Research Progress on the Isothermal Nucleic Acid Amplification Techniques in Rapid Detection of Microorganisms

doi:10.13560/j.cnki.biotech.bull.1985.2017-0106

Abstract

Abstract: In recent 20 years，isothermal amplification technology has been rapidly developed. Relying on the advantage of the isothermal reaction，it is gradually replacing the traditional in vitro PCR（polymerase chain reaction）amplification，and plays an important role in different fields such as clinical medicine，laboratory medicine，molecular biology，genomics，food safety，and especially in the detection of pathogenic bacteria，viruses and other microorganisms. This article reviews and compares more than 10 kinds of high-profile isothermal amplification technologies，mainly focusing on the reaction principles，advantages，disadvantages as well as the development and application，and finally prospects the trends of isothermal amplification techniques，in order to play a positive role in the development of the related research fields.

Key words: isothermal amplification, microorganisms, nucleic acid, rapid detection?

WANG Da-zhou ,GUO Tian-xiao ,ZHENG Shi, SHANG Ying, XU Wen-tao. Research Progress on the Isothermal Nucleic Acid Amplification Techniques in Rapid Detection of Microorganisms[J]. Biotechnology Bulletin, 2017, 33(7): 49-61.

References

[1] Zhao Y, Chen F, Li Q, et al. Isothermal amplification of nucleic acids[J] . Chemical Reviews, 2015, 115（22）：12491-12545.
[2] Compton J. Nucleic acid sequence-based amplification[J] . Nature, 1991, 350（6313）：91-92.
[3] Kwoh DY, Davis GR, Whitfield KM, et al. Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format[J] . Proceedings of the National Academy of Sciences of the United States of America, 1989, 86（4）：1173-1177.
[4] Guatelli JC, Whitfield KM, Kwoh DY, et al. Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication[J] . Proceedings of the National Academy of Sciences, 1990, 87（5）：1874-1878.
[5] Li J, Macdonald J. Advances in isothermal amplification：novel strategies inspired by biological processes[J] . Biosensors & Bioelectronics, 2015, 64：196-211.
[6] Deiman B, van Aarle P, Sillekens P. Characteristics and applications of nucleic acid sequence-based amplification（NASBA）[J] . Molecular Biotechnology, 2002, 20（2）：163-179.
[7] Deng H, Gao Z. Bioanalytical applications of isothermal nucleic acid amplification techniques[J] . Analytica Chimica Acta, 2015, 853：30-45.
[8] Gill P, Ghaemi A. Nucleic Acid Isothermal Amplification Technologies—a review[J] . Nucleosides, Nucleotides and Nucleic Acids, 2008, 27（3）：224-243.
[9] 汪琳, 罗英, 周琦, 等. 核酸恒温扩增技术研究进展[J] . 生物技术通讯, 2011, 22（2）：296-302.
[10] Lau LT, Reid SM, King DP, et al. Detection of foot-and-mouth disease virus by nucleic acid sequence-based amplification（NASBA）[J] . Veterinary Microbiology, 2008, 126（1）：101-110.
[11] Zhao X, Dong T, Yang Z, et al. Compatible immuno-NASBA LOC device for quantitative detection of waterborne pathogens：design and validation[J] . Lab on a Chip, 2012, 12（3）：602-612.
[12] Clancy E, Coughlan H, Higgins O, et al. Development of internally controlled duplex real-time NASBA diagnostics assays for the detection of microorganisms associated with bacterial meningitis[J] . Journal of Microbiological Methods, 2016, 127：197-202.
[13] H?nsvall BK, Robertson LJ. Real-time nucleic acid sequence-based amplification（NASBA）assay targeting MIC1 for detection of Cryptosporidium parvum and Cryptosporidium hominis oocysts[J] . Experimental Parasitology, 2017, 172：61-67.
[14] Zeng W, Yao W, Wang Y, et al. Molecular detection of genotype II grass carp reovirus based on nucleic acid sequence-based amplification combined with enzyme-linked immunosorbent assay（NASBA-ELISA）[J] . Journal of Virological Methods, 2017, 243：92-97.
[15] Fire A, Xu SQ. Rolling replication of short DNA circles[J] . Proceedings of the National Academy of Sciences, 1995, 92（10）：4641-4645.
