Table of Contents Author Guidelines Submit a Manuscript
BioMed Research International
Volume 2016 (2016), Article ID 2906484, 8 pages
http://dx.doi.org/10.1155/2016/2906484
Research Article

Enhancement of Polymerase Activity of the Large Fragment in DNA Polymerase I from Geobacillus stearothermophilus by Site-Directed Mutagenesis at the Active Site

1School of Bioscience & Bioengineering, South China University of Technology, Guangzhou 510006, China
2Guangdong Province Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China

Received 25 August 2016; Revised 13 October 2016; Accepted 19 October 2016

Academic Editor: Sujit S. Jagtap

Copyright © 2016 Yi Ma et al. 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. 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 Publisher · View at Google Scholar · View at Scopus
  2. I. P. Oscorbin, U. A. Boyarskikh, and M. L. Filipenko, “Large fragment of DNA polymerase I from Geobacillus sp. 777: cloning and comparison with DNA polymerases I in practical applications,” Molecular Biotechnology, vol. 57, no. 10, pp. 947–959, 2015. View at Publisher · View at Google Scholar · View at Scopus
  3. M. Imai, A. Ninomiya, H. Minekawa et al., “Development of H5-RT-LAMP (loop-mediated isothermal amplification) system for rapid diagnosis of H5 avian influenza virus infection,” Vaccine, vol. 24, no. 44-46, pp. 6679–6682, 2006. View at Publisher · View at Google Scholar · View at Scopus
  4. J. P. Dukes, D. P. King, and S. Alexandersen, “Novel reverse transcription loop-mediated isothermal amplification for rapid detection of foot-and-mouth disease virus,” Archives of Virology, vol. 151, no. 6, pp. 1093–1106, 2006. View at Publisher · View at Google Scholar · View at Scopus
  5. M. Parida, K. Horioke, H. Ishida et al., “Rapid detection and differentiation of dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplification assay,” Journal of Clinical Microbiology, vol. 43, no. 6, pp. 2895–2903, 2005. View at Publisher · View at Google Scholar · View at Scopus
  6. K. A. Curtis, D. L. Rudolph, and S. M. Owen, “Rapid detection of HIV-1 by reverse-transcription, loop-mediated isothermal amplification (RT-LAMP),” Journal of Virological Methods, vol. 151, no. 2, pp. 264–270, 2008. View at Publisher · View at Google Scholar · View at Scopus
  7. Y. Kurosaki, A. Takada, H. Ebihara et al., “Rapid and simple detection of Ebola virus by reverse transcription-loop-mediated isothermal amplification,” Journal of Virological Methods, vol. 141, no. 1, pp. 78–83, 2007. View at Publisher · View at Google Scholar · View at Scopus
  8. X. Ding, K. Nie, L. Shi et al., “Improved detection limit in rapid detection of human enterovirus 71 and coxsackievirus A16 by a novel reverse transcription-isothermal multiple-self-matching-initiated amplification assay,” Journal of Clinical Microbiology, vol. 52, no. 6, pp. 1862–1870, 2014. View at Publisher · View at Google Scholar · View at Scopus
  9. M. Delarue, O. Poch, N. Tordo, D. Moras, and P. Argos, “An attempt to unify the structure of polymerases,” Protein Engineering, vol. 3, no. 6, pp. 461–467, 1990. View at Publisher · View at Google Scholar · View at Scopus
  10. A. Hasan, A. A. Abedi, and S. Arjunan, “Molecular characterization of thermostable DNA polymerase of Bacillus stearothermophilus spp isolated from soil in Bangalore, India,” European Journal of Experimental Biology, vol. 4, no. 4, pp. 67–72, 2014. View at Google Scholar
  11. J. M. Aliotta, J. J. Pelletier, J. L. Ware, L. S. Moran, J. S. Benner, and H. Kong, “Thermostable Bst DNA polymerase I lacks a 3′ → 5′ proofreading exonuclease activity,” Genetic Analysis: Biomolecular Engineering, vol. 12, no. 5-6, pp. 185–195, 1996. View at Publisher · View at Google Scholar · View at Scopus
  12. T. A. Steitz, “DNA polymerases: structural diversity and common mechanisms,” Journal of Biological Chemistry, vol. 274, no. 25, pp. 17395–17398, 1999. View at Publisher · View at Google Scholar · View at Scopus
  13. S.-M. Phang, C.-Y. Teo, E. Lo, and V. W. Thi Wong, “Cloning and complete sequence of the DNA polymerase-encoding gene (BstpolI) and characterisation of the Klenow-like fragment from Bacillus stearothermophilus,” Gene, vol. 163, no. 1, pp. 65–68, 1995. View at Publisher · View at Google Scholar · View at Scopus
  14. F. C. Lawyer, S. Stoffel, R. K. Saiki et al., “High-level expression, purification, and enzymatic characterization of full-length Thermus aquaticus DNA polymerase and a truncated form deficient in 5′ to 3′ exonuclease activity,” Genome Research, vol. 2, pp. 275–287, 1993. View at Publisher · View at Google Scholar
