[논문]Ultrasensitive nucleic acid detection based on phosphorothioated hairpin-assisted isothermal amplification

Jung, Yujin; Song, Jayeon; Park, Hyun Gyu

doi:10.1038/s41598-021-87948-8

[해외논문] Ultrasensitive nucleic acid detection based on phosphorothioated hairpin-assisted isothermal amplification 원문보기

Scientific reports, v.11 no.1, 2021년, pp.8399 -

Jung, Yujin (Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141 Republic of Korea) , Song, Jayeon (Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141 Republic of Korea) , Park, Hyun Gyu (Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141 Republic of Korea)

Abstract ▼ AI-Helper

Herein, we describe a phosphorothioated hairpin-assisted isothermal amplification (PHAmp) method for detection of a target nucleic acid. The hairpin probe (HP) is designed to contain a 5′ phosphorothioate (PS)-modified overhang, a target recognition site, and a 3′ self-priming (SP) region. Upon binding to the target nucleic acid, the HP opens and the SP region is rearranged to serve as a primer. The subsequent process of strand displacement DNA synthesis recycles the bound target to open another HP and produces an extended HP (EP) with a PS-DNA/DNA duplex at the end, which would be readily denatured due to its reduced thermal stability. The trigger then binds to the denatured 3′ end of the EP and is extended, producing an intermediate double-stranded (ds) DNA product (IP). The trigger also binds to the denatured 3′ end of the IP, and its extension produces the final dsDNA product along with concomitant displacement and recycling of EP. By monitoring the dsDNA products, the target nucleic acid can be identified down to 0.29 fM with a wide dynamic range from 1 nM to 1 fM yielding an excellent specificity to discriminate even a single base-mismatched target. The unique design principle could provide new insights into the development of novel isothermal amplification methods for nucleic acid detection.

참고문헌 (47)

1. Li J Macdonald J Advances in isothermal amplification: novel strategies inspired by biological processes Biosens. Bioelectron. 2015 64 196 211 10.1016/j.bios.2014.08.069 25218104

상세보기
2. Gill P Ghaemi A Nucleic acid isothermal amplification technologies―a review Nucleos. Nucleot. Nucl. 2008 27 224 243 10.1080/15257770701845204

상세보기
3. Erlich HA Gelfand D Sninsky JJ Recent advances in the polymerase chain reaction Science 1991 252 1643 1651 10.1126/science.2047872 2047872

상세보기
4. Saiki RK Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase Science 1988 239 487 491 10.1126/science.239.4839.487 2448875

상세보기
5. Minero GAS Automated on-chip analysis of tuberculosis drug-resistance mutation with integrated DNA ligation and amplification Anal. Bioanal. Chem. 2020 2020 1 6
6. Walker GT Little MC Nadeau JG Shank DD Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system Proc. Natl. Acad. Sci. USA. 1992 89 392 396 10.1073/pnas.89.1.392 1309614

상세보기
7. Spargo C Detection ofM. tuberculosisDNA using thermophilic strand displacement amplification Mol. Cell. Probes. 1996 10 247 256 10.1006/mcpr.1996.0034 8865173

상세보기
8. Compton J Nucleic acid sequence-based amplification Nature 1991 350 91 92 10.1038/350091a0 1706072

상세보기
9. Guatelli JC Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication Proc. Natl. Acad. Sci. USA. 1990 87 1874 1878 10.1073/pnas.87.5.1874 2308948

상세보기
10. Fire A Xu S-Q Rolling replication of short DNA circles Proc. Natl. Acad. Sci. USA. 1995 92 4641 4645 10.1073/pnas.92.10.4641 7753856

상세보기
11. Lizardi PM Mutation detection and single-molecule counting using isothermal rolling-circle amplification Nat. Genet. 1998 19 225 10.1038/898 9662393

상세보기
12. Park KW Lee CY Batule BS Park KS Park HG Ultrasensitive DNA detection based on target-triggered rolling circle amplification and fluorescent poly (thymine)-templated copper nanoparticles RSC Adv. 2018 8 1958 1962 10.1039/C7RA11071E

상세보기
13. Vincent M Xu Y Kong H Helicase-dependent isothermal DNA amplification EMBO Rep. 2004 5 795 800 10.1038/sj.embor.7400200 15247927

