Title:
METHODS AND KITS FOR AMPLIFICATION AND DETECTION OF NUCLEIC ACIDS
Document Type and Number:
WIPO Patent Application WO/2021/147910
Kind Code:
A1
Abstract:
Provided herein is a method for denaturation bubble-mediated target nucleic acid amplification and related kits and uses thereof. The method facilitates the generation of denaturation bubbles in a duplex target nucleic acid molecule through the application of swift temperature changes during a thermal cycle, thereby accelerating the strand exchange amplification (SEA) reaction. The kits comprise specially designed primers and polymerase configured for performing the method. The methods and kits disclosed herein can be used under various scenarios, such as diagnosis of infectious or genetic diseases, sample quality control, and single nucleotide polymorphism (SNP) profiling.
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Inventors:
SHI CHAO (CN)
MA CUIPING (CN)
LIU MENGMENG (CN)
LI YANG (CN)
MA CUIPING (CN)
LIU MENGMENG (CN)
LI YANG (CN)
Application Number:
PCT/CN2021/072900
Publication Date:
July 29, 2021
Filing Date:
January 20, 2021
Export Citation:
Assignee:
QINGDAO NAVID BIOTECHNOLOGY CO LTD (CN)
International Classes:
C12Q1/6844
Foreign References:
| US20140045221A1 | 2014-02-13 | |||
| CN109136337A | 2019-01-04 | |||
| CN109136337A | 2019-01-04 | |||
| US5965408A | 1999-10-12 | |||
| CN105176971A | 2015-12-23 |
Other References:
SHI WENQIANG ET AL: "Rapid diagnosis of Mycoplasma pneumonia infection by denaturation bubble-mediated strand exchange amplification: comparison with LAMP and real- time PCR", SCIENTIFIC REPORTS |, vol. 9, 1 January 2019 (2019-01-01), pages 896, XP055801084, Retrieved from the Internet DOI: 10.1038/s41598-018-36751-z
ZHANG MEILING ET AL: "Rapid detection of foodborne pathogen Listeria monocytogenes by strand exchange amplification", ANALYTICAL BIOCHEMISTRY, vol. 545, 1 March 2018 (2018-03-01), Amsterdam, NL, pages 38 - 42, XP055801342, ISSN: 0003-2697, DOI: 10.1016/j.ab.2018.01.013
YANG CHEN ET AL: "Accurate, rapid and low-cost diagnosis ofvia fast narrow-thermal-cycling denaturation bubble-mediated strand exchange amplification", ANALYTICAL AND BIOANALYTICAL CHEMISTRY, vol. 412, no. 30, 11 October 2020 (2020-10-11), pages 8391 - 8399, XP037300502, ISSN: 1618-2642, DOI: 10.1007/S00216-020-02977-Y
DENG JIE ET AL: "Primer design strategy for denaturation bubble-mediated strand exchange amplification", ANALYTICAL BIOCHEMISTRY, ACADEMIC PRESS, AMSTERDAM, NL, vol. 593, 21 January 2020 (2020-01-21), XP086073669, ISSN: 0003-2697, [retrieved on 20200121], DOI: 10.1016/J.AB.2020.113593
SHI ET AL.: "Triggered isothermal PCR by denaturation bubble-mediated strand exchange amplification", CHEM COMMUN (CAMB, vol. 52, no. 77, 2016, pages 11551 - 4
