Estimation of binding constants of peptide nucleic acid and secondary-structured DNA by affinity capillary electrophoresis

Lal Mohan Kundu, Harumi Tsukada, Yukiharu Matsuoka, Naoki Kanayama, Tohru Takarada, Mizuo Maeda

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

An affinity capillary electrophoresis method was developed to determine a binding constant between a peptide nucleic acid (PNA) and a hairpin-structured DNA. A diblock copolymer composed of PNA and polyethylene glycol (PEG) was synthesized as a novel affinity probe. The base sequence of the probe's PNA segment was complementary to a hairpin-structured region of a 60-base single-stranded DNA (ssDNA). Upon applying a voltage, the DNA hairpin migrated slowly compared to a random sequence ssDNA in the presence of the PNA probe. This retardation was induced by strand invasion of the PNA into the DNA hairpin to form a hybridized complex, where the PEG segment received a large amount of hydrodynamic friction during electrophoresis. The binding constant between the PNA probe and the DNA hairpin was easily determined by mobility analysis. This simple method would be potentially beneficial in studying binding behaviors of various artificial nucleotides to natural DNA or RNA.

Original languageEnglish
Pages (from-to)5204-5209
Number of pages6
JournalAnalytical chemistry
Volume84
Issue number12
DOIs
Publication statusPublished - Jun 19 2012

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Peptide Nucleic Acids
Capillary electrophoresis
DNA
Nucleic Acid Probes
Single-Stranded DNA
Electrophoresis
Block copolymers
Hydrodynamics
Nucleotides
RNA
Friction
Electric potential

All Science Journal Classification (ASJC) codes

  • Analytical Chemistry

Cite this

Estimation of binding constants of peptide nucleic acid and secondary-structured DNA by affinity capillary electrophoresis. / Kundu, Lal Mohan; Tsukada, Harumi; Matsuoka, Yukiharu; Kanayama, Naoki; Takarada, Tohru; Maeda, Mizuo.

In: Analytical chemistry, Vol. 84, No. 12, 19.06.2012, p. 5204-5209.

Research output: Contribution to journalArticle

Kundu, Lal Mohan ; Tsukada, Harumi ; Matsuoka, Yukiharu ; Kanayama, Naoki ; Takarada, Tohru ; Maeda, Mizuo. / Estimation of binding constants of peptide nucleic acid and secondary-structured DNA by affinity capillary electrophoresis. In: Analytical chemistry. 2012 ; Vol. 84, No. 12. pp. 5204-5209.
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