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Drastic Stabilization of Parallel DNA Hybridizations by a Polylysine Comb‐Type Copolymer with Hydrophilic Graft Chain
Author(s) -
Miyoshi Daisuke,
Ueda Yumi,
Shimada Naohiko,
Nakano Shuichi,
Sugimoto Naoki,
Maruyama Atsushi
Publication year - 2014
Publication title -
chemmedchem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.817
H-Index - 100
eISSN - 1860-7187
pISSN - 1860-7179
DOI - 10.1002/cmdc.201402157
Subject(s) - antiparallel (mathematics) , polylysine , dna , oligonucleotide , copolymer , chemistry , dextran , cationic polymerization , molecular dynamics , duplex (building) , biophysics , molecule , crystallography , stereochemistry , polymer chemistry , biochemistry , computational chemistry , polymer , organic chemistry , biology , physics , quantum mechanics , magnetic field
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.