Structural origin of copper ion containing artificial DNA: a density functional study.
In order to investigate an origin of structural stability of a copper ion containing artificial DNA, we evaluated the stacking energy between [H-Cu(2+)-H] (H: hydroxypyridone) dimer by means of density functional theory (DFT) with an Anderson-Langreth-Lindqvist van der Waals (vdW) functional. The calculated distance between the copper ions is about 3.6 angstroms, which agrees well with the experimental data. Evaluated stacking energy is about 8-10 kcal/mol, which is slightly smaller than that of two base pairs in a natural B-DNA. This tendency does not change in [H-2H(+)-H], which does not contain copper ions. These results indicate that the vdW interaction dominates the inter-base-pair interaction over spin-spin interaction, in contrast to a conjecture by an experimental group. According to the results by the open-shell DFT, antiferromagnetic (singlet) and ferromagnetic (triplet) states are almost degenerated when the two bases are vertically located and both bases have a planar structure as found in the B-DNA.
Matsui
Toru
T
Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
Miyachi
Hideaki
H
Sato
Takeshi
T
Shigeta
Yasuteru
Y
Hirao
Kimihiko
K
D020029:Base Pairing; D003300:Copper / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular
D003300:Copper; D004247:DNA