JPWO2022038291A5 - - Google Patents
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- JPWO2022038291A5 JPWO2022038291A5 JP2023512403A JP2023512403A JPWO2022038291A5 JP WO2022038291 A5 JPWO2022038291 A5 JP WO2022038291A5 JP 2023512403 A JP2023512403 A JP 2023512403A JP 2023512403 A JP2023512403 A JP 2023512403A JP WO2022038291 A5 JPWO2022038291 A5 JP WO2022038291A5
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- JP
- Japan
- Prior art keywords
- oligonucleotide
- sequence
- pair
- binding
- strand
- 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.)
- Pending
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- 108091034117 Oligonucleotide Proteins 0.000 claims 168
- 238000000034 method Methods 0.000 claims 74
- 108020004707 nucleic acids Proteins 0.000 claims 73
- 102000039446 nucleic acids Human genes 0.000 claims 73
- 150000007523 nucleic acids Chemical class 0.000 claims 73
- JLCPHMBAVCMARE-UHFFFAOYSA-N [3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methyl [5-(6-aminopurin-9-yl)-2-(hydroxymethyl)oxolan-3-yl] hydrogen phosphate Polymers Cc1cn(C2CC(OP(O)(=O)OCC3OC(CC3OP(O)(=O)OCC3OC(CC3O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c3nc(N)[nH]c4=O)C(COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3CO)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cc(C)c(=O)[nH]c3=O)n3cc(C)c(=O)[nH]c3=O)n3ccc(N)nc3=O)n3cc(C)c(=O)[nH]c3=O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)O2)c(=O)[nH]c1=O JLCPHMBAVCMARE-UHFFFAOYSA-N 0.000 claims 42
- 230000005782 double-strand break Effects 0.000 claims 32
- 238000009396 hybridization Methods 0.000 claims 32
- 230000000295 complement effect Effects 0.000 claims 25
- 239000000758 substrate Substances 0.000 claims 19
- 238000012163 sequencing technique Methods 0.000 claims 14
- 108091092584 GDNA Proteins 0.000 claims 10
- 238000003776 cleavage reaction Methods 0.000 claims 8
- 239000012634 fragment Substances 0.000 claims 8
- 230000007017 scission Effects 0.000 claims 8
- 230000000694 effects Effects 0.000 claims 7
- 238000013467 fragmentation Methods 0.000 claims 7
- 238000006062 fragmentation reaction Methods 0.000 claims 7
- 230000001939 inductive effect Effects 0.000 claims 6
- 239000002773 nucleotide Substances 0.000 claims 6
- 125000003729 nucleotide group Chemical group 0.000 claims 6
- 230000003321 amplification Effects 0.000 claims 5
- 238000003199 nucleic acid amplification method Methods 0.000 claims 5
- 238000002360 preparation method Methods 0.000 claims 5
- 125000002467 phosphate group Chemical group [H]OP(=O)(O[H])O[*] 0.000 claims 4
- 238000005464 sample preparation method Methods 0.000 claims 4
- 235000011178 triphosphate Nutrition 0.000 claims 4
- 239000001226 triphosphate Substances 0.000 claims 4
- UNXRWKVEANCORM-UHFFFAOYSA-N triphosphoric acid Chemical compound OP(O)(=O)OP(O)(=O)OP(O)(O)=O UNXRWKVEANCORM-UHFFFAOYSA-N 0.000 claims 4
- 239000003795 chemical substances by application Substances 0.000 claims 3
- 230000004048 modification Effects 0.000 claims 3
- 238000012986 modification Methods 0.000 claims 3
- 108091093078 Pyrimidine dimer Proteins 0.000 claims 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 claims 2