COCO ET AL., NAT. BIOTECHNOL, vol. 19, 2001, pages 354 - 359
ZHAO ET AL., NAT. BIOTECHNOL, vol. 16, 1998, pages 258 - 261
SHI ET AL.: "Innate reverse transcriptase activity of DNA polymerase for isothermal RNA direct detection", J. AM. CHEM. SOC., vol. 137, 2015, pages 13804 - 13806, XP055701728, DOI: 10.1021/jacs.5b08144
BATZER, M.A. ET AL., NUCLEIC ACID RES., vol. 19, 1991, pages 5081 - 1585
OHTSUKA, E., J. BIOL. CHEM., vol. 260, 1985, pages 2605 - 2608
ROSSOLINI, G.M. ET AL., IWOL CELL. PROBES, vol. 8, 1994, pages 91 - 98
ZENG ET AL., STRAND DISPLACEMENT AMPLIFICATION FOR MULTIPLEX DETECTION OF NUCLEIC ACIDS, 2018
CHANDER ET AL.: "A novel thermostable polymerase for RNA and DNA loop-mediated isothermal amplification (LAMP", FRONT. ALICROBIOL., vol. 5, 2014, pages 395
SANCHEZ ET AL.: "DNA kinks and bubbles: temperature dependence of the elastic energy of sharply bent 10-nm-size DNA molecules", PHYSICAL REVIEW E, vol. 87, 2013, pages 22710
ADAMCIK ET AL.: "Quantifying supercoiling-induced denaturation bubbles in DNA", SOFT MATTER, vol. 8, 2012, pages 8651 - 8658
KUCERA ET AL.: "DNA-dependent DNA polymerases", CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, vol. 84, 2008, pages 3 - 5
KWOK ET AL.: "Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies", NUCLEIC ACIDS RES., vol. 18, 1990, pages 999 - 1005
RODRIGUEZ-LAZARO: "Real-time PCR in food science: introduction", CURR. ISSUES MOL. BIOL, vol. 529, 2013, pages 25 - 38
RAYMAEKERS: "Checklist for optimization and validation of real-time PCR assays", J. CLIN. LAB. ANAL., vol. 23, 2009, pages 145 - 151
MEAGHER ET AL.: "Impact of primer dimers and self-amplifying hairpins on reverse transcription loop-mediated isothermal amplification detection of viral RNA", ANALYST, vol. 143, 2018, pages 1924 - 1933
FOX, R.J. ET AL., TRENDS BIOTECHNOL., vol. 26, 2008, pages 132 - 138
FOX, R.J. ET AL., NATURE BIOTECHNOL, vol. 25, 2007, pages 338 - 344
HIBBERT, BIOMOL.ENG., vol. 22, 2005, pages 11 - 19
SEN ET AL., APPL. BIOCHEM.BIOTECHNOL., vol. 143, 2007, pages 212 - 223
BERGQUIST ET AL., BIOMOL. ENG., vol. 22, 2005, pages 63 - 72
PRITCHARD ET AL., J. THEOR.BIOL., vol. 234, 2005, pages 497 - 509
WONG ET AL., NUCLEIC ACIDS RES., vol. 32, 2004, pages el45
FUJII ET AL., NAT. PROTOC., vol. 1, 2006, pages 2493 - 2497
STEMMER, PROC. NATL. ACAD. SCI. U.S.A., vol. 91, 1994, pages 10747 - 10751
STEMMER, NATURE, vol. 370, 1994, pages 389 - 391
SHAO ET AL.: "DNA tetraplex formation in the control region of c-myc", NUCLEIC ACIDS RES., vol. 26, 1998, pages 1167 - 1172
VOLKOV ET AL., NUCLEIC ACIDS RES., vol. 27, 1999, pages el8
VOLKOV ET AL., METHODS ENZYMOL., vol. 328, 2000, pages 456 - 463
LEE ET AL., J. MOL. CAT., vol. 26, 2003, pages 119 - 129
BERGQUISTGIBBS, METHODS MOL. BIOI., vol. 352, 2007, pages 191 - 204
GIBBS ET AL., GENE, vol. 271, 2001, pages 13 - 20