[16] Liu D, Daubendiek SL, Zillman MA, et al. Rolling circle DNA synthesis：small circular oligonucleotides as efficient templates for DNA polymerases[J] . Journal of the American Chemical Society, 1996, 118（7）：1587-1594.
[17] Blanco L, Bernad A, Lázaro JM, et al. Highly efficient DNA synthesis by the phage Φ29 DNA polymerase. Symmetrical mode of DNA replication[J] . Journal of Biological Chemistry, 1989, 264（15）：8935-8940.
[18] 彭涛. 核酸等温扩增技术及其应用[D] . 北京：科学出版社, 2009.
[19] Lizardi PM, Huang X, Zhu Z, et al. Mutation detection and single-molecule counting using isothermal rolling-circle amplification[J] . Nature Genetics, 1998, 19（3）：225-232.
[20] Dean FB, Nelson JR, Giesler TL, et al. Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification[J] . Genome Research, 2001, 11（6）：1095-1099.
[21] 何艳, 蒋涛. 基于链置换反应的DNA等温扩增技术应用进展[J] . 医学综述, 2010, 16（1）：24-27.
[22] Daubendiek SL, Ryan K, Kool ET. Rolling-circle RNA synthesis：circular oligonucleotides as efficient substrates for T7 RNA polymerase[J] . Journal of the American Chemical Society, 1995, 117（29）：7818-7819.
[23] Dean FB, Hosono S, Fang L, et al. Comprehensive human genome amplification using multiple displacement amplification[J] . Proceedings of the National Academy of Sciences of the United States of America, 2002, 99（8）：5261-5266.
[24] Spits C, Le Caignec C, De Rycke M, et al. Optimization and evaluation of single-cell whole-genome multiple displacement amplification[J] . Human Mutation, 2006, 27（5）：496-503.
[25] Luthra R, Medeiros LJ. Isothermal multiple displacement amplification：a highly reliable approach for generating unlimited high molecular weight genomic DNA from clinical specimens[J] . The Journal of Molecular Diagnostics, 2004, 6（3）：236-242.
[26] Rockett R, Barraclough KA, Isbel NM, et al. Specific rolling circle amplification of low-copy human polyomaviruses BKV, HPyV6, HPyV7, TSPyV, and STLPyV[J] . Journal of Virological Methods, 2015, 215：17-21.
[27] Wen J, Li W, Li J, et al. Study on rolling circle amplification of Ebola virus and fluorescence detection based on graphene oxide[J] . Sensors and Actuators B：Chemical, 2016, 227：655-659.
[28] Hao L, Gu H, Duan N, et al. An enhanced chemiluminescence resonance energy transfer aptasensor based on rolling circle amplification and WS 2 nanosheet for Staphylococcus aureus detection[J] . Analytica Chimica Acta, 2017, 959：83-90.
[29] Gusev Y, Sparkowski J, Raghunathan A, et al. Rolling circle amplification：a new approach to increase sensitivity for immunohistochemistry and flow cytometry[J] . American Journal of Pathology 2001, 159（1）：63-69.
[30] Notomi T, Okayama H, Masubuchi H, et al. Loop-mediated isothermal amplification of DNA[J] . Nucleic Acids Research, 2000, 28（12）：e63.
[31] Nagamine K, Watanabe K, Ohtsuka K, et al. Loop-mediated isothermal amplification reaction using a nondenatured template[J] . Clinical Chemistry, 2001, 47（9）：1742-1743.
[32] Kaneko H, Kawana T, Fukushima E, et al. Tolerance of loop-mediated isothermal amplification to a culture medium and biological substances[J] . Journal of Biochemical and Biophysical Methods, 2007, 70（3）：499-501.
[33] Nagamine K, Hase T, Notomi T. Accelerated reaction by loop-mediated isothermal amplification using loop primers[J] . Molecular and Cellular Probes, 2002, 16（3）：223-229.
[34] Aonuma H, Yoshimura A, Kobayashi T, et al. A single fluorescence-based LAMP reaction for identifying multiple parasites in mosquitoes[J] . Experimental Parasitology, 2010, 125（2）：179-183.
[35] He L, Xu H. Development of a multiplex loop-mediated isothermal amplification（mLAMP）method for the simultaneous detection of white spot syndrome virus and infectious hypodermal and hematopoietic necrosis virus in penaeid shrimp[J] . Aquaculture, 2011, 311（1）：94-99.
[36] Liang C, Chu Y, Cheng S, et al. Multiplex loop-mediated isothermal amplification detection by sequence-based barcodes coupled with nicking endonuclease-mediated pyrosequencing[J] . Analytical Chemistry, 2012, 84（8）：3758-3763.
