Theoretical studies on sulfur and metal cation (Cu(II), Ni(II), Pd(II), and Pt(II))-containing artificial DNA.
We evaluated the stability, UV-vis spectra, and possibility of stacking of [S-M(II)-S] (M=Ni, Pd, Pt, S: hydroxypyridinethione) using density functional theory (DFT). We calculated the formation energies of modified bases with possible combinations of chalcogen atoms and metal cations. The results confirmed that [H-Ni(II)-H] (H: hydroxypyridone), [H-Cu(II)-H], and [S-Cu(II)-S] would form stable metal-base pairing; on the other hand, [H-Zn(II)-H], [S-Zn(II)-S], and [H-Pt(II)-H] would not. We predicted UV-vis excitations at 400-410 nm, mainly dominated by a d-pi* transition accompanied by a pi-pi* transition in [S-M(II)-S], where a metal-to-ligand charge transfer shifts the peak of S (without metal cations) by performing time-dependent density functional theory (TDDFT) calculations. By adding the Andersson-Langreth-Lundqvist van der Waals correction to the hybrid DFT results, we estimated the interaction energy between base pairs of [S-M(II)-S]. According to the results, the interaction between [S-M(II)-S] monomers for all cases is attractive, so that the selectivity of formation of the metal-containing DNA is governed mainly by the formation of the base pair in the aqueous phase and only slightly by the pi-pi stacking interaction between the modified bases.
Matsui
Toru
T
Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-8656, Japan. matsui@chem.sci.osaka-u.ac.jp
Miyachi
Hideaki
H
Nakanishi
Yasuyuki
Y
Shigeta
Yasuteru
Y
Sato
Takeshi
T
Kitagawa
Yasutaka
Y
Okumura
Mitsutaka
M
Hirao
Kimihiko
K
D020029:Base Pairing; D002413:Cations, Divalent / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D008670:Metals / Q000737:chemistry*; D009711:Nucleotides / Q000737:chemistry*; D013455:Sulfur / Q000737:chemistry*
D002413:Cations, Divalent; D008670:Metals; D009711:Nucleotides; D013455:Sulfur; D004247:DNA