OSTERMEIER ET AL., PROC. NAIL. ACAD. SCI. U.S.A., vol. 96, 1999, pages 3562 - 3567
OSTERMEIER ET AL., NAT. BIOTECHNOL., vol. 17, 1999, pages 1205 - 1209
LUTZ ET AL., NUCLEIC ACIDS RES., vol. 29, 2001, pages E16
LUTZ ET AL., PROC. NATL. ACAD. SCI. U.S.A., vol. 98, 2001, pages 11248 - 11253
WONG ET AL., BIOTECHNOL. J., vol. 3, 2008, pages 74 - 82
WONG ET AL., ANAL. BIOCHEM., vol. 341, 2005, pages 187 - 189
NESS ET AL., NAT. BIOTECHNOL., vol. 20, 2002, pages 1251 - 1255
WALKER ET AL., NUCLEIC ACIDS RES., vol. 20, no. 7, 11 April 1992 (1992-04-11), pages 1691 - 1696
SIEBER ET AL., NAT. BIOTECHNOL., vol. 19, 2001, pages 456 - 460
KRETZ, METHODS ENZYMOL., vol. 388, 2004, pages 3 - 11
REIDHAAR-OLSON ET AL., METHODS ENZYMOL., vol. 208, 1991, pages 564 - 586
REIDHAAR-OLSON ET AL., SCIENCE, vol. 241, 1988, pages 53 - 57
REETZ ET AL., ANGEW. CHEM. INT. ED ENGL., vol. 40, 2001, pages 3589 - 3591
SELIFONOVA ET AL., APPL. ENVIRON. MICROBIOL., vol. 67, 2001, pages 3645 - 3649
LOW ET AL., J. MOL. BIOL., vol. 260, 1996, pages 3659 - 3680
RAJPAL ET AL., PROC. NATL..ACAD. SCI. U.S.A., vol. 102, 2005, pages 8466 - 8471
HAYES, PROC. NATL. ACAD. SCI. U.S.A., vol. 99, 2002, pages 15926 - 15931
REETZ ET AL., NAT. PROTOC., vol. 2, 2007, pages 891 - 903
REETZ ET AL., ANGEW. CHEM. INT. ED ENGL., vol. 45, 2006, pages 7745 - 7751
SHIN, D.-S. ET AL., J. BIOCHEM. MOL. BIO., vol. 38, 2005, pages 517 - 525
GUO, NUCLEIC ACIDS RES., vol. 37, 1 February 2009 (2009-02-01), pages e20
RYCHLIK ET AL., NUCLEIC ACIDS RES., vol. 18, no. 21, 21 November 1990 (1990-11-21), pages 6409 - 6412
SHI, J. AM. CHEM. SOC., vol. 137, no. 43, 16 October 2015 (2015-10-16), pages 13804 - 13806
LANFORD ET AL., J. VIROL., vol. 69, no. 7, 21 April 1995 (1995-04-21), pages 4431 - 4439
HOLLAND ET AL., P. NATL. ACAD. SCI. USA, vol. 88, no. 16, 15 August 1991 (1991-08-15), pages 7276 - 7280
BEESE ET AL., EMBO J., vol. 10, no. 1, 1 January 1991 (1991-01-01), pages 25 - 33
ULLMAN, C.G., BRIEFINGS FUNCTIONAL GENOMICS, vol. 10, 2011, pages 125 - 134
SHI ET AL.: "Triggered isothermal PCR- by denaturation bubble-mediated strand exchange amplification", CHEM COMMUN (CAMB, vol. 52, no. 77, 2016, pages 11551 - 4
ZHANG ET AL.: "Rapid detection of foodborne pathogen Listeria monocytogenes by strand exchange amplification", ANALYTICAL BIOCHEMISTRY, vol. 545, 2018, pages 38 - 42
SHI ET AL.: "Rapid diagnosis of Mycoplasma pneumonia infection by denaturation bubble-mediated strand exchange amplification: comparison with LAMP and real-time PCR", SCIENTIFIC REPORTS, vol. 9, no. 896, 2019
LIU ET AL.: "Rapid and Simple Detection of Viable Foodborne Pathogen Staphylococcus aureus", FRONT CHEM., vol. 7, 12 March 2019 (2019-03-12), pages 124