  15. Y. Xu, O. Potapova, A. E. Leschziner, N. D. F. Grindley, and C. M. Joyce, “Contacts between the 5′ nuclease of DNA Polymerase I and Its DNA substrate,” Journal of Biological Chemistry, vol. 276, no. 32, pp. 30167–30177, 2001. View at Publisher · View at Google Scholar · View at Scopus
  16. M. G. Riggs, S. Tudor, M. Sivaram, and S. H. McDonough, “Construction of single amino acid substitution mutants of cloned Bacillus stearothermophilus DNA polymerase I which lack 5'3' exonuclease activity,” Biochimica et Biophysica Acta, vol. 1307, no. 2, pp. 178–186, 1996. View at Publisher · View at Google Scholar · View at Scopus
  17. F. Van Den Ent and J. Löwe, “RF cloning: a restriction-free method for inserting target genes into plasmids,” Journal of Biochemical and Biophysical Methods, vol. 67, no. 1, pp. 67–74, 2006. View at Publisher · View at Google Scholar · View at Scopus
  18. P. Chen, Z. Liu, S. Liu et al., “A LC-MS/MS method for the analysis of intracellular nucleoside triphosphate levels,” Pharmaceutical Research, vol. 26, no. 6, pp. 1504–1515, 2009. View at Publisher · View at Google Scholar · View at Scopus
  19. E. Kinai, H. Gatanaga, Y. Kikuchi, S. Oka, and S. Kato, “Ultrasensitive method to quantify intracellular zidovudine mono-, di- and triphosphate concentrations in peripheral blood mononuclear cells by liquid chromatography-tandem mass spectrometry,” Journal of Mass Spectrometry, vol. 50, no. 6, pp. 783–791, 2015. View at Publisher · View at Google Scholar · View at Scopus
  20. Y. Jing, W. X. Huang, H. W. Zeng et al., “Hand-foot-and-mouth disease,” in Diagnostic Imaging of Emerging Infectious Diseases, Springer, Amsterdam, The Netherlands, 2016. View at Google Scholar
  21. T. P. Van Boeckel, S. Takahashi, Q. Liao et al., “Hand, foot, and mouth disease in China: critical community size and spatial vaccination strategies,” Scientific Reports, vol. 6, Article ID 25248, 2016. View at Publisher · View at Google Scholar
  22. L.-J. Xu, T. Jiang, F.-J. Zhang et al., “Global transcriptomic analysis of human neuroblastoma cells in response to enterovirus type 71 infection,” PLoS ONE, vol. 8, no. 7, Article ID e65948, 2013. View at Publisher · View at Google Scholar · View at Scopus
  23. E. Dias and M. Dias, “Recurring hand foot mouth disease in a child,” Annals of Tropical Medicine and Public Health, vol. 5, no. 1, pp. 40–41, 2012. View at Publisher · View at Google Scholar · View at Scopus
  24. X. Wang, J.-P. Zhu, Q. Zhang et al., “Detection of enterovirus 71 using reverse transcription loop-mediated isothermal amplification (RT-LAMP),” The Journal of Virological Methods, vol. 179, no. 2, pp. 330–334, 2012. View at Publisher · View at Google Scholar · View at Scopus
  25. X. Ding, W. Wu, Q. Y. Zhu, T. Zhang, W. Jin, and Y. Mu, “Mixed-dye-based label-free and sensitive dual fluorescence for the product detection of nucleic acid isothermal multiple-self-matching-initiated amplification,” Analytical Chemistry, vol. 87, no. 20, pp. 10306–10314, 2015. View at Publisher · View at Google Scholar · View at Scopus
  26. H. Klenow and I. Henningsen, “Selective elimination of the exonuclease activity of the deoxyribonucleic acid polymerase from Escherichia coli B by limited proteolysis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 65, no. 1, pp. 168–175, 1970. View at Publisher · View at Google Scholar · View at Scopus
  27. D. L. Ollis, P. Brick, R. Hamlin, N. G. Xuong, and T. A. Steitz, “Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP,” Nature, vol. 313, no. 6005, pp. 762–766, 1985. View at Publisher · View at Google Scholar · View at Scopus
  28. A. H. Polesky, T. A. Steitz, N. D. F. Grindley, and C. M. Joyce, “Identification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I from Escherichia coli,” The Journal of Biological Chemistry, vol. 265, no. 24, pp. 14579–14591, 1990. View at Google Scholar · View at Scopus
  29. J. R. Kiefer, C. Mao, C. J. Hansen et al., “Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 Å resolution,” Structure, vol. 5, no. 1, pp. 95–108, 1997. View at Publisher · View at Google Scholar · View at Scopus
  30. C. A. Brautigam and T. A. Steitz, “Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes,” Current Opinion in Structural Biology, vol. 8, no. 1, pp. 54–63, 1998. View at Publisher · View at Google Scholar · View at Scopus
  31. Y. Zhao, D. Jeruzalmi, I. Moarefi, L. Leighton, R. Lasken, and J. Kuriyan, “Crystal structure of an archaebacterial DNA polymerase,” Structure, vol. 7, no. 10, pp. 1189–1199, 1999. View at Publisher · View at Google Scholar · View at Scopus