Title:
ROLLING CIRCLE BASED METHODS IDENTIFYING NUCLEIC ACIDS
Document Type and Number:
WIPO Patent Application WO/2014/030066
Kind Code:
A3
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.
Inventors:
BERNITZ MATS NILSSON (SE)
LARSSON CHATARINA (SE)
GRUNDBERG IDA (SE)
LARSSON CHATARINA (SE)
GRUNDBERG IDA (SE)
Application Number:
PCT/IB2013/002256
Publication Date:
May 22, 2014
Filing Date:
August 22, 2013
Export Citation:
Assignee:
BERNITZ MATS NILSSON (SE)
LARSSON CHATARINA (SE)
GRUNDBERG IDA (SE)
LARSSON CHATARINA (SE)
GRUNDBERG IDA (SE)
International Classes:
C12Q1/68
Domestic Patent References:
| WO2012110899A2 | 2012-08-23 |
Other References:
CHATARINA LARSSON ET AL: "In situ detection and genotyping of individual mRNA molecules -supplementary data", NATURE METHODS, vol. 7, no. 5, 11 April 2010 (2010-04-11), pages 395 - 397, XP055035175, ISSN: 1548-7091, DOI: 10.1038/nmeth.1448
HENRIKSSON, SARA: "Application of Padlock Probe Based Nucleic Acid Analysis in stitu", 1 December 2010 (2010-12-01), XP055035269, ISSN: 1651-6206, ISBN: 978-91-554-7842-1, Retrieved from the Internet [retrieved on 20120810]
J. GORANSSON ET AL: "A single molecule array for digital targeted molecular analyses", NUCLEIC ACIDS RESEARCH, vol. 37, no. 1, 1 January 2009 (2009-01-01), pages e7 - e7, XP055069029, ISSN: 0305-1048, DOI: 10.1093/nar/gkn921
QI X ET AL: "L-RCA (ligation-rolling circle amplification): a general method for genotyping of single nucleotide polymorphisms (SNPs)", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, GB, vol. 29, no. 22, 15 November 2001 (2001-11-15), pages E116, XP002244483, ISSN: 0305-1048, DOI: 10.1093/NAR/29.22.E116
NELSON J R ET AL: "TempliPhi: .Phi.29 DNA polymerase based rolling circle amplification of templates for DNA sequencing", BIOTECHNIQUES, INFORMA HEALTHCARE, US, vol. 32, 1 June 2002 (2002-06-01), pages S44 - S47, XP002705298, ISSN: 0736-6205
JOHNE R ET AL: "Rolling-circle amplification of viral DNA genomes using phi29 polymerase", TRENDS IN MICROBIOLOGY, ELSEVIER SCIENCE LTD., KIDLINGTON, GB, vol. 17, no. 5, 1 May 2009 (2009-05-01), pages 205 - 211, XP026095083, ISSN: 0966-842X, [retrieved on 20090415], DOI: 10.1016/J.TIM.2009.02.004
E. MERKIENE ET AL: "Direct detection of RNA in vitro and in situ by target-primed RCA: The impact of E. coli RNase III on the detection efficiency of RNA sequences distanced far from the 3'-end", RNA, vol. 16, no. 8, 28 June 2010 (2010-06-28), pages 1508 - 1515, XP055035267, ISSN: 1355-8382, DOI: 10.1261/rna.2068510
NILSSON M ET AL: "Analyzing genes using closing and replicating circles", TRENDS IN BIOTECHNOLOGY, ELSEVIER PUBLICATIONS, CAMBRIDGE, GB, vol. 24, no. 2, 1 February 2006 (2006-02-01), pages 83 - 88, XP027921656, ISSN: 0167-7799, [retrieved on 20060201]
HENRIKSSON, SARA: "Application of Padlock Probe Based Nucleic Acid Analysis in stitu", 1 December 2010 (2010-12-01), XP055035269, ISSN: 1651-6206, ISBN: 978-91-554-7842-1, Retrieved from the Internet
J. GORANSSON ET AL: "A single molecule array for digital targeted molecular analyses", NUCLEIC ACIDS RESEARCH, vol. 37, no. 1, 1 January 2009 (2009-01-01), pages e7 - e7, XP055069029, ISSN: 0305-1048, DOI: 10.1093/nar/gkn921
QI X ET AL: "L-RCA (ligation-rolling circle amplification): a general method for genotyping of single nucleotide polymorphisms (SNPs)", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, GB, vol. 29, no. 22, 15 November 2001 (2001-11-15), pages E116, XP002244483, ISSN: 0305-1048, DOI: 10.1093/NAR/29.22.E116
NELSON J R ET AL: "TempliPhi: .Phi.29 DNA polymerase based rolling circle amplification of templates for DNA sequencing", BIOTECHNIQUES, INFORMA HEALTHCARE, US, vol. 32, 1 June 2002 (2002-06-01), pages S44 - S47, XP002705298, ISSN: 0736-6205
JOHNE R ET AL: "Rolling-circle amplification of viral DNA genomes using phi29 polymerase", TRENDS IN MICROBIOLOGY, ELSEVIER SCIENCE LTD., KIDLINGTON, GB, vol. 17, no. 5, 1 May 2009 (2009-05-01), pages 205 - 211, XP026095083, ISSN: 0966-842X, [retrieved on 20090415], DOI: 10.1016/J.TIM.2009.02.004
E. MERKIENE ET AL: "Direct detection of RNA in vitro and in situ by target-primed RCA: The impact of E. coli RNase III on the detection efficiency of RNA sequences distanced far from the 3'-end", RNA, vol. 16, no. 8, 28 June 2010 (2010-06-28), pages 1508 - 1515, XP055035267, ISSN: 1355-8382, DOI: 10.1261/rna.2068510
NILSSON M ET AL: "Analyzing genes using closing and replicating circles", TRENDS IN BIOTECHNOLOGY, ELSEVIER PUBLICATIONS, CAMBRIDGE, GB, vol. 24, no. 2, 1 February 2006 (2006-02-01), pages 83 - 88, XP027921656, ISSN: 0167-7799, [retrieved on 20060201]
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