LIU ET AL.: "The Rapid detection of the Bursaphelenchus Xylophilus by Denaturation Bubble-mediated Strand Exchange Amplification", ANAL. SCI., 2019, pages 18,461P
LIU ET AL.: "A simple isothermal nucleic acid amplification method for the effective on-site identification for adulteration of pork source in mutton", FOOD CONTROL, vol. 98, 2019, pages 297 - 302
SHI ET AL.: "Innate reverse transcriptase activity of DNA polymerase for isothermal RNA direct detection", J AM. CHEM. SOC., vol. 137, 2015, pages 13804 - 13806, XP055701728, DOI: 10.1021/jacs.5b08144
THORNTON ET AL.: "Real-time PCR (qPCR) primer design using free online softwar", BIOCHEM. MOL. BIOI. EDU., vol. 39, 2011, pages 145 - 154, XP055198714, DOI: 10.1002/bmb.20461
LIM ET AL.: "Design and use of group-specific primers and probes for real-time quantitative PCR", FRONTIERS OF ENVIRONMENTAL SCIENCE & ENGINEERING IN CHINA, vol. 5, 2011, pages 28 - 39
ZHANG MEILING ET AL: "Rapid detection of foodborne pathogen Listeria monocytogenes by strand exchange amplification", ANALYTICAL BIOCHEMISTRY, vol. 545, 1 March 2018 (2018-03-01), Amsterdam, NL, pages 38 - 42, XP055801342, ISSN: 0003-2697, DOI: 10.1016/j.ab.2018.01.013
YANG CHEN ET AL: "Accurate, rapid and low-cost diagnosis ofvia fast narrow-thermal-cycling denaturation bubble-mediated strand exchange amplification", ANALYTICAL AND BIOANALYTICAL CHEMISTRY, vol. 412, no. 30, 11 October 2020 (2020-10-11), pages 8391 - 8399, XP037300502, ISSN: 1618-2642, DOI: 10.1007/S00216-020-02977-Y
DENG JIE ET AL: "Primer design strategy for denaturation bubble-mediated strand exchange amplification", ANALYTICAL BIOCHEMISTRY, ACADEMIC PRESS, AMSTERDAM, NL, vol. 593, 21 January 2020 (2020-01-21), XP086073669, ISSN: 0003-2697, [retrieved on 20200121], DOI: 10.1016/J.AB.2020.113593
SHI ET AL.: "Triggered isothermal PCR by denaturation bubble-mediated strand exchange amplification", CHEM COMMUN (CAMB, vol. 52, no. 77, 2016, pages 11551 - 4
COCO ET AL., NAT. BIOTECHNOL, vol. 19, 2001, pages 354 - 359
ZHAO ET AL., NAT. BIOTECHNOL, vol. 16, 1998, pages 258 - 261
SHI ET AL.: "Innate reverse transcriptase activity of DNA polymerase for isothermal RNA direct detection", J. AM. CHEM. SOC., vol. 137, 2015, pages 13804 - 13806, XP055701728, DOI: 10.1021/jacs.5b08144
BATZER, M.A. ET AL., NUCLEIC ACID RES., vol. 19, 1991, pages 5081 - 1585
OHTSUKA, E., J. BIOL. CHEM., vol. 260, 1985, pages 2605 - 2608
ROSSOLINI, G.M. ET AL., IWOL CELL. PROBES, vol. 8, 1994, pages 91 - 98
ZENG ET AL., STRAND DISPLACEMENT AMPLIFICATION FOR MULTIPLEX DETECTION OF NUCLEIC ACIDS, 2018
CHANDER ET AL.: "A novel thermostable polymerase for RNA and DNA loop-mediated isothermal amplification (LAMP", FRONT. ALICROBIOL., vol. 5, 2014, pages 395
SANCHEZ ET AL.: "DNA kinks and bubbles: temperature dependence of the elastic energy of sharply bent 10-nm-size DNA molecules", PHYSICAL REVIEW E, vol. 87, 2013, pages 22710
