Evaluation of single-base substitution rate in DNA by affinity capillary electrophoresis

Naoki Kanayama, Tohru Takarada, Hideaki Shibata, Ayumi Kimura, Mizuo Maeda

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Capillary electrophoretic separation of 60 mer single-stranded DNA (ssDNA) and a single-base-substituted ssDNA was demonstrated using a size- and composition-controlled poly(ethylene glycol)-oligodeoxyribonucleotide block copolymer (PEG-b-ODN) as an affinity ligand. Under appropriate conditions, PEG-b-ODN and ssDNA with a complementary sequence formed a reversible complex via hybridization during the electrophoresis, while the copolymer did not interact with the single-base-substituted ssDNA. The copolymer's PEG length determined the electrophoretic mobility of the ssDNA; upon formation of the complex, the electrically neutral PEG added hydrodynamic friction to ssDNA. Simultaneously using two types of PEG-b-ODN copolymers whose PEG segments were of different lengths, we achieved the complete separation of the 60 mer ssDNA, its single-base-substituted ssDNA, and impurities. This method was sensitive enough to quantify a slight amount (approximately 1%) of the single-base-substituted ssDNA. The present results suggest that our approach is applicable to quantitative detection of minor genotypes.

Original languageEnglish
Pages (from-to)101-109
Number of pages9
JournalAnalytica Chimica Acta
Volume619
Issue number1
DOIs
Publication statusPublished - Jun 30 2008
Externally publishedYes

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All Science Journal Classification (ASJC) codes

  • Analytical Chemistry
  • Biochemistry
  • Environmental Chemistry
  • Spectroscopy

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