İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri

ÜVEY, Mehmet; ÜNAL, NİLGÜN

İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri

Mehmet ÜVEY, (Aviagen Anadolu Veteriner Teşhis ve Analiz Laboratuvarı, Ankara, Türkiye)

Nilgün ÜNAL (Kırıkkale Üniversitesi Veteriner Fakültesi Mikrobiyoloji Anabilim Dalı, Kırıkkale, Türkiye)

Kocatepe Veterinary Journal

8 0

Yıl: 2018 Cilt: 11 Sayı: 1 Sayfa Aralığı: 86 - 95 Metin Dili: Türkçe İndeks Tarihi: 29-07-2022

İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri

Öz:

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

Anahtar Kelime:

Konular: Veterinerlik

Isothermal Amplification Methods Most Used in the Diagnosis of Infections

Öz:

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

Anahtar Kelime:

Konular: Veterinerlik

Belge Türü: Makale Makale Türü: Derleme Erişim Türü: Erişime Açık

hmed 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 loopmediated 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 YZ, Liu X-T, Cai X-P, Ma L-Q, Zhang Y-G, Liu Y-S. Reverse transcription loopmediated 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 helicasedependent 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 acidbased 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 HelicaseDependent 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 sequencebased 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. Realtime 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 nucleicacid 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.
Notomi T, Mori Y, Tomita N, Kanda H. Loopmediated isothermal amplification (LAMP): principle, features, and future prospects. J Microbiol. 2015; 53:1-5.
Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000; 28:e63-e63.
Ohtsuki R, Kawamoto K, Kato Y, Shah MM, Ezaki T,Makino SI. Rapid detection of Brucella spp. by the loop-mediated isothermal amplification method. J Appl Microbiol. 2008; 104:1815-1823.
Parida M, Sannarangaiah S, Dash PK, Rao PVL, Morita K. Loop mediated isothermal amplification (LAMP): a new generation of innovative gene amplification technique; perspectives in clinical diagnosis of infectious diseases. Rev Med Virol. 2008; 18:407-421.
Piepenburg O, Williams CH, Stemple DL, Armes NA. DNA detection using recombination proteins. PLoS Biol, 2006; 4:e204.
Sakuma T, Kurosaki Y, Fujinami Y, Takizawa T, Yasuda J. Rapid and simple detection of Clostridium botulinum types A and B by loop-mediated isothermal amplification. J Appl Microbiol., 2009; 106:1252-1259.
Sato K, Tachihara A, Renberg B, Mawatari K, Sato K, Tanaka Y, Jarvius J, Nilsson M, Kitamori T. Microbead-based rolling circle amplification in a microchip for sensitive DNA detection. Lab Chip. 2010; 10:1262-1266.
Sharma N, Hoshika S, Hutter D, Bradley KM, Benner SA. Recombinase-based isothermal amplification of nucleic acids with self-avoiding molecular recognition systems (SAMRS). Chem Bio Chem, 2014; 15:2268-2274.
Soliman H, El-Matbouli M. An inexpensive and rapid diagnostic method of Koi Herpesvirus (KHV) infection by loopmediated isothermal amplification. J Virol. 2005; 2:1-8.
Tan E, Erwin B, Dames S, Ferguson T, Buechel M, Irvine B, Voelkerding K, Niemz A. Specific versus nonspecific isothermal dna amplification through thermophilic polymerase and nicking enzyme activities. Biochemistry. 2008; 47: 9987-9999.
Tan E, Erwin B, Dames S, Voelkerding K, Niemz A. Isothermal DNA Amplification with Gold Nanosphere-Based Visual Colorimetric Readout for Herpes Simplex Virus Detection. Clin Chem. 2007; 53:2017-2020.
Tomita N, Mori Y, Kanda H, Notomi T. Loopmediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products. Nat Protoc. 2008; 3:877-882.
Tong Y, Mccarthy K, Kong H, Lemieux B. Development and comparison of a rapid isothermal nucleic acid amplification test for typing of herpes simplex virus types 1 and 2 on a portable fluorescence detector. J Mol Diagn. 2012; 14:569-576.
Tröger V, Niemann K, Gärtig C, Kuhlmeier D. Isothermal amplification and quantification of nucleic acids and its use in microsystems. J Nanomed Nanotechnol. 2015;6:1-19.
Tsai S-M, Liu H-J, Shien J-H, Lee L-H, Chang P-C, Wang C-Y. Rapid and sensitive detection of infectious bursal disease virus by reverse transcription loop-mediated isothermal amplification combined with a lateral flow dipstick. J Virol Methods. 2012; 181:117-124.
Ünal N, Çınar OD. Detection of stapylococcal enterotoxin, methicillin-resistant and Panton-Valentine leukocidin genes in coagulase-negative staphylococci isolated from cows and ewes with subclinical mastitis. Trop Anim Health Prod, 2012; 44: 369-375.
Van Ness J, Van Ness LK, Galas DJ. Isothermal reactions for the amplification of oligonucleotides. P Natl A Sci India B. 2003; 100:4504-4509.
Walker GT, Fraiser MS, Schram JL, Little MC, Nadeau JG, Malinowski DP. Strand displacement amplification—an isothermal, in vitro DNA amplification technique. Nucleic Acids Res. 1992; 20:1691-1696.
Walker GT. Empirical aspects of strand displacement amplification. Genome Res, 1993; 3: 1-6.
Walker GT, Nadeau JG, Spears PA, Schram JL, Nycz CM, Shank DD. Multiplex strand displacement amplification (SDA) and detection of DNA sequences from Mycobacterium tuberculosis and other mycobacteria. Nucleic Acids Res. 1994; 22:2670-2677.
Wang F, Jiang L, Yang Q, Prinyawiwatkul W, Ge B. Rapid and specific detection of Escherichia coli serogroups O26, O45, O103, O111, O121, O145, and O157 in ground beef, beef trim, and produce by loopmediated isothermal amplification. Appl Environ Microbiol. 2012; 78:2727-2736.
Won JY, Min J. Highly sensitive Escherichia coli O157: H7 detection in a large volume sample using a conical polymer tube chamber consisting of micro-glass beads. Biosens Bioelectron, 2010; 26:112-117.
Won JY, Min J, Park J-H. Bacteria adsorption on hydrophilic surfaces for the sensitive detection of pathogenic bacteria using a single tube chamber system. Biosens Bioelectron. 2010; 26:1763-1767.
Xie Q-M, Ji J, Pickens TT, Du L-Q, Cao Y-C, Li H-M, Wang L-G, Ma J-Y, Bi Y-Z. Rapid detection of infectious laryngotracheitis virus isolates by loopmediated isothermal amplification. J Virol Methods. 2010; 165:71-75.
Zhang F, Bao S, Yu S, Cheng J, Tan L, Qiu X, Song C, Dai Y, Fei R, Ding C. Development of a loop-mediated isothermal amplification targeting a gene within the pyruvate dehydrogenase complex, the pdhA gene, for rapid detection of Mycoplasma gallisepticum. J Vet Diagn Invest. 2015; 27:260-267.
Zhang G, Brown EW, González-Escalona N. Comparison of real-time PCR, reverse transcriptase real-time PCR, loop-mediated isothermal amplification, and the FDA conventional microbiological method for the detection of Salmonella spp. in produce. Appl Environ Microbiol. 2011; 77:6495- 6501.
Zhao W, Brook MA,Li Y, (2008) Periodic Assembly of Nanospecies on Repetitive DNA Sequences Generated on Gold Nanoparticles by Rolling Circle Amplification Nanostructure Design: Methods and Protocols. Eds: Gazit E, Nussinov R. Totowa, NJ Humana Press, p: 79-90.
Zhao Y, Chen F, Li Q, Wang L, Fan C. Isothermal amplification of nucleic acids. Chemical Rev. 2015; 115:12491-12545.

