PCR-free mutation detection of BRCA1 on a zip-code microarray using ligase chain reaction.

Agnishwar Girigoswami, Cheulhee Jung, Hyo Young Mun, Hyun Gyu Park

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)


We describe here ligation-based strategy to detect mutations in BRCA1 utilizing zip-code microarray technology. In our first approach, PCR was performed to amplify the genomic regions containing the mutation sites. The PCR products were then used as templates in a subsequent ligation reaction using two ligation primers that flanked the mutation site. The primary allele-specific primer is designed to contain a base of mutation site at its 3' end with 5' complementarity to the respective zip-code sequence while the secondary common primer is modified by biotin at its 3' end. Depending on the genotype of samples at the mutation site, the nick between the two ligation primers can be sealed in the presence of DNA ligase. The ligation products were then hybridized on the zip-code microarray followed by staining with streptavidine-cy3 to generate a fluorescent signal. Using this strategy we successfully genotyped selected Korean-specific mutation sites in exon 11 of BRCA1 with a wild type and two heterozygote mutant samples. Furthermore, we also demonstrated that ligase chain reaction using unamplified genomic DNA as direct templates is enough to generate sufficient signals for correct genotypings in a multiplexed manner, verifying first that PCR is not essential for this microarray-based strategy.

Original languageEnglish
Pages (from-to)897-902
Number of pages6
JournalJournal of Biochemical and Biophysical Methods
Issue number6
Publication statusPublished - 2008 Apr 24
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by the Brain Korea 21 (BK21) program, the Korea Research Foundation and the Centre for Ultramicrochemical Process Systems.

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry


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