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Superb nucleotide discrimination by a novel on/off switch for DNA polymerization and its applications

Molecular Biotechnology volume 29, pages 93–100 (2005)Cite this article

Abstract

With the use of polymerases having 3′ to 5′ exonuclease activity and 3′ phosphorothioate-modified allelespecific primers, we recently devised a SNP-operated on/off switch controlling DNA polymerization. One advantage of this novel on/off switch is its adaptability to arrayed primer extension. To further expand its application in genetic analysis, the new on/off switch was evaluated in discrimination of the match/mismatch status of single nucleotides upstream from the primer 3′ terminal. A set of seven amplicons was developed with the templates differing from each other by a single nucleotide. Using this set of amplicons, the new on/off switch was shown to be able to efficiently discriminate single nucleotide polymorphisms from the primer 3′ terminus to the −6 position from the primer 3′ terminus. These data, illustrating the broad single nucleotide discrimination ability of this novel on/off switch, explain why the SNP-operated on/off switch is powerful in SNP analysis, and also indicate useful applications to genetic analysis additional to SNP assay. First, these data broaden the application of the novel on/off switch in the analysis of mutations other than SNPs. Second, it raises a nucleotide-walking algorithm suitable for de novo array-based sequencing analysis.

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Author information

Affiliations

  1. SNP Institute, Hengyang, Hunan, China

    Kai Li, Jia Zhang & Linling Chen

  2. City of Hope National Medical Center, Duarte, CA, USA

    Kai Li & Sommer Steve S.

  3. Genomapping Inc., Tianjin, China

    Jia Zhang

Authors
  1. Kai Li
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  2. Jia Zhang
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  3. Linling Chen
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  4. Sommer Steve S.
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Correspondence to Kai Li.

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Li, K., Zhang, J., Chen, L. et al. Superb nucleotide discrimination by a novel on/off switch for DNA polymerization and its applications. Mol Biotechnol 29, 93–100 (2005). https://doi.org/10.1385/MB:29:2:093

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  • DOI: https://doi.org/10.1385/MB:29:2:093

Index Entries

  • Proofreading
  • exo+ polymerase
  • on/off switch
  • SNP
  • sequencing
  • microarrays