broad Institute Inc. | Protected guide rnas (pgrnas) |
WO2016100889A1 (en) | 2014-12-19 | 2016-06-23 | Sutro Biopharma, Inc. | Codon optimization for titer and fidelity improvement |
US20170369871A1 (en) | 2015-01-12 | 2017-12-28 | Synthorx, Inc. | Incorporation of unnatural nucleotides and methods thereof |
US11761007B2 (en) | 2015-12-18 | 2023-09-19 | The Scripps Research Institute | Production of unnatural nucleotides using a CRISPR/Cas9 system |
EP3393500B1 (en) | 2015-12-21 | 2021-10-13 | Duke University | Polymer conjugates having reduced antigenicity |
ES2929047T3 (es) | 2016-06-24 | 2022-11-24 | Scripps Research Inst | Transportador de nucleósido trifosfato novedoso y usos del mismo |
CA3069321A1 (en) | 2017-07-11 | 2019-01-17 | Synthorx, Inc. | Incorporation of unnatural nucleotides and methods thereof |
EP3651774A4 (en) | 2017-07-11 | 2021-07-07 | The Scripps Research Institute | INTEGRATION OF INNATURAL NUCLEOTIDES AND APPLICATION METHODS IN VIVO |
AU2018309166B2 (en) | 2017-08-03 | 2022-12-08 | Synthorx, Inc. | Cytokine conjugates for the treatment of proliferative and infectious diseases |
SG11202006101WA (en) | 2017-12-29 | 2020-07-29 | Scripps Research Inst | Unnatural base pair compositions and methods of use |
US11879145B2 (en) | 2019-06-14 | 2024-01-23 | The Scripps Research Institute | Reagents and methods for replication, transcription, and translation in semi-synthetic organisms |
MX2022003825A (es) | 2019-09-30 | 2022-05-11 | Scripps Research Inst | Organismos semisinteticos eucariotas. |
TW202128996A (zh) | 2019-10-10 | 2021-08-01 | 美商史基普研究協會 | 用於活體內合成非天然多肽的組合物及方法 |
EP4232570A1 (en) | 2020-10-23 | 2023-08-30 | The Scripps Research Institute | Reverse transcription of polynucleotides comprising unnatural nucleotides |
-
2018
- 2018-07-10 CA CA3069321A patent/CA3069321A1/en active Pending
- 2018-07-10 AR ARP180101920A patent/AR112756A1/es unknown
- 2018-07-10 KR KR1020207004044A patent/KR102649135B1/ko active IP Right Grant
- 2018-07-10 SG SG11202000167SA patent/SG11202000167SA/en unknown
- 2018-07-10 KR KR1020247008596A patent/KR20240038157A/ko active Search and Examination
- 2018-07-10 US US16/629,255 patent/US20200131555A1/en not_active Abandoned
- 2018-07-10 CN CN201880058859.4A patent/CN111051512A/zh active Pending
- 2018-07-10 TW TW107123898A patent/TWI821192B/zh active
- 2018-07-10 MA MA049578A patent/MA49578A/fr unknown
- 2018-07-10 EA EA202090090A patent/EA202090090A1/ru unknown
- 2018-07-10 AU AU2018300069A patent/AU2018300069A1/en active Pending
- 2018-07-10 JP JP2019572821A patent/JP7325341B2/ja active Active
- 2018-07-10 EP EP18831973.5A patent/EP3652316A4/en active Pending
- 2018-07-10 WO PCT/US2018/041509 patent/WO2019014267A1/en unknown
- 2018-07-10 NZ NZ761479A patent/NZ761479A/en unknown
-
2019
- 2019-08-02 US US16/530,742 patent/US20190376054A1/en not_active Abandoned
-
2020
- 2020-01-08 IL IL271903A patent/IL271903A/en unknown
-
2021
- 2021-03-09 US US17/196,151 patent/US11834689B2/en active Active
-
2023
- 2023-08-01 JP JP2023125730A patent/JP2023175678A/ja active Pending
- 2023-10-04 US US18/481,086 patent/US20240043823A1/en active Pending
Cited By (6)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US11634451B2 (en) | 2013-08-08 | 2023-04-25 | The Scripps Research Institute | Method for the site-specific enzymatic labelling of nucleic acids in vitro by incorporation of unnatural nucleotides |
