DK2610351T3 - Effektiv basebestemmelse i sekvenseringsreaktioner - Google Patents
Effektiv basebestemmelse i sekvenseringsreaktioner Download PDFInfo
- Publication number
- DK2610351T3 DK2610351T3 DK12191212.5T DK12191212T DK2610351T3 DK 2610351 T3 DK2610351 T3 DK 2610351T3 DK 12191212 T DK12191212 T DK 12191212T DK 2610351 T3 DK2610351 T3 DK 2610351T3
- Authority
- DK
- Denmark
- Prior art keywords
- adaptor
- nucleic acid
- probe
- sequencing
- target nucleic
- Prior art date
Links
- 238000012163 sequencing technique Methods 0.000 title claims description 269
- 238000006243 chemical reaction Methods 0.000 title description 115
- 239000000523 sample Substances 0.000 claims description 661
- 150000007523 nucleic acids Chemical class 0.000 claims description 518
- 238000000034 method Methods 0.000 claims description 498
- 102000039446 nucleic acids Human genes 0.000 claims description 482
- 108020004707 nucleic acids Proteins 0.000 claims description 482
- 125000003729 nucleotide group Chemical group 0.000 claims description 107
- 239000002773 nucleotide Substances 0.000 claims description 104
- 230000000295 complement effect Effects 0.000 claims description 85
- 238000009396 hybridization Methods 0.000 claims description 76
- 238000001514 detection method Methods 0.000 claims description 53
- 108091028732 Concatemer Proteins 0.000 claims description 25
- 239000000178 monomer Substances 0.000 claims description 17
- 108091028043 Nucleic acid sequence Proteins 0.000 claims description 15
- 238000004873 anchoring Methods 0.000 claims 6
- 239000003550 marker Substances 0.000 claims 1
- 239000012634 fragment Substances 0.000 description 156
- 108091008146 restriction endonucleases Proteins 0.000 description 147
- 230000008569 process Effects 0.000 description 140
- 108020004414 DNA Proteins 0.000 description 99
- 238000003199 nucleic acid amplification method Methods 0.000 description 87
- 230000003321 amplification Effects 0.000 description 86
- 108091034117 Oligonucleotide Proteins 0.000 description 79
- 238000013519 translation Methods 0.000 description 67
- 239000000047 product Substances 0.000 description 58
- ISAKRJDGNUQOIC-UHFFFAOYSA-N Uracil Chemical compound O=C1C=CNC(=O)N1 ISAKRJDGNUQOIC-UHFFFAOYSA-N 0.000 description 56
- 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 53
- 238000003752 polymerase chain reaction Methods 0.000 description 44
- 102000004190 Enzymes Human genes 0.000 description 41
- 108090000790 Enzymes Proteins 0.000 description 41
- 102000003960 Ligases Human genes 0.000 description 35
- 108090000364 Ligases Proteins 0.000 description 35
- 238000013467 fragmentation Methods 0.000 description 34
- 238000006062 fragmentation reaction Methods 0.000 description 34
- 230000000694 effects Effects 0.000 description 31
- 230000002255 enzymatic effect Effects 0.000 description 27
- 230000011987 methylation Effects 0.000 description 27
- 238000007069 methylation reaction Methods 0.000 description 27
- 229940035893 uracil Drugs 0.000 description 27
- 108010042407 Endonucleases Proteins 0.000 description 25
- 230000027455 binding Effects 0.000 description 24
- 229910019142 PO4 Inorganic materials 0.000 description 23
- 238000003776 cleavage reaction Methods 0.000 description 23
- 235000021317 phosphate Nutrition 0.000 description 23
- 230000007017 scission Effects 0.000 description 23
- 108060002716 Exonuclease Proteins 0.000 description 22
- 102000013165 exonuclease Human genes 0.000 description 22
- 239000000203 mixture Substances 0.000 description 22
- 108010008532 Deoxyribonuclease I Proteins 0.000 description 20
- 102000007260 Deoxyribonuclease I Human genes 0.000 description 20
- 238000003780 insertion Methods 0.000 description 20
- 230000037431 insertion Effects 0.000 description 20
- 238000003491 array Methods 0.000 description 19
- 238000006073 displacement reaction Methods 0.000 description 19
- 230000004048 modification Effects 0.000 description 19
- 238000012986 modification Methods 0.000 description 19
- 102000040430 polynucleotide Human genes 0.000 description 19
- 108091033319 polynucleotide Proteins 0.000 description 19
- 239000002157 polynucleotide Substances 0.000 description 19
- 102100031780 Endonuclease Human genes 0.000 description 18
- 239000000463 material Substances 0.000 description 18
- 210000004027 cell Anatomy 0.000 description 17
- 230000001419 dependent effect Effects 0.000 description 17
- NBIIXXVUZAFLBC-UHFFFAOYSA-K phosphate Chemical compound [O-]P([O-])([O-])=O NBIIXXVUZAFLBC-UHFFFAOYSA-K 0.000 description 17
- 239000010452 phosphate Substances 0.000 description 17
- 230000001276 controlling effect Effects 0.000 description 16
- 108091000080 Phosphotransferase Proteins 0.000 description 15
- 102000020233 phosphotransferase Human genes 0.000 description 15
- 239000011324 bead Substances 0.000 description 14
- 230000015572 biosynthetic process Effects 0.000 description 14
- 238000013461 design Methods 0.000 description 14
- 238000005516 engineering process Methods 0.000 description 14
- 230000002779 inactivation Effects 0.000 description 14
- 239000000758 substrate Substances 0.000 description 14
- 238000004458 analytical method Methods 0.000 description 13
- 125000002887 hydroxy group Chemical group [H]O* 0.000 description 13
- 239000010410 layer Substances 0.000 description 13
- 125000002467 phosphate group Chemical group [H]OP(=O)(O[H])O[*] 0.000 description 13
- 238000011282 treatment Methods 0.000 description 13
- 238000011144 upstream manufacturing Methods 0.000 description 13
- 102000002260 Alkaline Phosphatase Human genes 0.000 description 12
- 108020004774 Alkaline Phosphatase Proteins 0.000 description 12
- VYPSYNLAJGMNEJ-UHFFFAOYSA-N Silicium dioxide Chemical compound O=[Si]=O VYPSYNLAJGMNEJ-UHFFFAOYSA-N 0.000 description 12
- 108010006785 Taq Polymerase Proteins 0.000 description 12
- 102000006943 Uracil-DNA Glycosidase Human genes 0.000 description 12
- 108010072685 Uracil-DNA Glycosidase Proteins 0.000 description 12
- 230000015556 catabolic process Effects 0.000 description 12
- 238000006731 degradation reaction Methods 0.000 description 12
- 238000007841 sequencing by ligation Methods 0.000 description 12
- 239000012099 Alexa Fluor family Substances 0.000 description 11
