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Isothermal Amplification Methods Most Used in the Diagnosis of Infections

Year 2018, Volume: 11 Issue: 1 , 86 - 95 , 01.03.2018

Mehmet Üvey , Nilgün Ünal

https://izlik.org/JA43BY55AC

Abstract

Isothermal amplification of nucleic acid is one of the most commonly used methods to identify the infections, tumors, genetic abnormalities, and in forensic medicine. As isothermal amplification methods can be performed at one reaction temperature under simple conditions they are less complex in comparison to Polymerase Chain Reaction (PCR). These methods differ from each other with the diversity of enzymes, primers used, sensitivity and specificity. In this review, the most commonly used isothermal amplification methods, their principles, areas of use and innovations brought about are discussed.

Keywords

Isothermal Amplification LAMP NASBA SDA EXPAR

References

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İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri

Year 2018, Volume: 11 Issue: 1 , 86 - 95 , 01.03.2018

Mehmet Üvey , Nilgün Ünal

https://izlik.org/JA43BY55AC

Abstract

Nükleik asit amplifikasyonu, enfeksiyonların, tümörlerin, genetik anormalliklerin tanısında ve adli tıpta en fazla kullanılan yöntemlerdendir. İzotermal amplifikasyon yöntemleri, Polimeraz Zincir Reaksiyonu (PZR) metoduna göre sabit sıcaklıkta yapılmasıyla karmaşıklığı azaltır. Bu yöntemler, kullanılan enzim çeşitliliği, primerler, duyarlılıkları ile özgüllükleri bakımından farklılıklar göstermektedir. Bu derlemede izotermal amplifikasyon yöntemlerinden en sık kullanılanları, prensipleri, kullanım alanları ve getirdikleri yenilikler ele alınmıştır.