상세보기
14. An L Characterization of a thermostable UvrD helicase and its participation in helicase-dependent amplification J. Biol. Chem. 2005 280 28952 28958 10.1074/jbc.M503096200 15955821

상세보기
15. Piepenburg O Williams CH Stemple DL Armes NA DNA detection using recombination proteins PLoS Biol. 2006 4 e204 10.1371/journal.pbio.0040204 16756388

상세보기
16. Crannell ZA Rohrman B Richards-Kortum R Quantification of HIV-1 DNA using real-time recombinase polymerase amplification Anal. Chem. 2014 86 5615 5619 10.1021/ac5011298 24873435

상세보기
17. Van Ness J Van Ness LK Galas DJ Isothermal reactions for the amplification of oligonucleotides Proc. Natl. Acad. Sci. USA. 2003 100 4504 4509 10.1073/pnas.0730811100 12679520

상세보기
18. Park KW Batule BS Kang KS Park KS Park HG Rapid and ultrasensitive detection of microRNA by target-assisted isothermal exponential amplification coupled with poly (thymine)-templated fluorescent copper nanoparticles Nanotechnology 2016 27 425502 10.1088/0957-4484/27/42/425502 27622680

상세보기
19. Jung C Chung JW Kim UO Kim MH Park HG Isothermal target and signaling probe amplification method, based on a combination of an isothermal chain amplification technique and a fluorescence resonance energy transfer cycling probe technology Anal. Chem. 2010 82 5937 5943 10.1021/ac100606m 20575518

상세보기
20. Jung C Real-time colorimetric detection of target DNA using isothermal target and signaling probe amplification and gold nanoparticle cross-linking assay Biosens. Bioelectron. 2011 26 1953 1958 10.1016/j.bios.2010.07.088 20970981

상세보기
21. Notomi T Loop-mediated isothermal amplification of DNA Nucl. Acids Res. 2000 28 e63 e63 10.1093/nar/28.12.e63 10871386
22. Mori Y Hirano T Notomi T Sequence specific visual detection of LAMP reactions by addition of cationic polymers BMC Biotechnol. 2006 6 3 10.1186/1472-6750-6-3 16401354

상세보기
23. Lee S Jang H Kim HY Park HG Three-way junction-induced isothermal amplification for nucleic acid detection Biosens. Bioelectron. 2020 147 111762 10.1016/j.bios.2019.111762 31654822

상세보기
24. Jang H Lee CY Lee S Park KS Park HG Flap endonuclease-initiated enzymatic repairing amplification for ultrasensitive detection of target nucleic acids Nanoscale 2019 11 3633 3638 10.1039/C8NR06699J 30741288

상세보기
25. Song JY Jung Y Lee S Park HG Self-priming hairpin-utilized isothermal amplification enabling ultrasensitive nucleic acid detection Anal. Chem. 2020 92 10350 10356 10.1021/acs.analchem.0c00511 32551503

상세보기
26. Golinelli M-P Hughes SH Self-priming of retroviral minus-strand strong-stop DNAs Viorology 2001 285 278 290 10.1006/viro.2001.0970

상세보기
27. Zhang X Lowe SB Gooding JJ Brief review of monitoring methods for loop-mediated isothermal amplification (LAMP) Biosens. Bioelectron. 2014 61 491 499 10.1016/j.bios.2014.05.039 24949822

상세보기
28. Minero GAS Sequence-specific validation of LAMP amplicons in real-time optomagnetic detection of Dengue serotype 2 synthetic DNA Analyst 2017 142 3441 3450 10.1039/C7AN01023K 28828442

상세보기
29. Boczkowska M Guga P Stec WJ Stereodefined phosphorothioate analogues of DNA: relative thermodynamic stability of the model PS-DNA/DNA and PS-DNA/RNA complexes Biochemistry 2002 41 12483 12487 10.1021/bi026225z 12369839

