Classification of Multiple DNA Dyes Based on Inhibition Effects on Real-Time Loop-Mediated Isothermal Amplification (LAMP): Prospect for Point of Care Setting

Overview

Journal Front Microbiol

Specialty Microbiology

Date 2019 Nov 5

PMID 31681184

Citations 33

Authors

Than Linh Quyen

Tien Anh Ngo

Dang Duong Bang

Mogens Madsen

Anders Wolff

Affiliations

Soon will be listed here.

Abstract

LAMP has received great interest and is widely utilized in life sciences for nucleic acid analysis. To monitor a real-time LAMP assay, a fluorescence DNA dye is an indispensable component and therefore the selection of a suitable dye for real-time LAMP is a need. To aid this selection, we investigated the inhibition effects of twenty-three DNA dyes on real-time LAMP. Threshold time (T) values of each real-time LAMP were determined and used as an indicator of the inhibition effect. Based on the inhibition effects, the dyes were classified into four groups: (1) non-inhibition effect, (2) medium inhibition effect, (3) high inhibition effect, and (4) very high inhibition effect. The signal to noise ratio (SNR) and the limit of detection (LOD) of the dyes in groups 1, 2, and 3 were further investigated, and possible inhibition mechanisms of the DNA dyes on the real-time LAMP are suggested and discussed. Furthermore, a comparison of SYTO 9 in different LAMP reactions and different systems is presented. Of the 23 dyes tested, SYTO 9, SYTO 82, SYTO 16, SYTO 13, and Miami Yellow were the best dyes with no inhibitory effect, low LOD and high SNR in the real-time LAMP reactions. The present classification of the dyes will simplify the selection of fluorescence dye for real-time LAMP assays in point of care setting.

Citing Articles

Cleavable energy transfer labeled oligonucleotide probe for enhanced isothermal amplification detection and nano digital chip-based readout.

Liu L, Dollery S, Tobin G, Lu G, Du K Nanoscale. 2024; 17(3):1381-1391.

PMID: 39639742 PMC: 11750181. DOI: 10.1039/d4nr03142c.

Optimization of loop-mediated isothermal amplification assay for sunflower mildew disease detection.

Yeni O, Sen M, Hasancebi S, Kara N Sci Rep. 2024; 14(1):23224.

PMID: 39369029 PMC: 11455944. DOI: 10.1038/s41598-024-72228-y.

Integrating loop-mediated isothermal amplification with lateral flow assay to achieve a highly sensitive method for detecting Genome in raw pork.

Prompunt E, Thongkum W, Sumphanapai T, Kamseng P, Saoin S, Kloypan C Heliyon. 2024; 10(17):e36942.

PMID: 39281572 PMC: 11402220. DOI: 10.1016/j.heliyon.2024.e36942.

Research progress of loop-mediated isothermal amplification in the detection of Salmonella for food safety applications.

Zhuang L, Gong J, Zhang P, Zhang D, Zhao Y, Yang J Discov Nano. 2024; 19(1):124.

PMID: 39105889 PMC: 11303641. DOI: 10.1186/s11671-024-04075-9.

Evaluating Commercial Loop-Mediated Isothermal Amplification Master Mixes for Enhanced Detection of Foodborne Pathogens.

Costa-Ribeiro A, Lamas A, Garrido-Maestu A Foods. 2024; 13(11).

PMID: 38890864 PMC: 11172173. DOI: 10.3390/foods13111635.

References

Espy M, Uhl J, Sloan L, Buckwalter S, Jones M, Vetter E . Real-time PCR in clinical microbiology: applications for routine laboratory testing. Clin Microbiol Rev. 2006; 19(1):165-256. PMC: 1360278. DOI: 10.1128/CMR.19.1.165-256.2006. View

Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N . Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000; 28(12):E63. PMC: 102748. DOI: 10.1093/nar/28.12.e63. View

Kostic T, Ellis M, Williams M, Stedtfeld T, Kaneene J, Stedtfeld R . Thirty-minute screening of antibiotic resistance genes in bacterial isolates with minimal sample preparation in static self-dispensing 64 and 384 assay cards. Appl Microbiol Biotechnol. 2015; 99(18):7711-22. PMC: 4543423. DOI: 10.1007/s00253-015-6774-z. View

Hara-Kudo Y, Yoshino M, Kojima T, Ikedo M . Loop-mediated isothermal amplification for the rapid detection of Salmonella. FEMS Microbiol Lett. 2005; 253(1):155-61. DOI: 10.1016/j.femsle.2005.09.032. View

Sun Y, Quyen T, Hung T, Chin W, Wolff A, Bang D . A lab-on-a-chip system with integrated sample preparation and loop-mediated isothermal amplification for rapid and quantitative detection of Salmonella spp. in food samples. Lab Chip. 2015; 15(8):1898-904. DOI: 10.1039/c4lc01459f. View

