Home Shortening distance of forward and reverse primers for nucleic acid isothermal amplification
Article
Licensed
Unlicensed Requires Authentication

Shortening distance of forward and reverse primers for nucleic acid isothermal amplification

  • Qu Haitao EMAIL logo , Zhang Wenchao , Zhang Xiaohui , Wang Xiujun and Li Sulong
Published/Copyright: April 3, 2014

Abstract

Existent nucleic acid isothermal detection techniques for clinical diseases are difficult to promote greatly due to limitations in such aspects as methodology, costs of detection, amplification efficiency and conditions for operation. There is therefore an urgent need for a new isothermal amplification method with the characteristics of high accuracy, easy operation, short time of detection and low costs. We have devised a new method of nucleic acid isothermal amplification using Bst DNA polymerase under isothermal conditions (60–65°C). We call this method of amplification by shortening the distance between forward and reverse primers for nucleic acid isothermal amplification SDAMP. The results demonstrated that this technique is highly sensitive, specific and has short reaction times (40–60 min). Results of sequencing show that the products of SDAMP amplification are mainly polymers formed by series connection of monomers formed through linkage of forward primer and complementary sequences in reverse primer via a few bases. The method is different from current methods of nucleic acid amplification. Our study shows, however, that it is a specific method of nucleic acid isothermal amplification depending on interactions between primers and DNA template.


Corresponding author: Qu Haitao, Harbin Dege Biotechnology Co., Ltd., Room 1303, Building B, Hexing Shopping Mall, No.400, Xidazhi Street, Harbin, 150000, China, e-mail:

Acknowledgments

This work was supported by Heilongjiang Prevention and Treatment of Infectious Diseases Hospital and Huazhong Agricultural University.

References

Compton, J. (1991). Nucleic acid sequence-based amplification. Nature 350, 91–92.10.1038/350091a0Search in Google Scholar PubMed

Fang, R., Li, X., Hu, L., You, Q., Li, J., Wu, J., Xu, P., Zhong, H., Luo, Y., and Mei, J. (2009). Cross-priming amplification for rapid detection of Mycobacterium tuberculosis in sputum specimens. J. Clin. Microbiol. 47, 845–847.10.1128/JCM.01528-08Search in Google Scholar PubMed PubMed Central

Guatelli, J.C., Whitfield, K.M., Kwoh, D.Y., Barringer, K.J., Richman, D.D., and Gingeras, T.R. (1990). Isothermal in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proc. Nat. Acad. Sci. 87, 1874–1878.10.1073/pnas.87.5.1874Search in Google Scholar PubMed PubMed Central

Guo, Y., Park, J.M., Cui, B., Humes, E., Gangadharan, S., Hung, S., FitzGerald, P.C., Hoe, K-L., Grewal, S.I., and Craig, N.L. (2013). Integration profiling of gene function with dense maps of transposon integration. Genetics 195, 599–609.10.1534/genetics.113.152744Search in Google Scholar PubMed PubMed Central

Hafner, G., Yang, I., Wolter, L., Stafford, M., and Giffard, P. (2001). Isothermal amplification and multimerization of DNA by Bst DNA polymerase. Biotechniques 30, 852–867.10.2144/01304rr03Search in Google Scholar PubMed

Hellyer, T.J., DesJardin, L.E., Assaf, M.K., Bates, J.H., Cave, M.D., and Eisenach, K.D. (1996). Specificity of IS6110-based amplification assays for Mycobacterium tuberculosis complex. J Clin Microbiol. 34, 2843–2846.10.1128/jcm.34.11.2843-2846.1996Search in Google Scholar PubMed PubMed Central

Katter, K., Geurts, A.M., Hoffmann, O., Mátés, L., Landa, V., Hiripi, L., Moreno, C., Lazar, J., Bashir, S., and Zidek, V. (2013). Transposon-mediated transgenesis, transgenic rescue, and tissue-specific gene expression in rodents and rabbits. FASEB J. 27, 930–941.10.1096/fj.12-205526Search in Google Scholar PubMed PubMed Central

Lizardi, P.M., Huang, X., Zhu, Z., Bray-Ward, P., Thomas, D.C., and Ward, D.C. (1998). Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat. Genet. 19, 225–232.10.1038/898Search in Google Scholar PubMed

Martienssen, R.A., and Chandler, V.L. (2013). 5 molecular mechanisms of transposon epigenetic regulation. In: Plant Transposons and Genome Dynamics in Evolution (New York: Wiley and Sons), pp. 71–92.10.1002/9781118500156.ch5Search in Google Scholar

Notomi, T., Okayama, H., Masubuchi, H., Yonekawa, T., Watanabe, K., Amino, N., and Hase, T. (2000). Loop-mediated isothermal amplification of DNA. Nucl. Acids Res. 28, e63–e63.10.1093/nar/28.12.e63Search in Google Scholar PubMed PubMed Central

Ritis, K., Tzoanopoulos, D., Speletas, M., Papadopoulos, E., Arvanitidis, K., Kartali, S., and Sideras, P. (2000). Amplification of IS6110 sequence for detection of Mycobacterium tuberculosis complex in HIV-negative patients with fever of unknown origin (FUO) and evidence of extrapulmonary disease. J. Intern. Med. 248, 415–424.10.1046/j.1365-2796.2000.00750.xSearch in Google Scholar PubMed

Saiki, R.K., Scharf, S., Faloona, F., Mullis, K.B., Horn, G.T., Erlich, H.A., and Arnheim, N. (1985). Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230, 1350–1354.10.1126/science.2999980Search in Google Scholar PubMed

van Opijnen, T., and Camilli, A. (2013). Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms. Nat. Rev. Microbiol. 11, 435–442.10.1038/nrmicro3033Search in Google Scholar PubMed PubMed Central

Walker, G.T., Fraiser, M.S., Schram, J.L., Little, M.C., Nadeau, J.G., and Malinowski, D.P. (1992). Strand displacement amplification – an isothermal, in vitro DNA amplification technique. Nucl. Acids Res. 20, 1691–1696.10.1093/nar/20.7.1691Search in Google Scholar PubMed PubMed Central

Yong Zhang, D., Brandwein, M., Chun Hung Hsuih, T., and Li, H. (1998). Amplification of target-specific, ligation-dependent circular probe. Gene 211, 277–285.10.1016/S0378-1119(98)00113-9Search in Google Scholar

Received: 2014-1-9
Accepted: 2014-3-28
Published Online: 2014-4-3
Published in Print: 2014-6-1

©2014 by Walter de Gruyter Berlin/Boston

Downloaded on 22.9.2025 from https://www.degruyterbrill.com/document/doi/10.1515/hsz-2014-0103/html
Scroll to top button