- 230000001681 protective effect Effects 0.000 claims 2
- 230000005783 single-strand break Effects 0.000 claims 2
- FWMNVWWHGCHHJJ-SKKKGAJSSA-N 4-amino-1-[(2r)-6-amino-2-[[(2r)-2-[[(2r)-2-[[(2r)-2-amino-3-phenylpropanoyl]amino]-3-phenylpropanoyl]amino]-4-methylpentanoyl]amino]hexanoyl]piperidine-4-carboxylic acid Chemical compound C([C@H](C(=O)N[C@H](CC(C)C)C(=O)N[C@H](CCCCN)C(=O)N1CCC(N)(CC1)C(O)=O)NC(=O)[C@H](N)CC=1C=CC=CC=1)C1=CC=CC=C1 FWMNVWWHGCHHJJ-SKKKGAJSSA-N 0.000 claims 1
- UBKVUFQGVWHZIR-UHFFFAOYSA-N 8-oxoguanine Chemical compound O=C1NC(N)=NC2=NC(=O)N=C21 UBKVUFQGVWHZIR-UHFFFAOYSA-N 0.000 claims 1
- 208000035657 Abasia Diseases 0.000 claims 1
- 239000002126 C01EB10 - Adenosine Substances 0.000 claims 1
- 108010008286 DNA nucleotidylexotransferase Proteins 0.000 claims 1
- 102100029764 DNA-directed DNA/RNA polymerase mu Human genes 0.000 claims 1
- 102000004533 Endonucleases Human genes 0.000 claims 1
- 108010042407 Endonucleases Proteins 0.000 claims 1
- 108060002716 Exonuclease Proteins 0.000 claims 1
- 102000003960 Ligases Human genes 0.000 claims 1
- 108090000364 Ligases Proteins 0.000 claims 1
- 102000004160 Phosphoric Monoester Hydrolases Human genes 0.000 claims 1
- 108090000608 Phosphoric Monoester Hydrolases Proteins 0.000 claims 1
- 229960005305 adenosine Drugs 0.000 claims 1
- UPUOLJWYFICKJI-UHFFFAOYSA-N cyclobutane;pyrimidine Chemical class C1CCC1.C1=CN=CN=C1 UPUOLJWYFICKJI-UHFFFAOYSA-N 0.000 claims 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 claims 1
- 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 claims 1
- URGJWIFLBWJRMF-JGVFFNPUSA-N ddTTP Chemical compound O=C1NC(=O)C(C)=CN1[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)CC1 URGJWIFLBWJRMF-JGVFFNPUSA-N 0.000 claims 1
- 238000012217 deletion Methods 0.000 claims 1
- 230000037430 deletion Effects 0.000 claims 1
- 239000005546 dideoxynucleotide Substances 0.000 claims 1
- 102000013165 exonuclease Human genes 0.000 claims 1
- 238000000338 in vitro Methods 0.000 claims 1
- 238000011065 in-situ storage Methods 0.000 claims 1
- 238000007899 nucleic acid hybridization Methods 0.000 claims 1
- 239000008191 permeabilizing agent Substances 0.000 claims 1
- 150000008300 phosphoramidites Chemical class 0.000 claims 1
- 230000026731 phosphorylation Effects 0.000 claims 1
- 238000006366 phosphorylation reaction Methods 0.000 claims 1
- 102000004169 proteins and genes Human genes 0.000 claims 1
- 108090000623 proteins and genes Proteins 0.000 claims 1
- -1 spacer phosphoramidite Chemical class 0.000 claims 1
- RYYWUUFWQRZTIU-UHFFFAOYSA-K thiophosphate Chemical compound [O-]P([O-])([O-])=S RYYWUUFWQRZTIU-UHFFFAOYSA-K 0.000 claims 1
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| GB2013141.3 | 2020-08-21 | ||
| GBGB2013141.3A GB202013141D0 (en) | 2020-08-21 | 2020-08-21 | A screening method for the detection of DNA damage |
| PCT/EP2021/073203 WO2022038291A1 (en) | 2020-08-21 | 2021-08-20 | A method for the isolation of double-strand breaks |
Publications (3)
| Publication Number | Publication Date |
|---|---|
| JP2023539169A JP2023539169A (ja) | 2023-09-13 |
