SG10201808952WA - Systems and methods for clonal replication and amplification of nucleic acid molecules for genomic and therapeutic applications - Google Patents

Systems and methods for clonal replication and amplification of nucleic acid molecules for genomic and therapeutic applications

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Publication number
SG10201808952WA
SG10201808952WA SG10201808952WA SG10201808952WA SG10201808952WA SG 10201808952W A SG10201808952W A SG 10201808952WA SG 10201808952W A SG10201808952W A SG 10201808952WA SG 10201808952W A SG10201808952W A SG 10201808952WA SG 10201808952W A SG10201808952W A SG 10201808952WA
Authority
SG
Singapore
Prior art keywords
nucleic acid
amplification
replication
genomic
detection
Prior art date
Application number
SG10201808952WA
Inventor
Michael Metzker
Christopher Weier
Original Assignee
Redvault Biosciences Lp
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Publication date
Application filed by Redvault Biosciences Lp filed Critical Redvault Biosciences Lp
Publication of SG10201808952WA publication Critical patent/SG10201808952WA/en

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    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • C12Q1/6855—Ligating adaptors
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    • 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
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    • 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
    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/50—Other enzymatic activities
    • C12Q2521/501—Ligase
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    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/50—Other enzymatic activities
    • C12Q2521/507—Recombinase
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    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/50—Other enzymatic activities
    • C12Q2521/513—Winding/unwinding enzyme, e.g. helicase
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    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/50—Other enzymatic activities
    • C12Q2521/519—Topoisomerase
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    • C12Q2522/00—Reaction characterised by the use of non-enzymatic proteins
    • C12Q2522/10—Nucleic acid binding proteins
    • C12Q2522/101—Single or double stranded nucleic acid binding proteins
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    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/155—Modifications characterised by incorporating/generating a new priming site
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    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/179—Modifications characterised by incorporating arbitrary or random nucleotide sequences
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    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/30—Oligonucleotides characterised by their secondary structure
    • C12Q2525/301—Hairpin oligonucleotides
    • 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
    • C12Q2531/00—Reactions of nucleic acids characterised by
    • C12Q2531/10—Reactions of nucleic acids characterised by the purpose being amplify/increase the copy number of target nucleic acid
    • C12Q2531/125—Rolling circle

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • General Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Genetics & Genomics (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

SYSTEMSAND METHODS FOR CLONAL REPLICATION AND AMPLIFICATION OF NUCLEIC ACID MOLECULES FOR GENOMIC AND THERAPEUTIC APPLICATIONS The present invention provides for methods, reagents, apparatuses, and systems for the replication or amplification of nucleic acid molecules from biological samples. In one embodiment of the invention, the nucleic molecules are isolated from the sample, and subjected to fragmenting and joining using ligating agents of one or more hairpin structures to each end of the fragmented nucleic molecules to form one or more dumbbell templates. The one or more dumbbell templates are contacted with at least one substantially complementary primer attached to a substrate, and subjected to rolling circle replication or rolling circle amplification. The resulting replicated dumbbell templates or amplified dumbbell templates are used in numerous genomic applications, including whole genome de novo sequencing; sequence variant detection, structural variant detection, determining the phase of molecular haplotypes, molecular counting for aneuploidy detection; targeted sequencing of gene panels, whole exome, or chromosomal regions for sequence variant detection, structural variant detection, determining the phase of molecular haplotypes and/or molecular counting for aneuploidy detection; study of nucleic acid - nucleic acid binding interactions, nucleic acid - protein binding interactions, and nucleic acid molecule expression arrays; and testing of the effects of small molecule inhibitors or activators or nucleic acid therapeutics. No suitable figure
SG10201808952WA 2014-04-11 2015-04-11 Systems and methods for clonal replication and amplification of nucleic acid molecules for genomic and therapeutic applications SG10201808952WA (en)

Applications Claiming Priority (1)

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US201461978823P 2014-04-11 2014-04-11

Publications (1)

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SG10201808952WA true SG10201808952WA (en) 2018-11-29

