title: Estimation of binding constants of peptide nucleic acid and secondary-structured DNA by affinity capillary electrophoresis.
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.
authors.affiliation: Bioengineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
authors.forename: Lal Mohan
authors.initials: LM
authors.lastname: Kundu
authors.forename: Harumi
authors.initials: H
authors.lastname: Tsukada
authors.forename: Yukiharu
authors.initials: Y
authors.lastname: Matsuoka
authors.forename: Naoki
authors.initials: N
authors.lastname: Kanayama
authors.forename: Tohru
authors.initials: T
authors.lastname: Takarada
authors.forename: Mizuo
authors.initials: M
authors.lastname: Maeda
mesh_terms: D000345:Affinity Labels / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D019075:Electrophoresis, Capillary / Q000379:methods*; D055029:Inverted Repeat Sequences; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D020135:Peptide Nucleic Acids / Q000378:metabolism*; D011092:Polyethylene Glycols / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D000345:Affinity Labels; D020135:Peptide Nucleic Acids; D011092:Polyethylene Glycols; D004247:DNA