| JP2023539169A5 JP2023539169A5 (https=) | 2024-08-27 |
| JPWO2022038291A5 true JPWO2022038291A5 (https=) | 2024-08-27 |
Family
ID=72660690
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| JP2023512403A Pending JP2023539169A (ja) | 2020-08-21 | 2021-08-20 | 二本鎖切断を単離するための方法 |
Country Status (13)
| Country | Link |
|---|---|
| US (3) | US20240011095A1 (https=) |
| EP (2) | EP4368725B1 (https=) |
| JP (1) | JP2023539169A (https=) |
| KR (1) | KR20230057395A (https=) |
| CN (1) | CN116472356A (https=) |
| AU (1) | AU2021328724A1 (https=) |
| CA (1) | CA3188635A1 (https=) |
| DK (1) | DK4200443T3 (https=) |
| ES (1) | ES2984253T3 (https=) |
| FI (1) | FI4200443T3 (https=) |
| GB (1) | GB202013141D0 (https=) |
| IL (1) | IL300674A (https=) |
| WO (1) | WO2022038291A1 (https=) |
Families Citing this family (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| GB202013141D0 (en) | 2020-08-21 | 2020-10-07 | Univ College Cardiff Consultants Ltd | A screening method for the detection of DNA damage |
| GB202209189D0 (en) | 2022-06-22 | 2022-08-10 | Broken String Biosciences Ltd | Methods and compositions for nucleic acid sequencing |
| EP4569135A1 (en) | 2022-08-09 | 2025-06-18 | Institute of Molecular Biology gGmbH (IMB) | Method of parallel, rapid and sensitive detection of dna double strand breaks |
| EP4321630A1 (en) * | 2022-08-09 | 2024-02-14 | Institute of Molecular Biology gGmbH (IMB) | Method of parallel, rapid and sensitive detection of dna double strand breaks |
| GB202319988D0 (en) | 2023-12-22 | 2024-02-07 | Broken String Biosciences Ltd | Methods of detecting dsbs and mutations |
Family Cites Families (23)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| EP3722409A1 (en) | 2006-03-31 | 2020-10-14 | Illumina, Inc. | Systems and devices for sequence by synthesis analysis |
| CN104195227B (zh) | 2008-11-07 | 2017-04-12 | 适应生物技术公司 | 通过序列分析监测状况的方法 |
| WO2011086118A1 (en) | 2010-01-14 | 2011-07-21 | Deutsches Krebsforschungszentrum | In vivo determination of the lokalization of dna double-stand breaks and application thereof |
| US8951781B2 (en) | 2011-01-10 | 2015-02-10 | Illumina, Inc. | Systems, methods, and apparatuses to image a sample for biological or chemical analysis |
| WO2013006745A2 (en) | 2011-07-07 | 2013-01-10 | Immune Disease Institute, Inc. | High throughput genome-wide translocation sequencing |
| RU2694686C2 (ru) | 2013-03-12 | 2019-07-16 | Е.И.Дюпон Де Немур Энд Компани | Способы идентификации вариантных сайтов распознавания для редкощепящих сконструированных средств для индукции двунитевого разрыва, и композиции с ними, и их применения |
| DK2969479T3 (da) | 2013-03-13 | 2021-08-02 | Illumina Inc | Væskeanordninger i flere lag og fremgangsmåder til deres fremstilling |
| US10208338B2 (en) * | 2014-03-03 | 2019-02-19 | Swift Biosciences, Inc. | Enhanced adaptor ligation |
| EP3919621A1 (en) * | 2014-06-23 | 2021-12-08 | The General Hospital Corporation | Genomewide unbiased identification of dsbs evaluated by sequencing (guide-seq) |
| WO2016081798A1 (en) | 2014-11-20 | 2016-05-26 | Children's Medical Center Corporation | Methods relating to the detection of recurrent and non-specific double strand breaks in the genome |
