AFM-imaging diagnosis method for single nucleotide polymorphism using molecular beacon DNA as an intramolecular ligation template of target DNA and a viewable indicator

Hisao Yoshinaga, Koji Nakano, Nobuaki Soh, Toshihiko Imato

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

An AFM-imaging-based method for single nucleotide polymorphism (SNP) analysis is described. A stem-loop-forming 34-mer oligonucleotide (p34s) was designed. P34s contains the complementary sequence for K-ras (5'-GGT GGC-3', t6G), one of the human oncogenes, at the 5'-end for target-recognition and five successive phosphorothioate linkages in the loop. The functional probe, either alone or hybridized with target DNA (p34s/t6G), relaxed upon treatment with "opener" DNA. The template/target DNA interstrand hybridization product is covalently connected by ligase if the correct target is used, but not hybridized species including mismatches. With these results, developed was a solid-phase SNP assay by transferring an aliquot of the product onto an Au(111) substrate for self-assembly, followed by AFM imaging. Clear contrasts that allow the detection of SNPs, were observed for the ligated and non-ligated species representing the loop-to-linear conformational change. Simple statistical surface-roughness analysis determined the lowest concentration of the sample to be 5 × 10 -10 M, whose necessary sample quantity was 5 fmol. 2012

Original languageEnglish
Pages (from-to)939-945
Number of pages7
Journalanalytical sciences
Volume28
Issue number10
DOIs
Publication statusPublished - Jan 1 2012

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Polymorphism
Nucleotides
Imaging techniques
DNA
Ligases
Oligonucleotides
Self assembly
Assays
Surface roughness
Substrates

All Science Journal Classification (ASJC) codes

  • Analytical Chemistry

Cite this

AFM-imaging diagnosis method for single nucleotide polymorphism using molecular beacon DNA as an intramolecular ligation template of target DNA and a viewable indicator. / Yoshinaga, Hisao; Nakano, Koji; Soh, Nobuaki; Imato, Toshihiko.

In: analytical sciences, Vol. 28, No. 10, 01.01.2012, p. 939-945.

Research output: Contribution to journalArticle

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