Cationic Comb-Type Copolymer Excludes Intercalating Dye from DNA Without Inducing DNA Condensation
Atsushi Maruyama, Naotaka Sonda, Kohei Yamasaki, Masanori Hirano, Satoru Kidoaki, Naohiko Shimada, Masatoshi Maeshiro and Masaya Miyazaki
Affiliation: Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 B-57, Nagatsuta, Yokohama 226-8501, Japan.
Keywords: Coil-to-globule transition, Compaction, DNA, Flow-stretch, Graft copolymer, Inter polyelectrolyte complex, Polycation, Singlemolecular
The interaction of a single molecule of DNA with cationic comb-type copolymers has been observed using a flow-stretch assay.
We have shown that interaction with a copolymer with a high degree of grafting did not cause a coil-to-globule transition but resulted
in shrinkage of the DNA by 20%. In this study, a flow-stretch assay was employed in which changes in length and fluorescence intensity
of DNA were simultaneously observed. Upon binding of fluorescent intercalator dyes, the DNA length was extended. In the presence
of copolymer, dye binding was inhibited and DNA length was not significantly different than that in the absence of dye and copolymer.
Our data suggest that the copolymer does not influence DNA length. Our observation implies that use of the fluorescence dye
exclusion assay to estimate DNA condensing activity of polycations must be carefully carried out.
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