| EP3234192B1 (en) | 2014-12-19 | 2021-07-14 | The Broad Institute, Inc. | Unbiased identification of double-strand breaks and genomic rearrangement by genome-wide insert capture sequencing |
| WO2016138080A1 (en) | 2015-02-24 | 2016-09-01 | Trustees Of Boston University | Protection of barcodes during dna amplification using molecular hairpins |
| JP2018530536A (ja) * | 2015-09-11 | 2018-10-18 | ザ ジェネラル ホスピタル コーポレイション | ヌクレアーゼＤＳＢの完全照合およびシーケンシング（ＦＩＮＤ−ｓｅｑ） |
| RU2018121254A (ru) * | 2015-11-11 | 2019-12-16 | Резолюшн Байосайенс, Инк. | Высокоэффективное построение библиотек днк |
| CA3010199A1 (en) * | 2016-02-11 | 2017-08-17 | Htg Molecular Diagnostics, Inc. | Method of direct target sequencing using nuclease protection |
| WO2017218979A1 (en) * | 2016-06-17 | 2017-12-21 | The Broad Institute, Inc. | Unbiased detection of nucleic acid modifications |
| CA3046617C (en) * | 2017-01-27 | 2023-02-14 | Integrated Dna Technologies, Inc. | Construction of next generation sequencing (ngs) libraries using competitive strand displacement |
| JP7062681B2 (ja) | 2017-03-20 | 2022-05-06 | イルミナ インコーポレイテッド | 核酸ライブラリを調製するための方法および組成物 |
| WO2019126774A1 (en) | 2017-12-22 | 2019-06-27 | The Broad Institute, Inc. | Novel crispr enzymes and systems |
| WO2019217816A1 (en) * | 2018-05-11 | 2019-11-14 | Pioneer Hi-Bred International, Inc. | Methods for the identification and characterization of double-strand break sites and compositions and uses thereof |
| EP3999651B1 (en) | 2019-08-26 | 2026-03-18 | Adoc Ssf, Llc | Methods of performing guide-seq on primary human t cells |
| AU2021311713A1 (en) | 2020-07-23 | 2023-03-09 | Integrated Dna Technologies, Inc. | Methods for nomination of nuclease on-/off-target editing locations, designated "CTL-seq" (CRISPR tag linear-seq) |
| GB202013141D0 (en) | 2020-08-21 | 2020-10-07 | Univ College Cardiff Consultants Ltd | A screening method for the detection of DNA damage |
-
2020
- 2020-08-21 GB GBGB2013141.3A patent/GB202013141D0/en not_active Ceased
-
2021
- 2021-08-20 EP EP24165314.6A patent/EP4368725B1/en active Active
- 2021-08-20 FI FIEP21766455.6T patent/FI4200443T3/fi active
- 2021-08-20 CN CN202180072261.2A patent/CN116472356A/zh active Pending
- 2021-08-20 EP EP21766455.6A patent/EP4200443B1/en active Active
- 2021-08-20 KR KR1020237009611A patent/KR20230057395A/ko active Pending
- 2021-08-20 ES ES21766455T patent/ES2984253T3/es active Active
- 2021-08-20 JP JP2023512403A patent/JP2023539169A/ja active Pending
- 2021-08-20 IL IL300674A patent/IL300674A/en unknown
- 2021-08-20 CA CA3188635A patent/CA3188635A1/en active Pending
- 2021-08-20 US US18/042,193 patent/US20240011095A1/en active Pending
- 2021-08-20 DK DK21766455.6T patent/DK4200443T3/da active
- 2021-08-20 AU AU2021328724A patent/AU2021328724A1/en active Pending
- 2021-08-20 WO PCT/EP2021/073203 patent/WO2022038291A1/en not_active Ceased
-
2024
- 2024-03-28 US US18/620,640 patent/US12428683B2/en active Active
- 2024-03-28 US US18/620,644 patent/US12421554B2/en active Active
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