APA	ÜVEY M, ÜNAL N (2018). İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri. , 86 - 95.
Chicago	ÜVEY Mehmet,ÜNAL NİLGÜN İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri. (2018): 86 - 95.
MLA	ÜVEY Mehmet,ÜNAL NİLGÜN İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri. , 2018, ss.86 - 95.
AMA	ÜVEY M,ÜNAL N İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri. . 2018; 86 - 95.
Vancouver	ÜVEY M,ÜNAL N İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri. . 2018; 86 - 95.
IEEE	ÜVEY M,ÜNAL N "İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri." , ss.86 - 95, 2018.
ISNAD	ÜVEY, Mehmet - ÜNAL, NİLGÜN. "İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri". (2018), 86-95.

APA	ÜVEY M, ÜNAL N (2018). İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri. Kocatepe Veterinary Journal, 11(1), 86 - 95.
Chicago	ÜVEY Mehmet,ÜNAL NİLGÜN İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri. Kocatepe Veterinary Journal 11, no.1 (2018): 86 - 95.
MLA	ÜVEY Mehmet,ÜNAL NİLGÜN İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri. Kocatepe Veterinary Journal, vol.11, no.1, 2018, ss.86 - 95.
AMA	ÜVEY M,ÜNAL N İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri. Kocatepe Veterinary Journal. 2018; 11(1): 86 - 95.
Vancouver	ÜVEY M,ÜNAL N İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri. Kocatepe Veterinary Journal. 2018; 11(1): 86 - 95.
IEEE	ÜVEY M,ÜNAL N "İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri." Kocatepe Veterinary Journal, 11, ss.86 - 95, 2018.
ISNAD	ÜVEY, Mehmet - ÜNAL, NİLGÜN. "İnfeksiyonların Tanısında En Çok Kullanılan İzotermal Amplifikasyon Yöntemleri". Kocatepe Veterinary Journal 11/1 (2018), 86-95.