- 108010021757 Polynucleotide 5'-Hydroxyl-Kinase Proteins 0.000 description 11
- 102000008422 Polynucleotide 5'-hydroxyl-kinase Human genes 0.000 description 11
- 230000000875 corresponding effect Effects 0.000 description 11
- 230000001915 proofreading effect Effects 0.000 description 11
- 102000053602 DNA Human genes 0.000 description 10
- 230000008901 benefit Effects 0.000 description 10
- 239000000872 buffer Substances 0.000 description 10
- 238000007796 conventional method Methods 0.000 description 10
- 238000010369 molecular cloning Methods 0.000 description 10
- 239000011807 nanoball Substances 0.000 description 10
- 239000010453 quartz Substances 0.000 description 10
- -1 carbocyclic sugars Chemical class 0.000 description 9
- 238000007639 printing Methods 0.000 description 9
- 230000010076 replication Effects 0.000 description 9
- 238000003786 synthesis reaction Methods 0.000 description 9
- AHCYMLUZIRLXAA-SHYZEUOFSA-N Deoxyuridine 5'-triphosphate Chemical compound O1[C@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)[C@@H](O)C[C@@H]1N1C(=O)NC(=O)C=C1 AHCYMLUZIRLXAA-SHYZEUOFSA-N 0.000 description 8
- 102000004533 Endonucleases Human genes 0.000 description 8
- 102000004160 Phosphoric Monoester Hydrolases Human genes 0.000 description 8
- 108090000608 Phosphoric Monoester Hydrolases Proteins 0.000 description 8
- 239000003153 chemical reaction reagent Substances 0.000 description 8
- 238000005520 cutting process Methods 0.000 description 8
- 108010010677 Phosphodiesterase I Proteins 0.000 description 7
- 238000013459 approach Methods 0.000 description 7
- 230000000903 blocking effect Effects 0.000 description 7
- 230000029087 digestion Effects 0.000 description 7
- 239000011535 reaction buffer Substances 0.000 description 7
- 150000003839 salts Chemical class 0.000 description 7
- 239000000243 solution Substances 0.000 description 7
- XLYOFNOQVPJJNP-UHFFFAOYSA-N water Substances O XLYOFNOQVPJJNP-UHFFFAOYSA-N 0.000 description 7
- CSCPPACGZOOCGX-UHFFFAOYSA-N Acetone Chemical compound CC(C)=O CSCPPACGZOOCGX-UHFFFAOYSA-N 0.000 description 6
- 108010014303 DNA-directed DNA polymerase Proteins 0.000 description 6
- 102000016928 DNA-directed DNA polymerase Human genes 0.000 description 6
- ZHNUHDYFZUAESO-UHFFFAOYSA-N Formamide Chemical compound NC=O ZHNUHDYFZUAESO-UHFFFAOYSA-N 0.000 description 6
- 238000010790 dilution Methods 0.000 description 6
- 239000012895 dilution Substances 0.000 description 6
- 238000011534 incubation Methods 0.000 description 6
- UEZVMMHDMIWARA-UHFFFAOYSA-M phosphonate Chemical group [O-]P(=O)=O UEZVMMHDMIWARA-UHFFFAOYSA-M 0.000 description 6
- 150000003013 phosphoric acid derivatives Chemical class 0.000 description 6
- 108090000623 proteins and genes Proteins 0.000 description 6
- 238000000746 purification Methods 0.000 description 6
- 238000005096 rolling process Methods 0.000 description 6
- 108091093088 Amplicon Proteins 0.000 description 5
- 102000012410 DNA Ligases Human genes 0.000 description 5
- 108010061982 DNA Ligases Proteins 0.000 description 5
- 238000011166 aliquoting Methods 0.000 description 5
- 230000009286 beneficial effect Effects 0.000 description 5
- 239000012148 binding buffer Substances 0.000 description 5
- 150000001875 compounds Chemical class 0.000 description 5
- 238000010276 construction Methods 0.000 description 5
- 230000001351 cycling effect Effects 0.000 description 5
- 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 5
- 239000000975 dye Substances 0.000 description 5
- 238000005194 fractionation Methods 0.000 description 5
- 239000011521 glass Substances 0.000 description 5
- 238000010348 incorporation Methods 0.000 description 5
- 238000004519 manufacturing process Methods 0.000 description 5
- 108020004999 messenger RNA Proteins 0.000 description 5
- 238000006116 polymerization reaction Methods 0.000 description 5
- 238000001308 synthesis method Methods 0.000 description 5
- MPLHNVLQVRSVEE-UHFFFAOYSA-N texas red Chemical compound [O-]S(=O)(=O)C1=CC(S(Cl)(=O)=O)=CC=C1C(C1=CC=2CCCN3CCCC(C=23)=C1O1)=C2C1=C(CCC1)C3=[N+]1CCCC3=C2 MPLHNVLQVRSVEE-UHFFFAOYSA-N 0.000 description 5
- 238000012546 transfer Methods 0.000 description 5
- 238000005406 washing Methods 0.000 description 5
- SGTNSNPWRIOYBX-UHFFFAOYSA-N 2-(3,4-dimethoxyphenyl)-5-{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino}-2-(propan-2-yl)pentanenitrile Chemical compound C1=C(OC)C(OC)=CC=C1CCN(C)CCCC(C#N)(C(C)C)C1=CC=C(OC)C(OC)=C1 SGTNSNPWRIOYBX-UHFFFAOYSA-N 0.000 description 4
- 108020004635 Complementary DNA Proteins 0.000 description 4
- 102000008158 DNA Ligase ATP Human genes 0.000 description 4
- 108010060248 DNA Ligase ATP Proteins 0.000 description 4
- 241000238557 Decapoda Species 0.000 description 4
- 241000282412 Homo Species 0.000 description 4
- 229930010555 Inosine Natural products 0.000 description 4
- 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 4
- FKNQFGJONOIPTF-UHFFFAOYSA-N Sodium cation Chemical compound [Na+] FKNQFGJONOIPTF-UHFFFAOYSA-N 0.000 description 4
- 238000005119 centrifugation Methods 0.000 description 4
- 239000003795 chemical substances by application Substances 0.000 description 4
- 210000000349 chromosome Anatomy 0.000 description 4
- 238000012217 deletion Methods 0.000 description 4
- 230000037430 deletion Effects 0.000 description 4
- 238000004925 denaturation Methods 0.000 description 4
- 230000036425 denaturation Effects 0.000 description 4
- 238000005530 etching Methods 0.000 description 4
- 239000007850 fluorescent dye Substances 0.000 description 4
- 230000000977 initiatory effect Effects 0.000 description 4
- 229960003786 inosine Drugs 0.000 description 4
- 230000000670 limiting effect Effects 0.000 description 4
- 239000002777 nucleoside Substances 0.000 description 4
- 102000054765 polymorphisms of proteins Human genes 0.000 description 4
- 230000008439 repair process Effects 0.000 description 4
- 238000011160 research Methods 0.000 description 4
- PYWVYCXTNDRMGF-UHFFFAOYSA-N rhodamine B Chemical compound [Cl-].C=12C=CC(=[N+](CC)CC)C=C2OC2=CC(N(CC)CC)=CC=C2C=1C1=CC=CC=C1C(O)=O PYWVYCXTNDRMGF-UHFFFAOYSA-N 0.000 description 4
- 238000000926 separation method Methods 0.000 description 4
