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

Fingerprint

Capillary electrophoresis
Single-Stranded DNA
Capillary Electrophoresis
electrokinesis
substitution
Substitution reactions
Polyethylene glycols
DNA
Copolymers
rate
evaluation
Electrophoretic mobility
Ethylene Glycol
Friction
Oligodeoxyribonucleotides
Hydrodynamics
Electrophoresis
ethylene
ligand
Block copolymers

All Science Journal Classification (ASJC) codes

  • Analytical Chemistry
  • Biochemistry
  • Environmental Chemistry
  • Spectroscopy

Cite this

Evaluation of single-base substitution rate in DNA by affinity capillary electrophoresis. / Kanayama, Naoki; Takarada, Tohru; Shibata, Hideaki; Kimura, Ayumi; Maeda, Mizuo.

In: Analytica Chimica Acta, Vol. 619, No. 1, 30.06.2008, p. 101-109.

Research output: Contribution to journalArticle

Kanayama, Naoki ; Takarada, Tohru ; Shibata, Hideaki ; Kimura, Ayumi ; Maeda, Mizuo. / Evaluation of single-base substitution rate in DNA by affinity capillary electrophoresis. In: Analytica Chimica Acta. 2008 ; Vol. 619, No. 1. pp. 101-109.
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