[37] Tanner NA, Zhang Y, Evans Jr TC. Simultaneous multiple target detection in real-time loop-mediated isothermal amplification[J] . Biotechniques, 2012, 53（2）：81-89.
[38] Chen Y, Cheng N, Xu Y, et al. Point-of-care and visual detection of P. aeruginosa and its toxin genes by multiple LAMP and lateral flow nucleic acid biosensor[J] . Biosensors and Bioelectronics, 2016, 81：317-323.
[39] Vincent M, Xu Y, Kong H. Helicase-dependent isothermal DNA amplification[J] . EMBO Reports, 2004, 5（8）：795-800.
[40] An L, Wen T, Ranalli TA, et al. Characterization of a thermostable UvrD helicase and its participation in helicase dependent amplifi-cation[J] . Journal of Biological Chemistry, 2005, 280（32）：28952-28958.
[41] Li Y, Kumar N, Gopalakrishnan A, et al. Detection and species identification of malaria parasites by isothermal tHDA amplification directly from human blood without sample preparation[J] . Journal of Molecular Diagnostics, 2013, 15（5）：634-641.
[42] Motré A, Li Y, Kong H. Enhancing helicase-dependent amplification by fusing the helicase with the DNA polymerase[J] . Gene, 2008, 420（1）：17-22.
[43] Xu Y, Kim HJ, Kays A, et al. Simultaneous amplification and scr-eening of whole plasmids using the T7 bacteriophage replisome[J] . Nucleic Acids Research, 2006, 34（13）：e98-e98.
[44] Goldmeyer J, Kong H, Tang W. Development of a Novel one-tube isothermal reverse transcription thermophilic helicase-dependent amplification platform for rapid RNA detection[J] . The Journal of Molecular Diagnostics, 2007, 9（5）：639-644.
[45] Piepenburg O, Williams CH, Stemple DL, et al. DNA detection using recombination proteins[J] . PLoS Biology 2006, 4（7）：e204.
[46] 吕蓓, 程海荣, 严庆丰, 等. 用重组酶介导扩增技术快速扩增核酸[J] . 中国科学：生命科学, 2010, 40（10）：983-988.
[47] Liu J, Morrical SW. Assembly and dynamics of the bacteriophage T4 homologous recombination machinery[J] . Virology Journal, 2010, 7（1）：128-133.
[48] Euler M, Wang Y, Nentwich O, et al. Recombinase polymerase amplification assay for rapid detection of Rift Valley fever virus[J] . Journal of Clinical Virology, 2012, 54（4）：308-312.
[49] Tsaloglou MN, Watson RJ, Rushworth CM, et al. Real-time microfluidic recombinase polymerase amplification for the toxin B gene of Clostridium difficile on a SlipChip platform[J] . Analyst, 2015, 140（1）：258-264.
[50] Hang R, Yang M, Zhang G, et al. Development of a rapid recombinase polymerase amplification assay for detection of Brucella in blood samples[J] . Molecular & Cellular Probes, 2016, 30（2）：122-124.
[51] Wharam SD, Marsh P, Lloyd JS, et al. Specific detection of DNA and RNA targets using a novel isothermal nucleic acid amplification assay based on the formation of a three-way junction structure[J] . Nucleic Acids Research, 2001, 29（11）：e54.
[52] Hall MJ, Wharam SD, Weston A, et al. Use of signal-mediated amplification of RNA technology（SMART）to detect marine cyanophage DNA[J] . Biotechniques, 2002, 32（3）：604-611.
[53] Murakami, T, Sumaoka J, Komiyama M. Sensitive RNA detection by combining three-way junction formation and primer generation-rolling circle amplification[J] . Nucleic Acids Research, 2012, 40（3）：e22.
[54] 周敏, 张宏萍, 陆仁飞, 等. 三向连接构造组合引物介导的滚环扩增技术检测肠道病毒 71 型方法的建立[J] . 山东医药, 2015（28）：21-23 111.
[55] Yan L, Zhou J, Zheng Y, et al. Isothermal amplified detection of DNA and RNA[J] . Molecular Biosystems, 2014, 10（5）：970-1003.
[56] Kurn N, Chen P, Heath JD, et al. Novel isothermal, linear nucleic acid amplification systems for highly multiplexed applications[J] . Clinical Chemistry, 2005, 51（10）：1973-1981.
[57] 何水林. 基因工程[M] . 北京：科学出版社, 2008.
[58] Barker CS, Griffin C, Dolganov GM, et al. Increased DNA microarray hybridization specificity using sscDNA targets[J] . BMC Genomics, 2005, 6（1）：1-8.
[59] Guo X, Guo Y, Yan S, et al. A new molecular diagnosis method combined single primer isothermal amplification with rapid isothermal detection assay in detection of group B Streptococcus[J] . African Journal of Microbiology Research, 2013, 7（34）：4317-4322.
