Comb-type cationic copolymer expedites DNA strand exchange while stabilizing DNA duplex.
The accelerating effect of cationic substances on the DNA strand exchange reaction between a 20 bp DNA duplex and its complementary single strand was studied. A polycationic comb-type copolymer, that consists of a poly(L-lysine) backbone and a dextran graft chain (PLL-g-Dex) and known to stabilize triplex DNA, expedites the strand exchange reaction under physiological relevant conditions. Electrostatically a small excess of the copolymer let to a 300-1500-fold increase in the DNA strand exchange while large excess of spermine or cetyltrimethylammonium bromide, a cationic detergent known to promote markedly hybridization of complementary DNA strands, shows only a slight effect. The efficacy of the copolymer was not affected by a 10 mM Mg2+ concentration. Notably the copolymer promotes the strand exchange reaction while it stabilizes double-stranded DNA. The stabilization of strand exchange intermediates consisting of the parent duplex and the single strand by the copolymer is believed to be responsible for the observed acceleration behavior.
Kim
W J
WJ
Department of Biomolecular Engineering, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan.
Ishihara
T
T
Akaike
T
T
Maruyama
A
A
D002412:Cations / Q000737:chemistry; D002593:Cetrimonium Compounds / Q000737:chemistry; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D004586:Electrophoresis; D016650:Fluorescein-5-isothiocyanate / Q000378:metabolism; D005456:Fluorescent Dyes / Q000378:metabolism; D007700:Kinetics; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D011108:Polymers / Q000737:chemistry*; D013096:Spermine / Q000737:chemistry; D013816:Thermodynamics
D002412:Cations; D002593:Cetrimonium Compounds; D005456:Fluorescent Dyes; D009838:Oligodeoxyribonucleotides; D011108:Polymers; D013096:Spermine; D004247:DNA; D016650:Fluorescein-5-isothiocyanate