title: Drastic stabilization of parallel DNA hybridizations by a polylysine comb-type copolymer with hydrophilic graft chain.
abstract: Electrostatic interactions play a major role in protein-DNA interactions. As a model system of a cationic protein, herein we focused on a comb-type copolymer of a polycation backbone and dextran side chains, poly(L-lysine)-graft-dextran (PLL-g-Dex), which has been reported to form soluble interpolyelectrolyte complexes with DNA strands. We investigated the effects of PLL-g-Dex on the conformation and thermodynamics of DNA oligonucleotides forming various secondary structures. Thermodynamic analysis of the DNA structures showed that the parallel conformations involved in both DNA duplexes and triplexes were significantly and specifically stabilized by PLL-g-Dex. On the basis of thermodynamic parameters, it was further possible to design DNA switches that undergo structural transition responding to PLL-g-Dex from an antiparallel duplex to a parallel triplex even with mismatches in the third strand hybridization. These results suggest that polycationic molecules are able to induce structural polymorphism of DNA oligonucleotides, because of the conformation-selective stabilization effects.
authors.affiliation: Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047 (Japan). miyoshi@center.konan-u.ac.jp.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Miyoshi
authors.forename: Yu-Mi
authors.initials: YM
authors.lastname: Ueda
authors.forename: Naohiko
authors.initials: N
authors.lastname: Shimada
authors.forename: Shu-Ichi
authors.initials: S
authors.lastname: Nakano
authors.forename: Naoki
authors.initials: N
authors.lastname: Sugimoto
authors.forename: Atsushi
authors.initials: A
authors.lastname: Maruyama
mesh_terms: D004247:DNA / Q000187:drug effects*; D003911:Dextrans / Q000494:pharmacology*; D005812:Genes, Switch / Q000187:drug effects; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000378:metabolism; D011107:Polylysine / Q000031:analogs & derivatives* / Q000494:pharmacology; D013816:Thermodynamics
chemical_list: D003911:Dextrans; D009841:Oligonucleotides; C113090:poly(lysine)-graft-dextran; D011107:Polylysine; D004247:DNA
keywords: DNA structures; amino acids; cationic polymers; polymorphism; thermodynamics