Quantitative single-nucleotide polymorphism analysis in secondary-structured DNA by affinity capillary electrophoresis using a polyethylene glycol-peptide nucleic acid block copolymer

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

doi:10.1016/j.ab.2012.10.023

Quantitative single-nucleotide polymorphism analysis in secondary-structured DNA by affinity capillary electrophoresis using a polyethylene glycol-peptide nucleic acid block copolymer

Anal Biochem. 2013 Feb 15;433(2):150-2. doi: 10.1016/j.ab.2012.10.023. Epub 2012 Oct 26.

Authors

Harumi Tsukada¹, Lal Mohan Kundu, Yukiharu Matsuoka, Naoki Kanayama, Tohru Takarada, Mizuo Maeda

Affiliation

¹ Bioengineering Laboratory, RIKEN Advanced Science Institute, Wako, Saitama 351-0198, Japan.

PMID: 23103339
DOI: 10.1016/j.ab.2012.10.023

Abstract

To estimate allele frequency of single-nucleotide polymorphisms (SNPs) in pooled DNAs with secondary structures, an affinity capillary electrophoresis was developed using an allele-specific peptide nucleic acid probe modified with polyethylene glycol. This probe disrupted secondary structures of DNA analytes and hybridized to them during electrophoresis. Such DNA-binding capability allowed separation of the folded analytes with a single-base difference within 20 min. The feed ratio of the target allele was evaluated by calculating the peak area ratio. The averaged difference between the feed and observed ratio was 1.5%. This method should be of general applicability to quantitative SNP analyses.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alleles*
DNA / analysis*
DNA / chemistry
DNA / genetics*
Electrophoresis, Capillary / methods
Humans
Nucleic Acid Conformation*
Polymorphism, Single Nucleotide*

Substances

DNA