US11466279B2 (en) | 2014-04-09 | 2022-10-11 | The Scripps Research Institute | Import of unnatural or modified nucleoside triphosphates into cells via nucleic acid triphosphate transporters |
US11761007B2 (en) | 2015-12-18 | 2023-09-19 | The Scripps Research Institute | Production of unnatural nucleotides using a CRISPR/Cas9 system |
US11834479B2 (en) | 2016-06-24 | 2023-12-05 | The Scripps Research Institute | Nucleoside triphosphate transporter and uses thereof |
US11834689B2 (en) | 2017-07-11 | 2023-12-05 | The Scripps Research Institute | Incorporation of unnatural nucleotides and methods thereof |
US11879145B2 (en) | 2019-06-14 | 2024-01-23 | The Scripps Research Institute | Reagents and methods for replication, transcription, and translation in semi-synthetic organisms |
Also Published As
Publication number | Publication date |
---|---|
CA3069321A1 (en) | 2019-01-17 |
JP2023175678A (ja) | 2023-12-12 |
US20240043823A1 (en) | 2024-02-08 |
JP7325341B2 (ja) | 2023-08-14 |
NZ761479A (en) | 2024-03-22 |
WO2019014267A1 (en) | 2019-01-17 |
IL271903A (en) | 2020-02-27 |
JP2020526197A (ja) | 2020-08-31 |
US20210222147A1 (en) | 2021-07-22 |
EP3652316A4 (en) | 2021-04-07 |
US20190376054A1 (en) | 2019-12-12 |
SG11202000167SA (en) | 2020-02-27 |
EP3652316A1 (en) | 2020-05-20 |
AU2018300069A1 (en) | 2020-02-27 |
KR20200029531A (ko) | 2020-03-18 |
AR112756A1 (es) | 2019-12-11 |
KR102649135B1 (ko) | 2024-03-18 |
US11834689B2 (en) | 2023-12-05 |
KR20240038157A (ko) | 2024-03-22 |
EA202090090A1 (ru) | 2020-06-09 |
TW201920681A (zh) | 2019-06-01 |
MA49578A (fr) | 2021-04-07 |
TWI821192B (zh) | 2023-11-11 |
CN111051512A (zh) | 2020-04-21 |
Similar Documents
Publication | Publication Date | Title |
---|---|---|
US11834689B2 (en) | Incorporation of unnatural nucleotides and methods thereof | |
US20200224234A1 (en) | Incorporation of unnatural nucleotides and methods of use in vivo thereof | |
US20200024597A1 (en) | Incorporation of unnatural nucleotides and methods thereof | |
EP3475295B1 (en) | Novel nucleoside triphosphate transporter and uses thereof | |
US11879145B2 (en) | Reagents and methods for replication, transcription, and translation in semi-synthetic organisms | |
US20230392140A1 (en) | Reverse transcription of polynucleotides comprising unnatural nucleotides | |
AU2020363962A1 (en) | Compositions and methods for in vivo synthesis of unnatural polypeptides | |
EA042937B1 (ru) | Включение неприродных нуклеотидов и способы с ними |
Legal Events
Date | Code | Title | Description |
---|---|---|---|
STPP | Information on status: patent application and granting procedure in general |
Free format text: DOCKETED NEW CASE - READY FOR EXAMINATION |
|
AS | Assignment |
Owner name: SYNTHORX, INC., CALIFORNIA Free format text: ASSIGNMENT OF ASSIGNORS INTEREST;ASSIGNORS:PTACIN, JEROD;CAFFARO, CAROLINA;AERNI, HANS;SIGNING DATES FROM 20180801 TO 20180806;REEL/FRAME:056035/0613 Owner name: THE SCRIPPS RESEARCH INSTITUTE, CALIFORNIA Free format text: ASSIGNMENT OF ASSIGNORS INTEREST;ASSIGNORS:ZHANG, YORKE;FISCHER, EMIL C.;FELDMAN, AARON W.;AND OTHERS;SIGNING DATES FROM 20180716 TO 20180806;REEL/FRAME:056035/0812 |
|
STCB | Information on status: application discontinuation |
Free format text: EXPRESSLY ABANDONED -- DURING EXAMINATION |