Keywords

İzotermal Amplifikasyon LAMP NASBA SDA EXPAR

References

  • Ahmed A, Van Der Linden H, Hartskeerl RA. Development of a recombinase polymerase amplification assay for the detection of pathogenic Leptospira. Int J Environ Res Public Health. 2014; 11:4953-4964.
  • Altındiş M, Elmas M, Kılıç Ü, Aslan F G, Küçükkara G, Köroğlu M. Grup A Streptokokların hızlı moleküler tanısında loop-mediated isothermal amplifi cation PCR (LAMP-PCR). J Biotechnol Strategic Health Res. 2017;1:11-16.
  • Angamuthu R, Baskaran S, Gopal DR, Devarajan J, Kathaperumal K. Rapid detection of the marek's disease viral genome in chicken feathers by loop-mediated isothermal amplification. J Clin Microbiol. 2012; 50:961-965.
  • Banér J, Nilsson M, Mendel-Hartvig M, Landegren U. Signal amplification of padlock probes by rolling circle replication. Nucleic Acids Res. 1998; 26: 5073-5078.
  • Barkway CP, Pocock RL, Vrba V, Blake DP. Loop-mediated isothermal amplification (lamp) assays for the species-specific detection of Eimeria that infect chickens. JoVE. 2015:e52552.
  • Bulut E., Köker M. P., Ünal N., Yildirim M. Salmonella enterica’nın LAMP ile belirlenmesi XII. Ulusal Veteriner Hekimleri Mikrobiyoloji Kongresi (Uluslararası Katılımlı), Kongre Özet Kitabı p: 47-48 pp., 30 Ağustos-02 Eylül 2016 Kapadokya, Nevşehir, 2016.
  • Cao Y, Kim H-J, Li Y, Kong H, Lemieux B, (2013) Helicase-dependent amplification of nucleic acids current protocols in molecular biology. Eds: John Wiley & Sons, Inc., p: 15.11.01-15.11.012.
  • Chang C-C, Chen C-C, Wei S-C, Lu H-H, Liang Y-H, Lin C-W. Diagnostic devices for isothermal nucleic acid amplification. Sensors. 2012; 12: 8319-8337.
  • Chantratita N, Meumann E, Thanwisai A, Limmathurotsakul D, Wuthiekanun V, Wannapasni S, Tumapa S, Day NPJ, Peacock SJ. Loop-mediated isothermal amplification method targeting the tts1 gene cluster for detection of Burkholderia pseudomallei and diagnosis of melioidosis. J Clin Microbiol, 2008; 46: 568-573.
  • Chen H-T, Zhang J, Ma Y-P, Ma L-N, Ding Y-Z, Liu X-T, Cai X-P, Ma L-Q, Zhang Y-G, Liu Y-S. Reverse transcription loop-mediated isothermal amplification for the rapid detection of infectious bronchitis virus in infected chicken tissues. Mol Cell Probes. 2010; 24:104-106.
  • Chow WHA, Mccloskey C, Tong Y, Hu L, You Q, Kelly CP, Kong H, Tang Y-W, Tang W. Application of isothermal helicase-dependent amplification with a disposable detection device in a simple sensitive stool test for toxigenic Clostridium difficile. J Mol Diagn. 2008; 10:452-458.
  • Compton J. Nucleic acid sequence-based amplification. Nature. 1991; 350:91-92.
  • Conze T, Göransson J, Razzaghian HR, Ericsson O, Öberg D, Akusjärvi G, Landegren U, Nilsson M. Single molecule analysis of combinatorial splicing. Nucleic Acids Res. 2010; 38:e163-163.
  • Cui S-J, Fung Y-WW, Lau LT, Liu W-B, Wang Y-F, Tong G-Z, Chen J,Yu ACH. Detection of Newcastle disease virus using nucleic acid sequence-based amplification. Biologicals. 2007; 35:13-18.
  • Daher RK. Recombinase polymerase amplification technology: Assessment for nucleic acid-based point-of-care diagnostics, Doktora Tezi (Ph.D.), L'Université Laval, Québec, Canada, 2015.
  • Damen M, Sillekens P, Cuypers H, Frantzen I, Melsert R. Characterization of the quantitative HCV NASBA assay. J Virol Methods. 1999; 82:45-54.
  • Dean FB, Nelson JR, Giesler TL, Lasken RS. Rapid amplification of plasmid and phage DNA using phi29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res. 2001; 11: 1095-1099.
  • Doseeva V, Forbes T, Wolff J, Khripin Y, O'neil D, Rothmann T, Nazarenko I. Multiplex isothermal helicase-dependent amplification assay for detection of Chlamydia trachomatis and Neisseria gonorrhoeae. Diagn Microbiol Infect Dis. 2011; 71:354-365.
  • El Wahed AA, El-Deeb A, El-Tholoth M, El Kader HA, Ahmed A, Hassan S, Hoffmann B, Haas B, Shalaby MA, Hufert FT. A portable reverse transcription recombinase polymerase amplification assay for rapid detection of foot-and-mouth disease virus. PloS one. 2013; 8:e71642.
  • Frech GC, Munns D, Jenison RD, Hicke BJ. Direct detection of nasal Staphylococcus aureus carriage via helicase-dependent isothermal amplification and chip hybridization. BMC Res Notes. 2012; 5:430.
  • Ge Y, Cui L, Qi X, Shan J, Shan Y, Qi Y, Wu B, Wang H, Shi Z. Detection of novel swine origin influenza A virus (H1N1) by real-time nucleic acid sequence-based amplification. J Virol Methods. 2010; 163:495-497.
  • 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 Mol Diagn. 2007; 9:639-644.
  • Hara-Kudo Y, Konishi N, Ohtsuka K, Hiramatsu R, Tanaka H, Konuma H, Takatori K. Detection of Verotoxigenic Escherichia coli O157 and O26 in food by plating methods and LAMP method: A collaborative study. Int J Food Microbiol. 2008a; 122:156-161.
  • Hara-Kudo Y, Niizuma J, Goto I, Iizuka S, Kaji Y, Kamakura K, Suzuki S, Takatori K. Surveillance of shiga toxin–producing Escherichia coli in beef with effective procedures, independent of serotype. Foodborne Pathog Dis. 2008b; 5:97-103.
  • Hsieh K, Patterson AS, Ferguson BS, Plaxco KW, Soh HT. Rapid, sensitive, and quantitative detection of pathogenic dna at the point of care through microfluidic electrochemical quantitative loop-mediated isothermal amplification. Angewandte Chemie. 2012; 124:4980-4984.
  • Jayawardena S, Cheung CY, Barr I, Chan KH, Chen H, Guan Y, Peiris J, Poon L. Loop-mediated isothermal amplification for influenza A (H5N1) virus. Emerg Infect Dis. 2007; 13:899.
  • Jia H, Li Z, Liu C, Cheng Y. Ultrasensitive detection of microRNAs by exponential isothermal amplification. Angew Chem Int Ed. 2010; 49: 5498-5501.
  • Johne R, Müller H, Rector A, Van Ranst M, Stevens H. Rolling-circle amplification of viral DNA genomes using phi29 polymerase. Trends Microbiol. 2009; 17: 205-211.
  • Kaneko H, Kawana T, Fukushima E, Suzutani T. Tolerance of loop-mediated isothermal amplification to a culture medium and biological substances. J Biochem Biophys Methods. 2007; 70: 499-501.
  • Kaneko I, Miyamoto K, Mimura K, Yumine N, Utsunomiya H, Akimoto S, Mcclane BA. Detection of enterotoxigenic Clostridium perfringens in meat samples by using molecular methods. Appl Environ Microbiol. 2011; 77:7526-7532.
  • Keightley MC, Sillekens P, Schippers W, Rinaldo C, George KS. Real-time NASBA detection of SARS-associated coronavirus and comparison with real-time reverse transcription-PCR. J Med Virol. 2005; 77:602-608.
  • Kim H-J, Tong Y, Tang W, Quimson L, Cope VA, Pan X, Motre A, Kong R, Hong J, Kohn D. A rapid and simple isothermal nucleic acid amplification test for detection of herpes simplex virus types 1 and 2. J Clin Virol. 2011; 50:26-30.
  • Kursa O, Woźniakowski G, Tomczyk G, Sawicka A, Minta Z. Rapid detection of Mycoplasma synoviae by loop-mediated isothermal amplification. Arch Microbiol. 2015; 197:319-325.
  • Lau L-T, Banks J, Aherne R, Brown IH, Dillon N, Collins RA, Chan K-Y, Fung Y-WW, Xing J, Albert C. Nucleic acid sequence-based amplification methods to detect avian influenza virus. Biochem Biophys Res Commun. 2004; 313:336-342.
  • Lemieux B, Li Y, Kong H,Tang Y-W. Near instrument-free, simple molecular device for rapid detection of herpes simplex viruses. Expert Rev Mol Diagn. 2012; 12:437-443.
  • Li Q, Xue C, Qin J, Zhou Q, Chen F, Bi Y, Cao Y. An improved reverse transcription loop-mediated isothermal amplification assay for sensitive and specific detection of Newcastle disease virus. Arch Virol. 2009; 154:1433-1440.
  • Mader A, Riehle U, Brandstetter T, Stickeler E, Zur Hausen A, Rühe J. Microarray-based amplification and detection of RNA by nucleic acid sequence based amplification. Anal Bioanal Chem. 2010; 397:3533-3541.
  • Mahony J, Chong S, Bulir D, Ruyter A, Mwawasi K, Waltho D. Multiplex lamp (M-LAMP) assay for the detection of influenza A/H1, A/H3 and influenza B can provide a specimen-to-result diagnosis in 40 min with single genome copy sensitivity. J ClinVirol. 2013; 58:127-131.
  • Mori Y, Kanda H, Notomi T. Loop-mediated isothermal amplification (LAMP): recent progress in research and development. J Inf Chemother. 2013; 19:404-411.
  • Mori Y, Kitao M, Tomita N, Notomi T. Real-time turbidimetry of LAMP reaction for quantifying template DNA. J Biochem Biophys Methods. 2004; 59:145-157.
  • Murakami T, Sumaoka J, Komiyama M. Sensitive isothermal detection of nucleic-acid sequence by primer generation–rolling circle amplification. Nucleic Acids Res. 2009; 37:e19.
  • Nemoto M, Ohta M, Tsujimura K, Bannai H, Yamanaka T, Kondo T, Matsumura T. Direct detection of equine herpesvirus type 1 DNA in nasal swabs by loop-mediated isothermal amplification (LAMP). J Vet Med Sci. 2011; 73:1225-1227.
  • Nie K, Qi S-X, Zhang Y, Luo L, Xie Y, Yang M-J, Zhang Y, Li J, Shen H, Li Q, Ma X-J. Evaluation of a Direct Reverse Transcription Loop-Mediated Isothermal Amplification Method without RNA extraction for the detection of human enterovirus 71 subgenotype C4 in nasopharyngeal swab specimens. PLoS ONE, 2012; 7: e52486.
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There are 70 citations in total.

