WO2014030066A3 - Rolling circle based methods identifying nucleic acids - Google Patents

Rolling circle based methods identifying nucleic acids Download PDF

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Publication number
WO2014030066A3
WO2014030066A3 PCT/IB2013/002256 IB2013002256W WO2014030066A3 WO 2014030066 A3 WO2014030066 A3 WO 2014030066A3 IB 2013002256 W IB2013002256 W IB 2013002256W WO 2014030066 A3 WO2014030066 A3 WO 2014030066A3
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WIPO (PCT)
Prior art keywords
rolling circle
rna
nucleic acids
based methods
padlock probe
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PCT/IB2013/002256
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French (fr)
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WO2014030066A2 (en
Inventor
Mats Nilsson BERNITZ
Chatarina LARSSON
Ida GRUNDBERG
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Bernitz Mats Nilsson
Larsson Chatarina
Grundberg Ida
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Application filed by Bernitz Mats Nilsson, Larsson Chatarina, Grundberg Ida filed Critical Bernitz Mats Nilsson
Publication of WO2014030066A2 publication Critical patent/WO2014030066A2/en
Publication of WO2014030066A3 publication Critical patent/WO2014030066A3/en

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    • 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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • C—CHEMISTRY; METALLURGY
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    • 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
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    • 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
    • C12Q1/6841—In situ hybridisation
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    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/10—Nucleotidyl transfering
    • C12Q2521/107—RNA dependent DNA polymerase,(i.e. reverse transcriptase)
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/30—Phosphoric diester hydrolysing, i.e. nuclease
    • C12Q2521/327—RNAse, e.g. RNAseH
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    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/125—Modifications characterised by incorporating agents resulting in resistance to degradation
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    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/161—Modifications characterised by incorporating target specific and non-target specific sites
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    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/30—Oligonucleotides characterised by their secondary structure
    • C12Q2525/307—Circular oligonucleotides
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    • 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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    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/143—Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
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    • C12Q2543/00—Reactions characterised by the reaction site, e.g. cell or chromosome
    • C12Q2543/10—Reactions characterised by the reaction site, e.g. cell or chromosome the purpose being "in situ" analysis
    • C12Q2543/101—Reactions characterised by the reaction site, e.g. cell or chromosome the purpose being "in situ" analysis in situ amplification

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (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)

Abstract

Embodiments relate to the detection of RNA in a sample of cells. More particularly, methods concern the localized detection of RNA in situ. The method relies on the conversion of RNA to complementary DNA prior to the targeting of the cDNA with a padlock probe(s). The hybridization of the padlock probe(s) relies on the nucleotide sequence of the cDNA which is derived from the corresponding nucleotide sequence of the target RNA. Rolling circle amplification of the subsequently circularized padlock probe produces a rolling circle product which may be detected. Advantageously, this allows the RNA to be detected in situ. In additional methods, rolling circle amplification products are sequenced.
PCT/IB2013/002256 2012-08-22 2013-08-22 Methods for identifying nucleic acid sequences WO2014030066A2 (en)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US201261692208P 2012-08-22 2012-08-22
US61/692,208 2012-08-22
US201261705469P 2012-09-25 2012-09-25
US61/705,469 2012-09-25

Publications (2)

Publication Number Publication Date
WO2014030066A2 WO2014030066A2 (en) 2014-02-27
WO2014030066A3 true WO2014030066A3 (en) 2014-05-22

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PCT/IB2013/002256 WO2014030066A2 (en) 2012-08-22 2013-08-22 Methods for identifying nucleic acid sequences

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US20160108458A1 (en) * 2014-10-06 2016-04-21 The Board Of Trustees Of The Leland Stanford Junior University Multiplexed detection and quantification of nucleic acids in single-cells
US11046952B2 (en) 2015-03-16 2021-06-29 The Broad Institute, Inc. Encoding of DNA vector identity via iterative hybridization detection of a barcode transcript
WO2017081049A1 (en) * 2015-11-11 2017-05-18 Medizinische Universität Graz In vivo collection and localized quantification and profiling of circulating cells, proteins and nucleic acids
EP3472359B1 (en) 2016-06-21 2022-03-16 10X Genomics, Inc. Nucleic acid sequencing
CN111263819A (en) * 2017-10-06 2020-06-09 卡特阿纳公司 RNA templated ligation
EP4150126A2 (en) * 2020-05-12 2023-03-22 Singular Genomics Systems, Inc. Nucleic acid amplification methods
WO2021252375A1 (en) * 2020-06-08 2021-12-16 The Broad Institute, Inc. Single cell combinatorial indexing from amplified nucleic acids
WO2022032194A1 (en) 2020-08-06 2022-02-10 Singular Genomics Systems, Inc. Methods for in situ transcriptomics and proteomics
AU2022264021A1 (en) * 2021-04-29 2023-11-09 Illumina Cambridge Limited Amplification techniques for nucleic acid characterization
CN113481326B (en) * 2021-07-09 2022-11-22 安邦（厦门）生物科技有限公司 Isothermal nucleic acid amplification reaction reagent, isothermal nucleic acid amplification method and application thereof
CN113564230B (en) * 2021-07-27 2023-10-31 华侨大学 In-situ detection method for circular RNA
CN114921527A (en) * 2022-05-16 2022-08-19 华侨大学 Probe primer group for RNA in-situ detection and application thereof

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