- 229910001415 sodium ion Inorganic materials 0.000 description 4
- 239000007787 solid Substances 0.000 description 4
- 108010068698 spleen exonuclease Proteins 0.000 description 4
- 239000000126 substance Substances 0.000 description 4
- 239000006228 supernatant Substances 0.000 description 4
- 108091032973 (ribonucleotides)n+m Proteins 0.000 description 3
- IAZDPXIOMUYVGZ-UHFFFAOYSA-N Dimethylsulphoxide Chemical compound CS(C)=O IAZDPXIOMUYVGZ-UHFFFAOYSA-N 0.000 description 3
- KCXVZYZYPLLWCC-UHFFFAOYSA-N EDTA Chemical compound OC(=O)CN(CC(O)=O)CCN(CC(O)=O)CC(O)=O KCXVZYZYPLLWCC-UHFFFAOYSA-N 0.000 description 3
- HEMHJVSKTPXQMS-UHFFFAOYSA-M Sodium hydroxide Chemical compound [OH-].[Na+] HEMHJVSKTPXQMS-UHFFFAOYSA-M 0.000 description 3
- PPQRONHOSHZGFQ-LMVFSUKVSA-N aldehydo-D-ribose 5-phosphate Chemical group OP(=O)(O)OC[C@@H](O)[C@@H](O)[C@@H](O)C=O PPQRONHOSHZGFQ-LMVFSUKVSA-N 0.000 description 3
- 238000000137 annealing Methods 0.000 description 3
- 230000000692 anti-sense effect Effects 0.000 description 3
- 238000003556 assay Methods 0.000 description 3
- 210000004369 blood Anatomy 0.000 description 3
- 239000008280 blood Substances 0.000 description 3
- 150000001720 carbohydrates Chemical class 0.000 description 3
- 235000014633 carbohydrates Nutrition 0.000 description 3
- 238000005253 cladding Methods 0.000 description 3
- 238000010367 cloning Methods 0.000 description 3
- 230000002596 correlated effect Effects 0.000 description 3
- 230000007423 decrease Effects 0.000 description 3
- 230000003247 decreasing effect Effects 0.000 description 3
- 238000000151 deposition Methods 0.000 description 3
- 239000010432 diamond Substances 0.000 description 3
- 229910003460 diamond Inorganic materials 0.000 description 3
- 230000006862 enzymatic digestion Effects 0.000 description 3
- 238000002474 experimental method Methods 0.000 description 3
- 238000003205 genotyping method Methods 0.000 description 3
- 238000003384 imaging method Methods 0.000 description 3
- 230000008774 maternal effect Effects 0.000 description 3
- 230000001404 mediated effect Effects 0.000 description 3
- 238000002844 melting Methods 0.000 description 3
- 230000008018 melting Effects 0.000 description 3
- 239000003068 molecular probe Substances 0.000 description 3
- 238000001127 nanoimprint lithography Methods 0.000 description 3
- 230000036961 partial effect Effects 0.000 description 3
- 230000008775 paternal effect Effects 0.000 description 3
- 238000001020 plasma etching Methods 0.000 description 3
- 229920000642 polymer Polymers 0.000 description 3
- 238000000527 sonication Methods 0.000 description 3
- 238000010561 standard procedure Methods 0.000 description 3
- 238000013518 transcription Methods 0.000 description 3
- 230000035897 transcription Effects 0.000 description 3
- YBJHBAHKTGYVGT-ZKWXMUAHSA-N (+)-Biotin Chemical compound N1C(=O)N[C@@H]2[C@H](CCCCC(=O)O)SC[C@@H]21 YBJHBAHKTGYVGT-ZKWXMUAHSA-N 0.000 description 2
- VGIRNWJSIRVFRT-UHFFFAOYSA-N 2',7'-difluorofluorescein Chemical compound OC(=O)C1=CC=CC=C1C1=C2C=C(F)C(=O)C=C2OC2=CC(O)=C(F)C=C21 VGIRNWJSIRVFRT-UHFFFAOYSA-N 0.000 description 2
- JTBBWRKSUYCPFY-UHFFFAOYSA-N 2,3-dihydro-1h-pyrimidin-4-one Chemical class O=C1NCNC=C1 JTBBWRKSUYCPFY-UHFFFAOYSA-N 0.000 description 2
- 108010067770 Endopeptidase K Proteins 0.000 description 2
- 241000588724 Escherichia coli Species 0.000 description 2
- 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 2
- 102000009617 Inorganic Pyrophosphatase Human genes 0.000 description 2
- 108010009595 Inorganic Pyrophosphatase Proteins 0.000 description 2
- 108060004795 Methyltransferase Proteins 0.000 description 2
- 206010028980 Neoplasm Diseases 0.000 description 2
- 101710147059 Nicking endonuclease Proteins 0.000 description 2
- 101710163270 Nuclease Proteins 0.000 description 2
- 108020004711 Nucleic Acid Probes Proteins 0.000 description 2
- 238000012408 PCR amplification Methods 0.000 description 2
- 108700019535 Phosphoprotein Phosphatases Proteins 0.000 description 2
- 102000045595 Phosphoprotein Phosphatases Human genes 0.000 description 2
- 102000001253 Protein Kinase Human genes 0.000 description 2
- JUJWROOIHBZHMG-UHFFFAOYSA-N Pyridine Chemical compound C1=CC=NC=C1 JUJWROOIHBZHMG-UHFFFAOYSA-N 0.000 description 2
- 230000026279 RNA modification Effects 0.000 description 2
- 108010083644 Ribonucleases Proteins 0.000 description 2
- 102000006382 Ribonucleases Human genes 0.000 description 2
- 240000004808 Saccharomyces cerevisiae Species 0.000 description 2
- BLRPTPMANUNPDV-UHFFFAOYSA-N Silane Chemical compound [SiH4] BLRPTPMANUNPDV-UHFFFAOYSA-N 0.000 description 2
- 208000037065 Subacute sclerosing leukoencephalitis Diseases 0.000 description 2
- 206010042297 Subacute sclerosing panencephalitis Diseases 0.000 description 2
- HCHKCACWOHOZIP-UHFFFAOYSA-N Zinc Chemical compound [Zn] HCHKCACWOHOZIP-UHFFFAOYSA-N 0.000 description 2
- 239000002253 acid Substances 0.000 description 2
- 150000007513 acids Chemical class 0.000 description 2
- 230000004913 activation Effects 0.000 description 2
- 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 2
- 150000003838 adenosines Chemical class 0.000 description 2
- 150000001412 amines Chemical class 0.000 description 2
- 230000002457 bidirectional effect Effects 0.000 description 2
- 244000309466 calf Species 0.000 description 2
- 201000011510 cancer Diseases 0.000 description 2
- 230000001413 cellular effect Effects 0.000 description 2
- 230000008859 change Effects 0.000 description 2
- 239000002299 complementary DNA Substances 0.000 description 2
- OPTASPLRGRRNAP-UHFFFAOYSA-N cytosine Chemical compound NC=1C=CNC(=O)N=1 OPTASPLRGRRNAP-UHFFFAOYSA-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
- 238000013075 data extraction Methods 0.000 description 2
- 230000000593 degrading effect Effects 0.000 description 2
- 239000005546 dideoxynucleotide Substances 0.000 description 2
- 239000004205 dimethyl polysiloxane Substances 0.000 description 2
- 238000009826 distribution Methods 0.000 description 2
- 230000005782 double-strand break Effects 0.000 description 2
- 238000000609 electron-beam lithography Methods 0.000 description 2
- 238000006911 enzymatic reaction Methods 0.000 description 2
