SNPs detection by a single-strand specific nuclease on a PNA zip-code microarray

Hyo young Mun, Agnishwar Girigoswami, Cheulhee Jung, Dae Yeon Cho, Hyun Gyu Park

Research output: Contribution to journalArticlepeer-review

18 Citations (Scopus)


In this report, a reliable peptide nucleic acid (PNA) microarray-based method for accurately detecting single nucleotide polymorphism (SNP) in human genes is described. The technique relies on the mismatched cleavage activity of a single-strand specific (SSS) nuclease. PCR amplification was performed to prepare gene fragments containing the mutation sites. The amplified fragments were then employed as templates for the SSS nuclease reaction using chimeric probes, modified with biotin at the 5′ end and extended with a unique anchoring zip-code complement sequence at the 3′ end. The SSS nuclease promotes cleavage of heteroduplex DNAs at base mismatched positions to produce crumbled chimeric probes in the presence of imperfectly matching template strands. In contrast, the probes remain intact when they interact with perfectly matched template strands. Only the non-fragmented probes generate fluorescence signals after treatment with streptavidin-Cy3 on the PNA zip-code array. This methodology was used to successfully genotype selected Korean-specific BRCA mutation sites with wild type and mutant samples. The investigation has led to the development of a reliable SSS nuclease-based system for the diagnosis of human genetic mutations or SNPs.

Original languageEnglish
Pages (from-to)1706-1711
Number of pages6
JournalBiosensors and Bioelectronics
Issue number6
Publication statusPublished - 2009 Feb 15
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by the Brain Korea 21 (BK21) program, the Korea Research Foundation Grant funded by the Korean Government (MOEHRD) (KRF-2006-331-D00114) and the Centre for Ultramicrochemical Process Systems.


  • BRCA
  • Biochip
  • PNA
  • SNP
  • Single-strand specific (SSS) nuclease

ASJC Scopus subject areas

  • Biotechnology
  • Biophysics
  • Biomedical Engineering
  • Electrochemistry


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