[60] Wang J, Rui L, Hu L, et al. Development of a quantitative fluorescence single primer isothermal amplification-based method for the detection of Salmonella[J] . International Journal of Food Microbiology, 2015, 219：22-27.
[61] Mukai H, Sagawa H, Uemori T, et al. Method for amplifying nucleic acid sequence：US, 6951722[P] . 2005-10-4.
[62] Mukai H, Uemori T, O, Kobayashi E, et al. Highly efficient isothermal DNA amplification system using three elements of 5’-DNA-RNA-3’ chimeric primers, RNaseH and strand-displacing DNA polymerase[J] . Journal of Biochemistry, 2007, 142（2）：273-281.
[63] Uemori T, Mukai H, O, Moriyama M, et al. Investigation of the molecular mechanism of ICAN, a novel gene amplification method[J] . Journal of Biochemistry, 2007, 142（2）：283-292.
[64] Isogai E, Makungu C, Yabe J, et al. Detection of Salmonella invA by isothermal and chimeric primer-initiated amplification of nucleic acids（ICAN）in Zambia[J] . Comparative Immunology Microbiology & Infectious Diseases, 2005, 28（5）：363-370.
[65] Horii T, Monji A, Uemura K, et al. Rapid detection of fluoroquino-lone resistance by isothermal chimeric primer-initiated amplifica-tion of nucleic acids from clinical isolates of Neisseria gonorrho-eae［J］. Journal of Microbiological Methods, 2006, 65（3）：557-561.
［66］ Urasaki N, Kawano S, Mukai H, et al. Rapid and sensitive detection of “Candidatus Liberibacter asiaticus” by cycleave isothermal and chimeric primer-initiated amplification of nucleic acids［J］. Journal of General Plant Pathology, 2008, 74（2）：151-155.
［67］ Walker GT, Little MC, Nadeau JG, et al. Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system［J］. Proceedings of the National Academy of Sciences of the United States of America, 1992, 89（1）：392-396.
［68］ Little MC, Andrews J, Moore R, et al. Strand displacement amplification and homogeneous real-time detection incorporated in a second-generation DNA probe system, BDProbeTecET［J］. Clinical Chemistry, 1999, 45（6）：777-784.
［69］ Nuovo GJ. In situ strand displacement amplification：an improved technique for the detection of low copy nucleic acids［J］. Diagnostic Molecular Pathology, 2000, 9（4）：195-202.
［70］ Li W, Yang Y, Chen J, et al. Detection of lead（II）ions with a DNAzyme and isothermal strand displacement signal amplification［J］. Biosensors and Bioelectronics, 2014, 53：245-249.
［71］ Yao Z, Lidgard G. Methods for rapid, single-step strand displacem-ent amplification of nucleic acids：US, 11/838, 024［P］. 2007-8-13.
［72］尤其敏, 净汪, 林胡, 等. 切口酶扩增靶核酸序列的方法及用于扩增靶核酸序列的试剂盒及其应用：中国, 200610057262［P］. 2006-10-25.
［73］马丽敏, 卢亦愚. 核酸等温扩增技术研究进展［J］. 浙江预防医学, 2013, 25（1）：24-27.
［74］ Van Ness J, Van Ness LK, et al. Isothermal reactions for the amplification of oligonucleotides［J］. Proceedings of the National Academy of Sciences, 2003, 100（8）：4504-4509.
［75］ Nie J, Zhang DW, Cai T, et al. G-quadruplex based two-stage isothermal exponential amplification reaction for label-free DNA colorimetric detection［J］. Biosensors & Bioelectronics, 2014, 56：237-242.
［76］ Ma F, Yang Y, Zhang CY. Ultrasensitive detection of transcription factors using transcription-mediated isothermally exponential amplification-induced chemiluminescence［J］. Analytical Chemistry, 2014, 86（12）：6006-6011.
［77］ Yu Y, Chen Z, Jian W, et al. Ultrasensitive electrochemical detection of avian influenza A（H7N9）virus DNA based on isothermal exponential amplification coupled with hybridization chain reaction of DNAzyme nanowires［J］. Biosensors and Bioelectronics, 2015, 64：566-571.
［78］ Craw P, Balachandran W. Isothermal nucleic acid amplification technologies for point-of-care diagnostics：a critical review［J］. Lab on a Chip, 2012, 12（14）：2469-2486.
［79］ Singh R, Maganti RJ, Jabba SV, et al. Microarray-based comparison of three amplification methods for nanogram amounts of total RNA［J］. American Journal of Physiology-Cell Physiology, 2005, 288（5）：C1179-C1189.