- 238000012869 ethanol precipitation Methods 0.000 description 2
- 239000000835 fiber Substances 0.000 description 2
- GNBHRKFJIUUOQI-UHFFFAOYSA-N fluorescein Chemical compound O1C(=O)C2=CC=CC=C2C21C1=CC=C(O)C=C1OC1=CC(O)=CC=C21 GNBHRKFJIUUOQI-UHFFFAOYSA-N 0.000 description 2
- 230000006870 function Effects 0.000 description 2
- 238000007306 functionalization reaction Methods 0.000 description 2
- 230000014509 gene expression Effects 0.000 description 2
- KWIUHFFTVRNATP-UHFFFAOYSA-N glycine betaine Chemical compound C[N+](C)(C)CC([O-])=O KWIUHFFTVRNATP-UHFFFAOYSA-N 0.000 description 2
- UYTPUPDQBNUYGX-UHFFFAOYSA-N guanine Chemical compound O=C1NC(N)=NC2=C1N=CN2 UYTPUPDQBNUYGX-UHFFFAOYSA-N 0.000 description 2
- 230000010354 integration Effects 0.000 description 2
- 230000003993 interaction Effects 0.000 description 2
- 230000000968 intestinal effect Effects 0.000 description 2
- DRAVOWXCEBXPTN-UHFFFAOYSA-N isoguanine Chemical compound NC1=NC(=O)NC2=C1NC=N2 DRAVOWXCEBXPTN-UHFFFAOYSA-N 0.000 description 2
- 238000005304 joining Methods 0.000 description 2
- 238000007169 ligase reaction Methods 0.000 description 2
- 239000006249 magnetic particle Substances 0.000 description 2
- 238000013507 mapping Methods 0.000 description 2
- 238000010297 mechanical methods and process Methods 0.000 description 2
- 238000002493 microarray Methods 0.000 description 2
- 238000002156 mixing Methods 0.000 description 2
- 230000009871 nonspecific binding Effects 0.000 description 2
- 238000007899 nucleic acid hybridization Methods 0.000 description 2
- 239000002853 nucleic acid probe Substances 0.000 description 2
- 150000003833 nucleoside derivatives Chemical class 0.000 description 2
- 238000002515 oligonucleotide synthesis Methods 0.000 description 2
- 238000000206 photolithography Methods 0.000 description 2
- 239000013612 plasmid Substances 0.000 description 2
- 239000004033 plastic Substances 0.000 description 2
- 229920003023 plastic Polymers 0.000 description 2
- 229920000435 poly(dimethylsiloxane) Polymers 0.000 description 2
- 238000002360 preparation method Methods 0.000 description 2
- 238000012545 processing Methods 0.000 description 2
- 108060006633 protein kinase Proteins 0.000 description 2
- 102000004169 proteins and genes Human genes 0.000 description 2
- BBEAQIROQSPTKN-UHFFFAOYSA-N pyrene Chemical compound C1=CC=C2C=CC3=CC=CC4=CC=C1C2=C43 BBEAQIROQSPTKN-UHFFFAOYSA-N 0.000 description 2
- 239000011541 reaction mixture Substances 0.000 description 2
- 230000008707 rearrangement Effects 0.000 description 2
- 230000009467 reduction Effects 0.000 description 2
- 238000009877 rendering Methods 0.000 description 2
- 230000035945 sensitivity Effects 0.000 description 2
- 238000002864 sequence alignment Methods 0.000 description 2
- 229910000077 silane Inorganic materials 0.000 description 2
- 238000006467 substitution reaction Methods 0.000 description 2
- 235000000346 sugar Nutrition 0.000 description 2
- WGTODYJZXSJIAG-UHFFFAOYSA-N tetramethylrhodamine chloride Chemical compound [Cl-].C=12C=CC(N(C)C)=CC2=[O+]C2=CC(N(C)C)=CC=C2C=1C1=CC=CC=C1C(O)=O WGTODYJZXSJIAG-UHFFFAOYSA-N 0.000 description 2
- RWQNBRDOKXIBIV-UHFFFAOYSA-N thymine Chemical compound CC1=CNC(=O)NC1=O RWQNBRDOKXIBIV-UHFFFAOYSA-N 0.000 description 2
- 230000005945 translocation Effects 0.000 description 2
- 239000001226 triphosphate Substances 0.000 description 2
- 235000011178 triphosphate Nutrition 0.000 description 2
- 238000007740 vapor deposition Methods 0.000 description 2
- 238000003260 vortexing Methods 0.000 description 2
- 239000002699 waste material Substances 0.000 description 2
- 239000011701 zinc Substances 0.000 description 2
- 229910052725 zinc Inorganic materials 0.000 description 2
- HDTRYLNUVZCQOY-UHFFFAOYSA-N α-D-glucopyranosyl-α-D-glucopyranoside Natural products OC1C(O)C(O)C(CO)OC1OC1C(O)C(O)C(O)C(CO)O1 HDTRYLNUVZCQOY-UHFFFAOYSA-N 0.000 description 1
- IOOMXAQUNPWDLL-UHFFFAOYSA-N 2-[6-(diethylamino)-3-(diethyliminiumyl)-3h-xanthen-9-yl]-5-sulfobenzene-1-sulfonate Chemical compound C=12C=CC(=[N+](CC)CC)C=C2OC2=CC(N(CC)CC)=CC=C2C=1C1=CC=C(S(O)(=O)=O)C=C1S([O-])(=O)=O IOOMXAQUNPWDLL-UHFFFAOYSA-N 0.000 description 1
- XQCZBXHVTFVIFE-UHFFFAOYSA-N 2-amino-4-hydroxypyrimidine Chemical compound NC1=NC=CC(O)=N1 XQCZBXHVTFVIFE-UHFFFAOYSA-N 0.000 description 1
- GLISOBUNKGBQCL-UHFFFAOYSA-N 3-[ethoxy(dimethyl)silyl]propan-1-amine Chemical group CCO[Si](C)(C)CCCN GLISOBUNKGBQCL-UHFFFAOYSA-N 0.000 description 1
- 208000035657 Abasia Diseases 0.000 description 1
- 229930024421 Adenine Natural products 0.000 description 1
- GFFGJBXGBJISGV-UHFFFAOYSA-N Adenine Chemical compound NC1=NC=NC2=C1N=CN2 GFFGJBXGBJISGV-UHFFFAOYSA-N 0.000 description 1
- 108700028369 Alleles Proteins 0.000 description 1
- 108091023037 Aptamer Proteins 0.000 description 1
- 102000007347 Apyrase Human genes 0.000 description 1
- 108010007730 Apyrase Proteins 0.000 description 1
- 241000894006 Bacteria Species 0.000 description 1
- 208000035143 Bacterial infection Diseases 0.000 description 1
- 239000002126 C01EB10 - Adenosine Substances 0.000 description 1
- 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 1
- 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 1
- HMFHBZSHGGEWLO-SOOFDHNKSA-N D-ribofuranose Chemical compound OC[C@H]1OC(O)[C@H](O)[C@@H]1O HMFHBZSHGGEWLO-SOOFDHNKSA-N 0.000 description 1
- 102000004594 DNA Polymerase I Human genes 0.000 description 1
- 108010017826 DNA Polymerase I Proteins 0.000 description 1
- 108050009160 DNA polymerase 1 Proteins 0.000 description 1
- 108090000626 DNA-directed RNA polymerases Proteins 0.000 description 1
- 102000004163 DNA-directed RNA polymerases Human genes 0.000 description 1
- 108010082610 Deoxyribonuclease (Pyrimidine Dimer) Proteins 0.000 description 1
- 102000004099 Deoxyribonuclease (Pyrimidine Dimer) Human genes 0.000 description 1
- 229910052693 Europium Inorganic materials 0.000 description 1
- 108010007577 Exodeoxyribonuclease I Proteins 0.000 description 1
- 102100029075 Exonuclease 1 Human genes 0.000 description 1
- 208000026350 Inborn Genetic disease Diseases 0.000 description 1
- 108091092195 Intron Proteins 0.000 description 1
- 241000124008 Mammalia Species 0.000 description 1