Details

Primary Language Turkish
Journal Section Review
Authors

Mehmet Üvey

Nilgün Ünal This is me

Acceptance Date December 20, 2017
Publication Date March 1, 2018
IZ https://izlik.org/JA43BY55AC
Published in Issue Year 2018 Volume: 11 Issue: 1

Cite

APA Üvey, M., & Ünal, N. (2018). İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri. Kocatepe Veterinary Journal, 11(1), 86-95. https://izlik.org/JA43BY55AC
AMA 1.Üvey M, Ünal N. İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri. kvj. 2018;11(1):86-95. https://izlik.org/JA43BY55AC
Chicago Üvey, Mehmet, and Nilgün Ünal. 2018. “İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri”. Kocatepe Veterinary Journal 11 (1): 86-95. https://izlik.org/JA43BY55AC.
EndNote Üvey M, Ünal N (March 1, 2018) İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri. Kocatepe Veterinary Journal 11 1 86–95.
IEEE [1]M. Üvey and N. Ünal, “İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri”, kvj, vol. 11, no. 1, pp. 86–95, Mar. 2018, [Online]. Available: https://izlik.org/JA43BY55AC
ISNAD Üvey, Mehmet - Ünal, Nilgün. “İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri”. Kocatepe Veterinary Journal 11/1 (March 1, 2018): 86-95. https://izlik.org/JA43BY55AC.
JAMA 1.Üvey M, Ünal N. İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri. kvj. 2018;11:86–95.
MLA Üvey, Mehmet, and Nilgün Ünal. “İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri”. Kocatepe Veterinary Journal, vol. 11, no. 1, Mar. 2018, pp. 86-95, https://izlik.org/JA43BY55AC.
Vancouver 1.Mehmet Üvey, Nilgün Ünal. İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri. kvj [Internet]. 2018 Mar. 1;11(1):86-95. Available from: https://izlik.org/JA43BY55AC

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