ADAMCIK ET AL.: "Quantifying supercoiling-induced denaturation bubbles in DNA", SOFT MATTER, vol. 8, 2012, pages 8651 - 8658
KUCERA ET AL.: "DNA-dependent DNA polymerases", CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, vol. 84, 2008, pages 3 - 5
KWOK ET AL.: "Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies", NUCLEIC ACIDS RES., vol. 18, 1990, pages 999 - 1005
RODRIGUEZ-LAZARO: "Real-time PCR in food science: introduction", CURR. ISSUES MOL. BIOL, vol. 529, 2013, pages 25 - 38
RAYMAEKERS: "Checklist for optimization and validation of real-time PCR assays", J. CLIN. LAB. ANAL., vol. 23, 2009, pages 145 - 151
MEAGHER ET AL.: "Impact of primer dimers and self-amplifying hairpins on reverse transcription loop-mediated isothermal amplification detection of viral RNA", ANALYST, vol. 143, 2018, pages 1924 - 1933
FOX, R.J. ET AL., TRENDS BIOTECHNOL., vol. 26, 2008, pages 132 - 138
FOX, R.J. ET AL., NATURE BIOTECHNOL, vol. 25, 2007, pages 338 - 344
HIBBERT, BIOMOL.ENG., vol. 22, 2005, pages 11 - 19
SEN ET AL., APPL. BIOCHEM.BIOTECHNOL., vol. 143, 2007, pages 212 - 223
BERGQUIST ET AL., BIOMOL. ENG., vol. 22, 2005, pages 63 - 72
PRITCHARD ET AL., J. THEOR.BIOL., vol. 234, 2005, pages 497 - 509
WONG ET AL., NUCLEIC ACIDS RES., vol. 32, 2004, pages el45
FUJII ET AL., NAT. PROTOC., vol. 1, 2006, pages 2493 - 2497
STEMMER, PROC. NATL. ACAD. SCI. U.S.A., vol. 91, 1994, pages 10747 - 10751
STEMMER, NATURE, vol. 370, 1994, pages 389 - 391
SHAO ET AL.: "DNA tetraplex formation in the control region of c-myc", NUCLEIC ACIDS RES., vol. 26, 1998, pages 1167 - 1172
VOLKOV ET AL., NUCLEIC ACIDS RES., vol. 27, 1999, pages el8
VOLKOV ET AL., METHODS ENZYMOL., vol. 328, 2000, pages 456 - 463
LEE ET AL., J. MOL. CAT., vol. 26, 2003, pages 119 - 129
BERGQUISTGIBBS, METHODS MOL. BIOI., vol. 352, 2007, pages 191 - 204
GIBBS ET AL., GENE, vol. 271, 2001, pages 13 - 20
OSTERMEIER ET AL., PROC. NAIL. ACAD. SCI. U.S.A., vol. 96, 1999, pages 3562 - 3567
OSTERMEIER ET AL., NAT. BIOTECHNOL., vol. 17, 1999, pages 1205 - 1209
LUTZ ET AL., NUCLEIC ACIDS RES., vol. 29, 2001, pages E16
LUTZ ET AL., PROC. NATL. ACAD. SCI. U.S.A., vol. 98, 2001, pages 11248 - 11253
WONG ET AL., BIOTECHNOL. J., vol. 3, 2008, pages 74 - 82
WONG ET AL., ANAL. BIOCHEM., vol. 341, 2005, pages 187 - 189
NESS ET AL., NAT. BIOTECHNOL., vol. 20, 2002, pages 1251 - 1255
WALKER ET AL., NUCLEIC ACIDS RES., vol. 20, no. 7, 11 April 1992 (1992-04-11), pages 1691 - 1696
SIEBER ET AL., NAT. BIOTECHNOL., vol. 19, 2001, pages 456 - 460
KRETZ, METHODS ENZYMOL., vol. 388, 2004, pages 3 - 11
REIDHAAR-OLSON ET AL., METHODS ENZYMOL., vol. 208, 1991, pages 564 - 586
REIDHAAR-OLSON ET AL., SCIENCE, vol. 241, 1988, pages 53 - 57
REETZ ET AL., ANGEW. CHEM. INT. ED ENGL., vol. 40, 2001, pages 3589 - 3591
