ABSTRACT: We investigate the energetics of the antiparallel, hybrid and parallel type G-quadruplex structures of the human telomere DNA sequence. We find that both the conformational energy and solvation free energy of these structures are roughly inversely proportional to their radii of gyration. We rationalize this finding in terms of the dominance of the electrostatic contributions. We also show that the solvation free energy is more significant than the conformational energy in determining the G-quadruplex structures, which is in contrast to the canonical B-DNA structures. Our work will contribute to an understanding of the molecular mechanisms dictating various G-quadruplex topologies.

KEYWORDS: DNA, Conformational energy, Solvation free energy, Molecular dynamics simulation, Integral-equation theory,

Author : Jinkeong Lee, Haeri Im, Song-Ho Chong, and Sihyun Ham

Journal :  Chemical Physics letters, 693, 2018, 216-221

Publication Date : 2018.02

This publication is from

Prof. Sihyun Ham’s lab