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Single Locked Nucleic Acid-Enhanced Nanopore Genetic Discrimination of Pathogenic Serotypes and Cancer Driver Mutations.

Authors
  • Tian, Kai
  • Chen, Xiaowei
  • Luan, Binquan1
  • Singh, Prashant
  • Yang, Zhiyu
  • Gates, Kent S
  • Lin, Mengshi
  • Mustapha, Azlin
  • Gu, Li-Qun
  • 1 Computational Biology Center , IBM Thomas J. Watson Research , Yorktown Heights , New York 10598 , United States. , (United States)
Type
Published Article
Journal
ACS Nano
Publisher
American Chemical Society
Publication Date
May 22, 2018
Volume
12
Issue
5
Pages
4194–4205
Identifiers
DOI: 10.1021/acsnano.8b01198
PMID: 29664612
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Accurate and rapid detection of single-nucleotide polymorphism (SNP) in pathogenic mutants is crucial for many fields such as food safety regulation and disease diagnostics. Current detection methods involve laborious sample preparations and expensive characterizations. Here, we investigated a single locked nucleic acid (LNA) approach, facilitated by a nanopore single-molecule sensor, to accurately determine SNPs for detection of Shiga toxin producing Escherichia coli (STEC) serotype O157:H7, and cancer-derived EGFR L858R and KRAS G12D driver mutations. Current LNA applications that require incorporation and optimization of multiple LNA nucleotides. But we found that in the nanopore system, a single LNA introduced in the probe is sufficient to enhance the SNP discrimination capability by over 10-fold, allowing accurate detection of the pathogenic mutant DNA mixed in a large amount of the wild-type DNA. Importantly, the molecular mechanistic study suggests that such a significant improvement is due to the effect of the single-LNA that both stabilizes the fully matched base-pair and destabilizes the mismatched base-pair. This sensitive method, with a simplified, low cost, easy-to-operate LNA design, could be generalized for various applications that need rapid and accurate identification of single-nucleotide variations.

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