- 229910021380 Manganese Chloride Inorganic materials 0.000 description 1
- GLFNIEUTAYBVOC-UHFFFAOYSA-L Manganese chloride Chemical compound Cl[Mn]Cl GLFNIEUTAYBVOC-UHFFFAOYSA-L 0.000 description 1
- 108010059724 Micrococcal Nuclease Proteins 0.000 description 1
- JGFZNNIVVJXRND-UHFFFAOYSA-N N,N-diisopropylethylamine Substances CCN(C(C)C)C(C)C JGFZNNIVVJXRND-UHFFFAOYSA-N 0.000 description 1
- CTQNGGLPUBDAKN-UHFFFAOYSA-N O-Xylene Chemical compound CC1=CC=CC=C1C CTQNGGLPUBDAKN-UHFFFAOYSA-N 0.000 description 1
- AWZJFZMWSUBJAJ-UHFFFAOYSA-N OG-514 dye Chemical compound OC(=O)CSC1=C(F)C(F)=C(C(O)=O)C(C2=C3C=C(F)C(=O)C=C3OC3=CC(O)=C(F)C=C32)=C1F AWZJFZMWSUBJAJ-UHFFFAOYSA-N 0.000 description 1
- 108020005187 Oligonucleotide Probes Proteins 0.000 description 1
- 108010038807 Oligopeptides Proteins 0.000 description 1
- 102000015636 Oligopeptides Human genes 0.000 description 1
- 108091081548 Palindromic sequence Proteins 0.000 description 1
- 108091093037 Peptide nucleic acid Proteins 0.000 description 1
- 108010002747 Pfu DNA polymerase Proteins 0.000 description 1
- 101710188536 RNA ligase 1 Proteins 0.000 description 1
- 101710188535 RNA ligase 2 Proteins 0.000 description 1
- 108010092799 RNA-directed DNA polymerase Proteins 0.000 description 1
- 101710093506 RNA-editing ligase 1, mitochondrial Proteins 0.000 description 1
- 101710204104 RNA-editing ligase 2, mitochondrial Proteins 0.000 description 1
- 108091028664 Ribonucleotide Proteins 0.000 description 1
- PYMYPHUHKUWMLA-LMVFSUKVSA-N Ribose Natural products OC[C@@H](O)[C@@H](O)[C@@H](O)C=O PYMYPHUHKUWMLA-LMVFSUKVSA-N 0.000 description 1
- 238000012300 Sequence Analysis Methods 0.000 description 1
- 108020004682 Single-Stranded DNA Proteins 0.000 description 1
- VMHLLURERBWHNL-UHFFFAOYSA-M Sodium acetate Chemical compound [Na+].CC([O-])=O VMHLLURERBWHNL-UHFFFAOYSA-M 0.000 description 1
- PJANXHGTPQOBST-VAWYXSNFSA-N Stilbene Natural products C=1C=CC=CC=1/C=C/C1=CC=CC=C1 PJANXHGTPQOBST-VAWYXSNFSA-N 0.000 description 1
- 108010090804 Streptavidin Proteins 0.000 description 1
- 229910052771 Terbium Inorganic materials 0.000 description 1
- HDTRYLNUVZCQOY-WSWWMNSNSA-N Trehalose Natural products O[C@@H]1[C@@H](O)[C@@H](O)[C@@H](CO)O[C@@H]1O[C@@H]1[C@H](O)[C@@H](O)[C@@H](O)[C@@H](CO)O1 HDTRYLNUVZCQOY-WSWWMNSNSA-N 0.000 description 1
- 239000007983 Tris buffer Substances 0.000 description 1
- 238000005411 Van der Waals force Methods 0.000 description 1
- 208000036142 Viral infection Diseases 0.000 description 1
- 241000700605 Viruses Species 0.000 description 1
- 101710185494 Zinc finger protein Proteins 0.000 description 1
- 102100023597 Zinc finger protein 816 Human genes 0.000 description 1
- 238000010306 acid treatment Methods 0.000 description 1
- 239000011149 active material Substances 0.000 description 1
- 229960000643 adenine Drugs 0.000 description 1
- 229960005305 adenosine Drugs 0.000 description 1
- HDTRYLNUVZCQOY-LIZSDCNHSA-N alpha,alpha-trehalose Chemical compound O[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1O[C@@H]1[C@H](O)[C@@H](O)[C@H](O)[C@@H](CO)O1 HDTRYLNUVZCQOY-LIZSDCNHSA-N 0.000 description 1
- HMFHBZSHGGEWLO-UHFFFAOYSA-N alpha-D-Furanose-Ribose Natural products OCC1OC(O)C(O)C1O HMFHBZSHGGEWLO-UHFFFAOYSA-N 0.000 description 1
- 230000004075 alteration Effects 0.000 description 1
- 150000001408 amides Chemical class 0.000 description 1
- 239000007864 aqueous solution Substances 0.000 description 1
- 210000004436 artificial bacterial chromosome Anatomy 0.000 description 1
- 210000001106 artificial yeast chromosome Anatomy 0.000 description 1
- 125000004429 atom Chemical group 0.000 description 1
- 230000001580 bacterial effect Effects 0.000 description 1
- 208000022362 bacterial infectious disease Diseases 0.000 description 1
- 230000004888 barrier function Effects 0.000 description 1
- 229960003237 betaine Drugs 0.000 description 1
- 125000002619 bicyclic group Chemical group 0.000 description 1
- 102000023732 binding proteins Human genes 0.000 description 1
- 108091008324 binding proteins Proteins 0.000 description 1
- 239000012472 biological sample Substances 0.000 description 1
- 229960002685 biotin Drugs 0.000 description 1
- 235000020958 biotin Nutrition 0.000 description 1
- 239000011616 biotin Substances 0.000 description 1
- OMWQUXGVXQELIX-UHFFFAOYSA-N bitoscanate Chemical compound S=C=NC1=CC=C(N=C=S)C=C1 OMWQUXGVXQELIX-UHFFFAOYSA-N 0.000 description 1
- 239000002981 blocking agent Substances 0.000 description 1
- 238000009640 blood culture Methods 0.000 description 1
- 210000001124 body fluid Anatomy 0.000 description 1
- 238000004422 calculation algorithm Methods 0.000 description 1
- 238000004364 calculation method Methods 0.000 description 1
- 150000001768 cations Chemical class 0.000 description 1
- 238000004113 cell culture Methods 0.000 description 1
- 239000000919 ceramic Substances 0.000 description 1
- 210000003756 cervix mucus Anatomy 0.000 description 1
- VYXSBFYARXAAKO-WTKGSRSZSA-N chembl402140 Chemical compound Cl.C1=2C=C(C)C(NCC)=CC=2OC2=C\C(=N/CC)C(C)=CC2=C1C1=CC=CC=C1C(=O)OCC VYXSBFYARXAAKO-WTKGSRSZSA-N 0.000 description 1
- 239000013043 chemical agent Substances 0.000 description 1
- 239000003086 colorant Substances 0.000 description 1
- 239000003431 cross linking reagent Substances 0.000 description 1
- DMSZORWOGDLWGN-UHFFFAOYSA-N ctk1a3526 Chemical compound NP(N)(N)=O DMSZORWOGDLWGN-UHFFFAOYSA-N 0.000 description 1
- 230000009089 cytolysis Effects 0.000 description 1
- 229940104302 cytosine Drugs 0.000 description 1
- 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 1
- 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 1
- 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 1
- 125000001295 dansyl group Chemical group [H]C1=C([H])C(N(C([H])([H])[H])C([H])([H])[H])=C2C([H])=C([H])C([H])=C(C2=C1[H])S(*)(=O)=O 0.000 description 1
- 238000007405 data analysis Methods 0.000 description 1
- 230000008021 deposition Effects 0.000 description 1
- 230000000368 destabilizing effect Effects 0.000 description 1
- 238000011161 development Methods 0.000 description 1
- 238000000502 dialysis Methods 0.000 description 1
- 239000013024 dilution buffer Substances 0.000 description 1