상세보기
30. LaPlanche LA Phosphorothioate-modified oligodeoxyribonucleotides. III. NMR and UV spectroscoptc studies of the R p-R p, S p-S p, and R p-S p duplexes,[d (GGsAATTCC)] 2, derived from diastereomeric O-ethyl phosphorothioates Nucl. Acids Res. 1986 14 9081 9093 10.1093/nar/14.22.9081 3786144
31. Cai S Jung C Bhadra S Ellington AD Phosphorothioated primers lead to loop-mediated isothermal amplification at low temperatures Anal. Chem. 2018 90 8290 8294 10.1021/acs.analchem.8b02062 29968462

상세보기
32. Jung C Ellington AD A primerless molecular diagnostic: phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) Anal. Bioanal. Chem. 2016 408 8583 8591 10.1007/s00216-016-9479-y 27032410

상세보기
33. Walker GT Strand displacement amplification―an isothermal, in vitro DNA amplification technique Nucl. Acids Res. 1992 20 1691 1696 10.1093/nar/20.7.1691 1579461

상세보기
34. Huang WE RT-LAMP for rapid diagnosis of coronavirus SARS-CoV-2 Microb. Biotechnol. 2020 13 950 961 10.1111/1751-7915.13586 32333644

상세보기
35. Kim HY Ahn JK Lee CY Park HG A hairpin probe-mediated isothermal amplification method to detect target nucleic acid Anal. Chim. Acta. 2020 1114 7 14 10.1016/j.aca.2020.04.003 32359517

상세보기
36. Tyagi S Bratu DP Kramer FR Multicolor molecular beacons for allele discrimination Nat. Biotechnol. 1998 16 49 10.1038/nbt0198-49 9447593

상세보기
37. Bonnet G Tyagi S Libchaber A Kramer FR Thermodynamic basis of the enhanced specificity of structured DNA probes Proc. Natl. Acad. Sci. USA. 1999 96 6171 6176 10.1073/pnas.96.11.6171 10339560

상세보기
38. Zinkova A Brynychova I Svacina A Jirkovska M Korabecna M Cell-free DNA from human plasma and serum differs in content of telomeric sequences and its ability to promote immune response Sci. Rep 2017 7 1 8 10.1038/s41598-017-02905-8 28127051

상세보기
39. Jackson JB Multiplex preamplification of serum DNA to facilitate reliable detection of extremely rare cancer mutations in circulating DNA by digital PCR J. Mol. Diagn. 2016 18 235 243 10.1016/j.jmoldx.2015.10.004 26752305

상세보기
40. Lefkowitz RB Clinical validation of a noninvasive prenatal test for genomewide detection of fetal copy number variants Am. J. Obstet. Gynecol. 2016 215 221 227 10.1016/j.ajog.2016.02.030 27143399

상세보기
41. Kalishwaralal K Kwon WY Park KS Exosomes for non-invasive cancer monitoring Biotechnol. J. 2019 14 1800430 10.1002/biot.201800430

상세보기
42. Poon LL Rapid detection of the severe acute respiratory syndrome (SARS) coronavirus by a loop-mediated isothermal amplification assay Clin. Chem. 2004 50 1050 1052 10.1373/clinchem.2004.032011 15054079

상세보기
43. Shirato K Detection of Middle East respiratory syndrome coronavirus using reverse transcription loop-mediated isothermal amplification (RT-LAMP) Virol. J. 2014 11 1 11 10.1186/1743-422X-11-139 24393133

상세보기
44. Baylis S Standardization of nucleic acid amplification technique (NAT)-based assays for different genotypes of parvovirus B19: a meeting summary Vox Sang. 2008 94 74 80 10.1111/j.1423-0410.2008.01023.x 18171331

상세보기
45. Bauer B Riley L Antemortem detection of mouse parvovirus and mice minute virus by polymerase chain reaction (PCR) of faecal samples Lab. Anim. 2006 40 144 152 10.1258/002367706776319079 16600074

상세보기
46. Tobiasch E Burguete T Klein-Bauernschmitt P Heilbronn R Schlehofer JR Discrimination between different types of human adeno-associated viruses in clinical samples by PCR J. Virol. Methods 1998 71 17 25 10.1016/S0166-0934(97)00198-5 9628217

상세보기
47. Chung W-Y A sexually transmitted disease (STD) DNA chip for the diagnosis of genitourinary infections Biosens. Bioelectron. 2011 26 4314 4319 10.1016/j.bios.2011.04.024 21665459

상세보기

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