Table of Contents
ISRN Bioinformatics
Volume 2012, Article ID 696758, 5 pages
http://dx.doi.org/10.5402/2012/696758
Research Article

Electric LAMP: Virtual Loop-Mediated Isothermal AMPlification

1Cullman Program for Molecular Systematics, The New York Botanical Garden, Bronx, NY 10458, USA
2The Graduate Center, The City University of New York, New York, NY 10016, USA

Received 23 August 2012; Accepted 20 September 2012

Academic Editors: D. A. McClellan and F. Pappalardo

Copyright © 2012 Nelson R. Salinas and Damon P. Little. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. K. B. Mullis and F. A. Faloona, “Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction,” Methods in Enzymology, vol. 155, pp. 335–350, 1987. View at Publisher · View at Google Scholar · View at Scopus
  2. R. K. Saiki, D. H. Gelfand, S. Stoffel et al., “Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase,” Science, vol. 239, no. 4839, pp. 487–491, 1988. View at Google Scholar · View at Scopus
  3. T. Notomi, H. Okayama, H. Masubuchi et al., “Loop-mediated isothermal amplification of DNA,” Nucleic Acids Research, vol. 28, no. 12, article e63, 2000. View at Google Scholar · View at Scopus
  4. P. Gill and A. Ghaemi, “Nucleic acid isothermal amplification technologies—a review,” Nucleosides, Nucleotides and Nucleic Acids, vol. 27, no. 3, pp. 224–243, 2008. View at Publisher · View at Google Scholar · View at Scopus
  5. N. Tomita, Y. Mori, H. Kanda, and T. Notomi, “Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products,” Nature Protocols, vol. 3, no. 5, pp. 877–882, 2008. View at Publisher · View at Google Scholar · View at Scopus
  6. M. Goto, E. Honda, A. Ogura, A. Nomoto, and K. I. Hanaki, “Colorimetric detection of loop-mediated isothermal amplification reaction by using hydroxy naphthol blue,” BioTechniques, vol. 46, no. 3, pp. 167–172, 2009. View at Publisher · View at Google Scholar · View at Scopus
  7. Anonymous, A Guide to LAMP Primer Designing, Eiken Chemical, 2009.
  8. K. Nagamine, T. Hase, and T. Notomi, “Accelerated reaction by loop-mediated isothermal amplification using loop primers,” Molecular and Cellular Probes, vol. 16, no. 3, pp. 223–229, 2002. View at Publisher · View at Google Scholar · View at Scopus
  9. Y. Tanaka, Y. Kimura, Y. Mitani et al., “Effects of the turn-back primer on intermediate product generation in isothermal DNA amplification,” BioTechniques, vol. 49, no. 6, pp. 888–892, 2010. View at Publisher · View at Google Scholar · View at Scopus
  10. R. Sommer and D. Tautz, “Minimal homology requirements for PCR primers,” Nucleic Acids Research, vol. 17, no. 16, p. 6749, 1989. View at Google Scholar · View at Scopus
  11. S. Kwok, D. E. Kellogg, N. McKinney et al., “Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies,” Nucleic Acids Research, vol. 18, no. 4, pp. 999–1005, 1990. View at Google Scholar · View at Scopus
  12. G. Sarkar, J. Cassady, C. D. K. Bottema, and S. S. Sommer, “Characterization of polymerase chain reaction amplification of specific alleles,” Analytical Biochemistry, vol. 186, no. 1, pp. 64–68, 1990. View at Google Scholar · View at Scopus
  13. M. M. Huang, N. Arnheim, and M. F. Goodman, “Extension of base mispairs by Taq DNA polymerase: implications for single nucleotide discrimination in PCR,” Nucleic Acids Research, vol. 20, no. 17, pp. 4567–4573, 1992. View at Google Scholar · View at Scopus
  14. S. Ayyadevara, J. J. Thaden, and R. J. S. Reis, “Discrimination of primer 3-nucleotide mismatch by Taq DNA polymerase during polymerase chain reaction,” Analytical Biochemistry, vol. 284, no. 1, pp. 11–18, 2000. View at Publisher · View at Google Scholar · View at Scopus
  15. Z. K. Njiru, A. S. Mikosza, T. Armstrong, J. C. Enyaru, J. M. Ndung'u, and A. R. Thompson, “Loop-mediated isothermal amplification (LAMP) method for rapid detection of Trypanosoma brucei rhodesiense,” PLoS Neglected Tropical Diseases, vol. 2, no. 1, article e147, 2008. View at Google Scholar · View at Scopus
  16. S. J. Harper, L. I. Ward, and G. R. G. Clover, “Development of LAMP and real-time PCR methods for the rapid detection of Xylella fastidiosa for quarantine and field applications,” Phytopathology, vol. 100, no. 12, pp. 1282–1288, 2010. View at Publisher · View at Google Scholar · View at Scopus
  17. J. A. Tomlinson, N. Boonham, and M. Dickinson, “Development and evaluation of a one-hour DNA extraction and loop-mediated isothermal amplification assay for rapid detection of phytoplasmas,” Plant Pathology, vol. 59, no. 3, pp. 465–471, 2010. View at Publisher · View at Google Scholar · View at Scopus
  18. D. T. Dinh, M. T. Q. Le, C. D. Vuong, F. Hasebe, and K. Morita, “An updated loop-mediated isothermal amplification method for rapid diagnosis of H5N1 Avian Influenza Viruses,” Tropical Medicine and Health, vol. 39, no. 1, pp. 3–7, 2011. View at Publisher · View at Google Scholar · View at Scopus
  19. F. Wang, L. Jiang, Q. Yang, W. Prinyawiwatkul, and B. Ge, “Rapid and specific detection of Escherichia coli serogroups O26, O45, O103, O111, O121, O145, and O157 in ground beef, beef trim, and produce by loop-mediated isothermal amplification,” Applied and Environmental Microbiology, vol. 78, pp. 2727–2736, 2012. View at Google Scholar
  20. Anonymous, Primer Explorer, Eiken Chemical Co., Tokyo, Japan, 2009.
  21. C. Torres, E. A. Vitalis, B. R. Baker, S. N. Gardner, M. W. Torres, and J. M. Dzenitis, “LAVA: an open-source approach to designing lAMP (Loop-Mediated Isothermal Amplification) DNA signatures,” BMC Bioinformatics, vol. 12, article 240, 2011. View at Publisher · View at Google Scholar · View at Scopus
  22. G. D. Schuler, “Sequence mapping by electronic PCR,” Genome Research, vol. 7, no. 5, pp. 541–550, 1997. View at Google Scholar · View at Scopus
  23. S. Wu and U. Manber, “Fast text searching: allowing errors,” Communications of the ACM, vol. 35, pp. 83–91, 1992. View at Google Scholar
  24. D. C. Holt, M. T. G. Holden, S. Y. C. Tong et al., “A very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin,” Genome Biology and Evolution, vol. 3, pp. 881–895, 2011. View at Google Scholar