- NAGJZTKCGNOGPW-UHFFFAOYSA-K dioxido-sulfanylidene-sulfido-$l^{5}-phosphane Chemical compound [O-]P([O-])([S-])=S NAGJZTKCGNOGPW-UHFFFAOYSA-K 0.000 description 1
- 201000010099 disease Diseases 0.000 description 1
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 description 1
- 238000011143 downstream manufacturing Methods 0.000 description 1
- 230000002616 endonucleolytic effect Effects 0.000 description 1
- 238000003366 endpoint assay Methods 0.000 description 1
- 238000012407 engineering method Methods 0.000 description 1
- 230000007613 environmental effect Effects 0.000 description 1
- YQGOJNYOYNNSMM-UHFFFAOYSA-N eosin Chemical compound [Na+].OC(=O)C1=CC=CC=C1C1=C2C=C(Br)C(=O)C(Br)=C2OC2=C(Br)C(O)=C(Br)C=C21 YQGOJNYOYNNSMM-UHFFFAOYSA-N 0.000 description 1
- IINNWAYUJNWZRM-UHFFFAOYSA-L erythrosin B Chemical compound [Na+].[Na+].[O-]C(=O)C1=CC=CC=C1C1=C2C=C(I)C(=O)C(I)=C2OC2=C(I)C([O-])=C(I)C=C21 IINNWAYUJNWZRM-UHFFFAOYSA-L 0.000 description 1
- OGPBJKLSAFTDLK-UHFFFAOYSA-N europium atom Chemical compound [Eu] OGPBJKLSAFTDLK-UHFFFAOYSA-N 0.000 description 1
- 108010052305 exodeoxyribonuclease III Proteins 0.000 description 1
- 238000000605 extraction Methods 0.000 description 1
- 229920005570 flexible polymer Polymers 0.000 description 1
- GVEPBJHOBDJJJI-UHFFFAOYSA-N fluoranthrene Natural products C1=CC(C2=CC=CC=C22)=C3C2=CC=CC3=C1 GVEPBJHOBDJJJI-UHFFFAOYSA-N 0.000 description 1
- MHMNJMPURVTYEJ-UHFFFAOYSA-N fluorescein-5-isothiocyanate Chemical compound O1C(=O)C2=CC(N=C=S)=CC=C2C21C1=CC=C(O)C=C1OC1=CC(O)=CC=C21 MHMNJMPURVTYEJ-UHFFFAOYSA-N 0.000 description 1
- 238000002073 fluorescence micrograph Methods 0.000 description 1
- 125000000524 functional group Chemical group 0.000 description 1
- 230000005021 gait Effects 0.000 description 1
- 108010055863 gene b exonuclease Proteins 0.000 description 1
- 208000016361 genetic disease Diseases 0.000 description 1
- 230000002068 genetic effect Effects 0.000 description 1
- 239000003365 glass fiber Substances 0.000 description 1
- 229940029575 guanosine Drugs 0.000 description 1
- 238000010438 heat treatment Methods 0.000 description 1
- 238000012165 high-throughput sequencing Methods 0.000 description 1
- 229910052739 hydrogen Inorganic materials 0.000 description 1
- 239000001257 hydrogen Substances 0.000 description 1
- 230000002209 hydrophobic effect Effects 0.000 description 1
- 230000005661 hydrophobic surface Effects 0.000 description 1
- 238000007654 immersion Methods 0.000 description 1
- 230000000415 inactivating effect Effects 0.000 description 1
- 230000000155 isotopic effect Effects 0.000 description 1
- 238000002372 labelling Methods 0.000 description 1
- 229910052747 lanthanoid Inorganic materials 0.000 description 1
- 150000002602 lanthanoids Chemical class 0.000 description 1
- 239000012035 limiting reagent Substances 0.000 description 1
- 125000005647 linker group Chemical group 0.000 description 1
- DLBFLQKQABVKGT-UHFFFAOYSA-L lucifer yellow dye Chemical compound [Li+].[Li+].[O-]S(=O)(=O)C1=CC(C(N(C(=O)NN)C2=O)=O)=C3C2=CC(S([O-])(=O)=O)=CC3=C1N DLBFLQKQABVKGT-UHFFFAOYSA-L 0.000 description 1
- 210000002751 lymph Anatomy 0.000 description 1
- 239000011565 manganese chloride Substances 0.000 description 1
- 235000002867 manganese chloride Nutrition 0.000 description 1
- 239000011159 matrix material Substances 0.000 description 1
- 230000007246 mechanism Effects 0.000 description 1
- 230000035772 mutation Effects 0.000 description 1
- 239000002102 nanobead Substances 0.000 description 1
- 239000002105 nanoparticle Substances 0.000 description 1
- 239000002077 nanosphere Substances 0.000 description 1
- 238000007826 nucleic acid assay Methods 0.000 description 1
- 102000044158 nucleic acid binding protein Human genes 0.000 description 1
- 108700020942 nucleic acid binding protein Proteins 0.000 description 1
- 238000001921 nucleic acid quantification Methods 0.000 description 1
- 125000003835 nucleoside group Chemical group 0.000 description 1
- 230000005257 nucleotidylation Effects 0.000 description 1
- 238000002966 oligonucleotide array Methods 0.000 description 1
- 239000002751 oligonucleotide probe Substances 0.000 description 1
- 238000005580 one pot reaction Methods 0.000 description 1
- 239000013307 optical fiber Substances 0.000 description 1
- 239000003960 organic solvent Substances 0.000 description 1
- VYNDHICBIRRPFP-UHFFFAOYSA-N pacific blue Chemical compound FC1=C(O)C(F)=C2OC(=O)C(C(=O)O)=CC2=C1 VYNDHICBIRRPFP-UHFFFAOYSA-N 0.000 description 1
- 244000052769 pathogen Species 0.000 description 1
- 230000001717 pathogenic effect Effects 0.000 description 1
- 230000026731 phosphorylation Effects 0.000 description 1
- 238000006366 phosphorylation reaction Methods 0.000 description 1
- 229920002401 polyacrylamide Polymers 0.000 description 1
- 239000013641 positive control Substances 0.000 description 1
- 239000002243 precursor Substances 0.000 description 1
- 125000002924 primary amino group Chemical group [H]N([H])* 0.000 description 1
- 239000012521 purified sample Substances 0.000 description 1
- UMJSCPRVCHMLSP-UHFFFAOYSA-N pyridine Natural products COC1=CC=CN=C1 UMJSCPRVCHMLSP-UHFFFAOYSA-N 0.000 description 1
- 239000002096 quantum dot Substances 0.000 description 1
- 238000010791 quenching Methods 0.000 description 1
- 230000000171 quenching effect Effects 0.000 description 1
- 230000002285 radioactive effect Effects 0.000 description 1
- 239000000376 reactant Substances 0.000 description 1
- 238000010188 recombinant method Methods 0.000 description 1
- 230000002829 reductive effect Effects 0.000 description 1
- 230000002441 reversible effect Effects 0.000 description 1
- XFKVYXCRNATCOO-UHFFFAOYSA-M rhodamine 6G Chemical compound [Cl-].C=12C=C(C)C(NCC)=CC2=[O+]C=2C=C(NCC)C(C)=CC=2C=1C1=CC=CC=C1C(=O)OCC XFKVYXCRNATCOO-UHFFFAOYSA-M 0.000 description 1
- 239000002336 ribonucleotide Substances 0.000 description 1
- 125000002652 ribonucleotide group Chemical group 0.000 description 1
- 150000003290 ribose derivatives Chemical group 0.000 description 1
- 125000000548 ribosyl group Chemical group C1([C@H](O)[C@H](O)[C@H](O1)CO)* 0.000 description 1
- 210000003296 saliva Anatomy 0.000 description 1
- 239000012266 salt solution Substances 0.000 description 1
- 238000013515 script Methods 0.000 description 1