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SG11201608486SA SG11201608486SA (en) 2014-04-11 2015-04-11 Systems and methods for clonal replication and amplification of nucleic acid molecules for genomic and therapeutic applications
SG10201808952WA SG10201808952WA (en) 2014-04-11 2015-04-11 Systems and methods for clonal replication and amplification of nucleic acid molecules for genomic and therapeutic applications

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Country Status (10)

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US (1) US20170067097A1 (en)
EP (1) EP3129505B1 (en)
JP (2) JP7058502B2 (en)
KR (1) KR102592367B1 (en)
CN (2) CN106460065A (en)
AU (1) AU2015243130B2 (en)
CA (1) CA2945358C (en)
DK (1) DK3129505T3 (en)
SG (2) SG11201608486SA (en)
WO (1) WO2015157747A1 (en)

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WO2018081666A1 (en) * 2016-10-28 2018-05-03 Silgentech Inc. Methods of single dna/rna molecule counting
EP3714064A1 (en) * 2017-11-21 2020-09-30 4Basebio SL Methods and kits for amplification of double stranded dna
KR102131494B1 (en) * 2018-04-17 2020-07-07 건국대학교 산학협력단 Detection of Target Nucleic Acid Sequences by PCR-coupled Rolling Circle Amplification
CN109055488B (en) * 2018-08-17 2021-11-02 中山康源基因技术科技有限公司 Method for preparing long probe by using annular single-chain probe and application of long probe in gene chip production
EP3650559B1 (en) * 2018-11-08 2022-06-29 Siemens Healthcare GmbH Direct rna nanopore sequencing with help of a stem-loop polynucleotide
CN118222672A (en) * 2018-12-05 2024-06-21 青岛华大智造科技有限责任公司 Rolling circle amplification method, sequencing library preparation method and DNA nanospheres prepared by adopting rolling circle amplification method
CN111378750A (en) * 2018-12-29 2020-07-07 北京福安华生物科技有限公司 Artificial mimic nucleic acid molecular beacon and kit for detecting rs885004 site polymorphism of SLC28A3 gene
GB201911421D0 (en) * 2019-08-09 2019-09-25 Dnae Diagnostics Ltd Methods of multiplexed isothermal amplification of nucleic acid sequences
CN111139289A (en) * 2019-12-25 2020-05-12 中国海洋大学 Constant-temperature rolling ring amplification method based on dumbbell ring template
CA3164390A1 (en) * 2020-01-31 2021-08-05 Tyris Therapeutics, S.L. Closed linear dna with modified nucleotides
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WO2023049937A2 (en) * 2021-09-27 2023-03-30 Intergalactic Therapeutics, Inc. Synthetic production of circular dna vectors
WO2024175089A1 (en) * 2023-02-23 2024-08-29 Centre For Novostics Single-molecule strand-specific end modalities

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CA2360342A1 (en) * 1999-12-02 2001-06-07 Molecular Staging Inc. Generation of single-strand circular dna from linear self-annealing segments
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WO2005059157A2 (en) * 2003-12-11 2005-06-30 The Board Of Trustees Of The Leland Stanford Junior University METHODS AND COMPOSITIONS FOR USE IN PREPARING HAIRPIN RNAs
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Also Published As

Publication number Publication date
AU2015243130B2 (en) 2021-08-26
KR20160138579A (en) 2016-12-05
JP2017512071A (en) 2017-05-18
WO2015157747A9 (en) 2016-08-25
EP3129505A4 (en) 2017-12-06
JP7100680B2 (en) 2022-07-13
DK3129505T3 (en) 2021-10-04
JP2020188774A (en) 2020-11-26
WO2015157747A1 (en) 2015-10-15
AU2015243130A1 (en) 2016-11-03
SG11201608486SA (en) 2016-11-29
CN106460065A (en) 2017-02-22
JP7058502B2 (en) 2022-04-22
EP3129505B1 (en) 2021-06-30
EP3129505A1 (en) 2017-02-15
CA2945358C (en) 2022-12-06
KR102592367B1 (en) 2023-10-26
CN113528628A (en) 2021-10-22
US20170067097A1 (en) 2017-03-09
CA2945358A1 (en) 2015-10-15

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