Monis P, Giglio S, Saint C . Comparison of SYTO9 and SYBR Green I for real-time polymerase chain reaction and investigation of the effect of dye concentration on amplification and DNA melting curve analysis. Anal Biochem. 2005; 340(1):24-34. DOI: 10.1016/j.ab.2005.01.046. View

Wilson J, Wigenius J, Pitter D, Qiu Y, Abrahamsson M, Westerlund F . Base pair sensitivity and enhanced ON/OFF ratios of DNA-binding: donor-acceptor-donor fluorophores. J Phys Chem B. 2013; 117(40):12000-6. DOI: 10.1021/jp406993m. View

Bustin S, Benes V, Garson J, Hellemans J, Huggett J, Kubista M . The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009; 55(4):611-22. DOI: 10.1373/clinchem.2008.112797. View

Tuma R, Beaudet M, Jin X, Jones L, Cheung C, Yue S . Characterization of SYBR Gold nucleic acid gel stain: a dye optimized for use with 300-nm ultraviolet transilluminators. Anal Biochem. 1999; 268(2):278-88. DOI: 10.1006/abio.1998.3067. View

10.

Horakova H, Polakovicova I, Shaik G, Eitler J, Bugajev V, Draberova L . 1,2-propanediol-trehalose mixture as a potent quantitative real-time PCR enhancer. BMC Biotechnol. 2011; 11:41. PMC: 3102612. DOI: 10.1186/1472-6750-11-41. View

11.

Oscorbin I, Belousova E, Zakabunin A, Boyarskikh U, Filipenko M . Comparison of fluorescent intercalating dyes for quantitative loop-mediated isothermal amplification (qLAMP). Biotechniques. 2016; 61(1):20-5. DOI: 10.2144/000114432. View

12.

Tourlousse D, Ahmad F, Stedtfeld R, Seyrig G, Tiedje J, Hashsham S . A polymer microfluidic chip for quantitative detection of multiple water- and foodborne pathogens using real-time fluorogenic loop-mediated isothermal amplification. Biomed Microdevices. 2012; 14(4):769-78. DOI: 10.1007/s10544-012-9658-3. View

13.

Cao D, Hu L, Lin M, Li M, Ye Z, Sun H . Real-time fluorescence Loop-Mediated Isothermal Amplification (LAMP) for rapid and reliable diagnosis of pulmonary tuberculosis. J Microbiol Methods. 2014; 109:74-8. DOI: 10.1016/j.mimet.2014.12.013. View

14.

Stedtfeld R, Stedtfeld T, Kronlein M, Seyrig G, Steffan R, Cupples A . DNA extraction-free quantification of Dehalococcoides spp. in groundwater using a hand-held device. Environ Sci Technol. 2014; 48(23):13855-63. DOI: 10.1021/es503472h. View

15.

Nixon G, Svenstrup H, Donald C, Carder C, Stephenson J, Morris-Jones S . A novel approach for evaluating the performance of real time quantitative loop-mediated isothermal amplification-based methods. Biomol Detect Quantif. 2016; 2:4-10. PMC: 5121211. DOI: 10.1016/j.bdq.2014.11.001. View

16.

Chen S, Ge B . Development of a toxR-based loop-mediated isothermal amplification assay for detecting Vibrio parahaemolyticus. BMC Microbiol. 2010; 10:41. PMC: 2838873. DOI: 10.1186/1471-2180-10-41. View

17.

de Paz H, Brotons P, Munoz-Almagro C . Molecular isothermal techniques for combating infectious diseases: towards low-cost point-of-care diagnostics. Expert Rev Mol Diagn. 2014; 14(7):827-43. PMC: 7103708. DOI: 10.1586/14737159.2014.940319. View

18.

Xie L, Xie Z, Zhao G, Liu J, Pang Y, Deng X . A loop-mediated isothermal amplification assay for the visual detection of duck circovirus. Virol J. 2014; 11:76. PMC: 4013541. DOI: 10.1186/1743-422X-11-76. View

19.

Tian C, Lin Z, He X, Luo Q, Luo C, Yu H . Development of a fluorescent-intercalating-dye-based reverse transcription loop-mediated isothermal amplification assay for rapid detection of seasonal Japanese B encephalitis outbreaks in pigs. Arch Virol. 2012; 157(8):1481-8. DOI: 10.1007/s00705-012-1330-y. View

20.

Mao F, Leung W, Xin X . Characterization of EvaGreen and the implication of its physicochemical properties for qPCR applications. BMC Biotechnol. 2007; 7:76. PMC: 2213645. DOI: 10.1186/1472-6750-7-76. View