- 210000000582 semen Anatomy 0.000 description 1
- 210000002966 serum Anatomy 0.000 description 1
- 238000010008 shearing Methods 0.000 description 1
- 238000004904 shortening Methods 0.000 description 1
- 229910052710 silicon Inorganic materials 0.000 description 1
- 239000010703 silicon Substances 0.000 description 1
- 239000000377 silicon dioxide Substances 0.000 description 1
- 239000002356 single layer Substances 0.000 description 1
- 239000001632 sodium acetate Substances 0.000 description 1
- 235000017281 sodium acetate Nutrition 0.000 description 1
- 239000001488 sodium phosphate Substances 0.000 description 1
- 229910000162 sodium phosphate Inorganic materials 0.000 description 1
- 239000002689 soil Substances 0.000 description 1
- 230000006641 stabilisation Effects 0.000 description 1
- 238000011105 stabilization Methods 0.000 description 1
- PJANXHGTPQOBST-UHFFFAOYSA-N stilbene Chemical compound C=1C=CC=CC=1C=CC1=CC=CC=C1 PJANXHGTPQOBST-UHFFFAOYSA-N 0.000 description 1
- 235000021286 stilbenes Nutrition 0.000 description 1
- 239000004575 stone Substances 0.000 description 1
- 230000002194 synthesizing effect Effects 0.000 description 1
- GZCRRIHWUXGPOV-UHFFFAOYSA-N terbium atom Chemical compound [Tb] GZCRRIHWUXGPOV-UHFFFAOYSA-N 0.000 description 1
- RYYWUUFWQRZTIU-UHFFFAOYSA-K thiophosphate Chemical compound [O-]P([O-])([O-])=S RYYWUUFWQRZTIU-UHFFFAOYSA-K 0.000 description 1
- 229940113082 thymine Drugs 0.000 description 1
- 230000009466 transformation Effects 0.000 description 1
- 238000000844 transformation Methods 0.000 description 1
- BPSIOYPQMFLKFR-UHFFFAOYSA-N trimethoxy-[3-(oxiran-2-ylmethoxy)propyl]silane Chemical compound CO[Si](OC)(OC)CCCOCC1CO1 BPSIOYPQMFLKFR-UHFFFAOYSA-N 0.000 description 1
- 125000002264 triphosphate group Chemical class [H]OP(=O)(O[H])OP(=O)(O[H])OP(=O)(O[H])O* 0.000 description 1
- LENZDBCJOHFCAS-UHFFFAOYSA-N tris Chemical compound OCC(N)(CO)CO LENZDBCJOHFCAS-UHFFFAOYSA-N 0.000 description 1
- RYFMWSXOAZQYPI-UHFFFAOYSA-K trisodium phosphate Chemical compound [Na+].[Na+].[Na+].[O-]P([O-])([O-])=O RYFMWSXOAZQYPI-UHFFFAOYSA-K 0.000 description 1
- 210000002700 urine Anatomy 0.000 description 1
- 239000013598 vector Substances 0.000 description 1
- 230000009385 viral infection Effects 0.000 description 1
- 238000012070 whole genome sequencing analysis Methods 0.000 description 1
- 239000008096 xylene Substances 0.000 description 1
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6869—Methods for sequencing
- C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6813—Hybridisation assays
- C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6813—Hybridisation assays
- C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
Landscapes
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Organic Chemistry (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Microbiology (AREA)
- Immunology (AREA)
- Biotechnology (AREA)
- Molecular Biology (AREA)
- Biophysics (AREA)
- Analytical Chemistry (AREA)
- Physics & Mathematics (AREA)
- Biochemistry (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
- General Health & Medical Sciences (AREA)
- Genetics & Genomics (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Claims (13)
1. Fremgangsmåde til bestemmelse af identifikationen af et første nukleotid ved en detekteringsposition af en målsekvens omfattende en flerhed af detekteringspositioner, hvilken fremgangsmåde omfatter: a) tilvejebringelse af en flerhed af nukleinsyrekonstrukter, hvor hvert nukleinsyrekonstrukt omfatter en flerhed af monomerer og hver monomer omfatter: i) et første målområde af målsekvensen omfattende et første sæt af måldetekteringspositioner og ii) en første adapter omfattende et forankringssted; b) hybridisering af en første forankringssonde til forankringsstedet; c) hybridisering af en anden forankringssonde til en sekvens, der støder op til og er sammenhængende med forankringsstedet, hvor den anden forankringssonde er delvist eller helt degenereret og den hybridiserede anden forankringssonde kan ligeres til den hybridiserede første forankringssonde; d) hybridisering af én, to eller tre supplerende forankringssonder til målsekvensen mellem det første målområde og stedet for hybridisering af den anden forankringssonde; hvor den eller de supplerende forankringssonder er fuldt degenererede; e) hybridisering af mindst en første sekvenseringssonde til det første målområde, hvor den første sekvenseringssonde omfatter: i) et første sondeområde, der er komplementært til målområdet; ii) et unikt nukleotid ved en første spørgeposition og iii) en markør; under forhold, hvor sekvenseringssonden hybridiserer til målområdet, hvis det unikke nukleotid er komplementært til et første nukleotid i det første sæt af måldetekteringspositioner; hvor den hybridiserede første forankringssonde, anden forankringssonde, den eller de supplerende forankringssonder og den første sekvenseringssonde er hybridiseret til tilstødende sekvenser og kan ligeres for at danne et ligeringsprodukt; og f) ligering af forankringssondeme og sekvenseringssonden for at danne et sondeligeringsprodukt; og derefter g) detektering af sondeligeringsproduktet for derved at identificere det første nukleotid.
2. Fremgangsmåde ifølge krav 1, hvor nukleinsyrekonstrukteme befinder sig på en overflade.
3. Fremgangsmåde ifølge krav 2, hvor hvert nukleinsyrekonstrukt er en concatemer, der omfatter en flerhed af monomerer, og hver monomer omfatter målområdet og adapteren.
4. Fremgangsmåde ifølge krav 3, hvor overfladen omfatter en flerhed af rumligt adskilte områder, hvortil individuelle concatemerer er bundet.
5. Fremgangsmåde ifølge krav 4, hvor de rumligt adskilte områder er indrettet som et regelmæssigt system.
6. Fremgangsmåde ifølge krav 4, hvor concatemereme er ikke-kovalent bundet til overfladen.
7. Fremgangsmåde ifølge krav 1, hvor trin b) - f) gentages i flere cyklusser for derved at identificere nukleotider ved supplerende måldetekteringspositioner i sættet af måldetekteringspositioner, hvor der i forskellige cyklusser anvendes forskellige sekvenseringssonder, hvor de forskellige sekvenseringssonder adskiller sig fra hinanden ved at have et unikt nukleotid ved forskellige spørgepositioner.