SELIFONOVA ET AL., APPL. ENVIRON. MICROBIOL., vol. 67, 2001, pages 3645 - 3649
LOW ET AL., J. MOL. BIOL., vol. 260, 1996, pages 3659 - 3680
RAJPAL ET AL., PROC. NATL..ACAD. SCI. U.S.A., vol. 102, 2005, pages 8466 - 8471
HAYES, PROC. NATL. ACAD. SCI. U.S.A., vol. 99, 2002, pages 15926 - 15931
REETZ ET AL., NAT. PROTOC., vol. 2, 2007, pages 891 - 903
REETZ ET AL., ANGEW. CHEM. INT. ED ENGL., vol. 45, 2006, pages 7745 - 7751
SHIN, D.-S. ET AL., J. BIOCHEM. MOL. BIO., vol. 38, 2005, pages 517 - 525
GUO, NUCLEIC ACIDS RES., vol. 37, 1 February 2009 (2009-02-01), pages e20
RYCHLIK ET AL., NUCLEIC ACIDS RES., vol. 18, no. 21, 21 November 1990 (1990-11-21), pages 6409 - 6412
SHI, J. AM. CHEM. SOC., vol. 137, no. 43, 16 October 2015 (2015-10-16), pages 13804 - 13806
LANFORD ET AL., J. VIROL., vol. 69, no. 7, 21 April 1995 (1995-04-21), pages 4431 - 4439
HOLLAND ET AL., P. NATL. ACAD. SCI. USA, vol. 88, no. 16, 15 August 1991 (1991-08-15), pages 7276 - 7280
BEESE ET AL., EMBO J., vol. 10, no. 1, 1 January 1991 (1991-01-01), pages 25 - 33
ULLMAN, C.G., BRIEFINGS FUNCTIONAL GENOMICS, vol. 10, 2011, pages 125 - 134
SHI ET AL.: "Triggered isothermal PCR- by denaturation bubble-mediated strand exchange amplification", CHEM COMMUN (CAMB, vol. 52, no. 77, 2016, pages 11551 - 4
ZHANG ET AL.: "Rapid detection of foodborne pathogen Listeria monocytogenes by strand exchange amplification", ANALYTICAL BIOCHEMISTRY, vol. 545, 2018, pages 38 - 42
SHI ET AL.: "Rapid diagnosis of Mycoplasma pneumonia infection by denaturation bubble-mediated strand exchange amplification: comparison with LAMP and real-time PCR", SCIENTIFIC REPORTS, vol. 9, no. 896, 2019
LIU ET AL.: "Rapid and Simple Detection of Viable Foodborne Pathogen Staphylococcus aureus", FRONT CHEM., vol. 7, 12 March 2019 (2019-03-12), pages 124
LIU ET AL.: "The Rapid detection of the Bursaphelenchus Xylophilus by Denaturation Bubble-mediated Strand Exchange Amplification", ANAL. SCI., 2019, pages 18,461P
LIU ET AL.: "A simple isothermal nucleic acid amplification method for the effective on-site identification for adulteration of pork source in mutton", FOOD CONTROL, vol. 98, 2019, pages 297 - 302
SHI ET AL.: "Innate reverse transcriptase activity of DNA polymerase for isothermal RNA direct detection", J AM. CHEM. SOC., vol. 137, 2015, pages 13804 - 13806, XP055701728, DOI: 10.1021/jacs.5b08144
THORNTON ET AL.: "Real-time PCR (qPCR) primer design using free online softwar", BIOCHEM. MOL. BIOI. EDU., vol. 39, 2011, pages 145 - 154, XP055198714, DOI: 10.1002/bmb.20461
LIM ET AL.: "Design and use of group-specific primers and probes for real-time quantitative PCR", FRONTIERS OF ENVIRONMENTAL SCIENCE & ENGINEERING IN CHINA, vol. 5, 2011, pages 28 - 39
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