8. Fremgangsmåde ifølge krav 1, hvor hver af monomeme omfatter en flerhed af adaptere.
9. Fremgangsmåde ifølge krav 1, hvor målsekvensen eller -sekvenserne er en genomisk nukleinsyresekvens.
10. Fremgangsmåde ifølge krav 9, hvor den eller de genomiske nukleinsyresekvenser er humane.
11. Fremgangsmåde ifølge krav 1-10, hvor trin (d) omfatter hybridisering af én supplerende forankringssonde.
12. Fremgangsmåde ifølge krav 1-10, hvor trin (d) omfatter hybridisering af to supplerende forankringssonder.
13. Fremgangsmåde ifølge krav 1-10, hvor trin (d) omfatter hybridisering af tre supplerende forankringssonder.
Applications Claiming Priority (9)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US99248507P | 2007-12-05 | 2007-12-05 | |
| US2633708P | 2008-02-05 | 2008-02-05 | |
| US3591408P | 2008-03-12 | 2008-03-12 | |
| US6113408P | 2008-06-13 | 2008-06-13 | |
| US10258608P | 2008-10-03 | 2008-10-03 | |
| US12/265,593 US7901890B2 (en) | 2007-11-05 | 2008-11-05 | Methods and oligonucleotide designs for insertion of multiple adaptors employing selective methylation |
| US12/266,385 US7897344B2 (en) | 2007-11-06 | 2008-11-06 | Methods and oligonucleotide designs for insertion of multiple adaptors into library constructs |
| US11619308P | 2008-11-19 | 2008-11-19 | |
| EP12164915.6A EP2565279B1 (en) | 2007-12-05 | 2008-12-05 | Efficient base determination in sequencing reactions |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| DK2610351T3 true DK2610351T3 (da) | 2015-09-28 |
Family
ID=52465106
Family Applications (2)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| DK12191212.5T DK2610351T3 (da) | 2007-12-05 | 2008-12-05 | Effektiv basebestemmelse i sekvenseringsreaktioner |
| DK12164915.6T DK2565279T3 (da) | 2007-12-05 | 2008-12-05 | Effektiv basebestemmelse i sekvenseringsreaktioner |
Family Applications After (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| DK12164915.6T DK2565279T3 (da) | 2007-12-05 | 2008-12-05 | Effektiv basebestemmelse i sekvenseringsreaktioner |
Country Status (3)
| Country | Link |
|---|---|
| EP (2) | EP2565279B1 (da) |
| CN (1) | CN103290106B (da) |
| DK (2) | DK2610351T3 (da) |
Families Citing this family (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN107002291B (zh) * | 2014-11-26 | 2019-03-26 | 深圳华大智造科技有限公司 | 一种核酸的双接头单链环状文库的构建方法和试剂 |
| WO2016082129A1 (zh) * | 2014-11-26 | 2016-06-02 | 深圳华大基因研究院 | 一种核酸的双接头单链环状文库的构建方法和试剂 |
| HK1247662B (en) | 2015-10-07 | 2019-11-01 | Selma Diagnostics Aps | Flow system and methods for digital counting |
| WO2018020024A1 (en) | 2016-07-29 | 2018-02-01 | Selma Diagnostics Aps | Improvements in methods for digital counting |
| WO2022104138A1 (en) * | 2020-11-14 | 2022-05-19 | Life Technologies Corporation | System and method for automated repeat sequencing |
Family Cites Families (36)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US2633708A (en) | 1948-07-07 | 1953-04-07 | American Steel Foundries | Control for hydraulic presses |
| US3591408A (en) | 1967-12-06 | 1971-07-06 | Owens Corning Fiberglass Corp | Process for coloring glass fibers and fabrics |
| 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 |
| US5034506A (en) | 1985-03-15 | 1991-07-23 | Anti-Gene Development Group | Uncharged morpholino-based polymers having achiral intersubunit linkages |
| US5235033A (en) | 1985-03-15 | 1993-08-10 | Anti-Gene Development Group | Alpha-morpholino ribonucleoside derivatives and polymers thereof |
| US5216141A (en) | 1988-06-06 | 1993-06-01 | Benner Steven A | Oligonucleotide analogs containing sulfur linkages |
| US5143854A (en) | 1989-06-07 | 1992-09-01 | Affymax Technologies N.V. | Large scale photolithographic solid phase synthesis of polypeptides and receptor binding screening thereof |
| US5602240A (en) | 1990-07-27 | 1997-02-11 | Ciba Geigy Ag. | Backbone modified oligonucleotide analogs |
| US5386023A (en) | 1990-07-27 | 1995-01-31 | Isis Pharmaceuticals | Backbone modified oligonucleotide analogs and preparation thereof through reductive coupling |
| US5426180A (en) | 1991-03-27 | 1995-06-20 | Research Corporation Technologies, Inc. | Methods of making single-stranded circular oligonucleotides |
| US5644048A (en) | 1992-01-10 | 1997-07-01 | Isis Pharmaceuticals, Inc. | Process for preparing phosphorothioate oligonucleotides |
| US5473060A (en) | 1993-07-02 | 1995-12-05 | Lynx Therapeutics, Inc. | Oligonucleotide clamps having diagnostic applications |
| US6401267B1 (en) | 1993-09-27 | 2002-06-11 | Radoje Drmanac | Methods and compositions for efficient nucleic acid sequencing |
| SE9400522D0 (sv) | 1994-02-16 | 1994-02-16 | Ulf Landegren | Method and reagent for detecting specific nucleotide sequences |
| US5637684A (en) | 1994-02-23 | 1997-06-10 | Isis Pharmaceuticals, Inc. | Phosphoramidate and phosphorothioamidate oligomeric compounds |
| US5750341A (en) | 1995-04-17 | 1998-05-12 | Lynx Therapeutics, Inc. | DNA sequencing by parallel oligonucleotide extensions |
| US5774305A (en) | 1995-06-07 | 1998-06-30 | Seagate Technology, Inc. | Head gimbal assembly to reduce slider distortion due to thermal stress |
| CN1153825A (zh) * | 1995-09-18 | 1997-07-09 | 株式会社日立制作所 | Dna碱基序列的测序方法及用于该方法的样品调制方法 |
| DK0862656T3 (da) | 1995-11-21 | 2001-04-09 | Univ Yale | Unimolekylær segmentamplifikation og -detektering |
| US5854033A (en) | 1995-11-21 | 1998-12-29 | Yale University | Rolling circle replication reporter systems |
| GB9620209D0 (en) | 1996-09-27 | 1996-11-13 | Cemu Bioteknik Ab | Method of sequencing DNA |
| US6309824B1 (en) | 1997-01-16 | 2001-10-30 | Hyseq, Inc. | Methods for analyzing a target nucleic acid using immobilized heterogeneous mixtures of oligonucleotide probes |
| US6113408A (en) | 1998-10-21 | 2000-09-05 | Lyall Assemblies, Inc. | Non-arcing fluorescent lamp holder |
| US6864052B1 (en) | 1999-01-06 | 2005-03-08 | Callida Genomics, Inc. | Enhanced sequencing by hybridization using pools of probes |
| GB9901475D0 (en) | 1999-01-22 | 1999-03-17 | Pyrosequencing Ab | A method of DNA sequencing |
| US6818395B1 (en) | 1999-06-28 | 2004-11-16 | California Institute Of Technology | Methods and apparatus for analyzing polynucleotide sequences |
| AU7537200A (en) | 1999-09-29 | 2001-04-30 | Solexa Ltd. | Polynucleotide sequencing |
| WO2006073504A2 (en) | 2004-08-04 | 2006-07-13 | President And Fellows Of Harvard College | Wobble sequencing |
| EP1879906A4 (en) | 2005-01-05 | 2009-07-22 | Advanced Genetic Analysis Corp | REVERSIBLE NUCLEOTIDE TERMINATORS AND USES THEREOF |
| EP3257949A1 (en) * | 2005-06-15 | 2017-12-20 | Complete Genomics Inc. | Nucleic acid analysis by random mixtures of non-overlapping fragments |
| WO2007120208A2 (en) | 2005-11-14 | 2007-10-25 | President And Fellows Of Harvard College | Nanogrid rolling circle dna sequencing |
| CN101432439B (zh) | 2006-02-24 | 2013-07-24 | 考利达基因组股份有限公司 | Dna阵列上的高通量基因组测序 |
| CN101495654A (zh) * | 2006-04-19 | 2009-07-29 | 阿普里拉股份有限公司 | 无凝胶珠基测序的试剂、方法和文库 |
| WO2014143762A2 (en) | 2013-03-15 | 2014-09-18 | Armour Technologies, Inc. | Medical device curving apparatus, system, and method of use |
| MA43271A (fr) | 2015-06-17 | 2018-09-26 | Dispersol Technologies Llc | Formulations améliorées de déférasirox et leurs procédés de fabrication |
| WO2019151396A1 (ja) | 2018-02-01 | 2019-08-08 | イーグル工業株式会社 | 摺動部品 |
-
2008
- 2008-12-05 EP EP12164915.6A patent/EP2565279B1/en active Active
- 2008-12-05 CN CN201310051522.XA patent/CN103290106B/zh active Active
- 2008-12-05 DK DK12191212.5T patent/DK2610351T3/da active
- 2008-12-05 DK DK12164915.6T patent/DK2565279T3/da active
- 2008-12-05 EP EP12191212.5A patent/EP2610351B1/en active Active
Also Published As
| Publication number | Publication date |
|---|---|
| EP2610351A1 (en) | 2013-07-03 |
| CN103290106B (zh) | 2015-07-29 |
| EP2610351B1 (en) | 2015-07-08 |
| CN103290106A (zh) | 2013-09-11 |
| EP2565279A1 (en) | 2013-03-06 |
| EP2565279B1 (en) | 2014-12-03 |
| DK2565279T3 (da) | 2015-02-16 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| EP2227563B1 (en) | Efficient base determination in sequencing reactions | |
| US9267172B2 (en) | Efficient base determination in sequencing reactions | |
| US11835437B2 (en) | Treatment for stabilizing nucleic acid arrays | |
| US9023769B2 (en) | cDNA library for nucleic acid sequencing | |
| US8518640B2 (en) | Nucleic acid sequencing and process | |
| EP2443236B1 (en) | Methods and compositions for long fragment read sequencing | |
| DK2610351T3 (da) | Effektiv basebestemmelse i sekvenseringsreaktioner | |
| HK1187078B (en) | Efficient base determination in sequencing reactions | |
| AU2013202989A1 (en) | Efficient base determination in sequencing reactions | |
| HK1176095B (en) | Efficient base determination in sequencing reactions | |
| HK1214303B (en) | Method for long fragment read sequencing | |
| HK1201778B (en) | Treatment for stabilizing nucleic acid arrays | |
| HK1169679B (en) | Methods and compositions for long fragment read sequencing |