Open AccessThe Role of Hydrogen Bonds in the Stabilization of Silver-Mediated Cytosine Tetramers
Author(s) -
Leonardo Andrés Espinosa Leal,
Alexander S. Karpenko,
Steven M. Swasey,
E. G. Gwinn,
V. Rojas-Cervellera,
Carme Rovira,
Olga Lopez-Acevedo
Publication year - 2015
Publication title -
the journal of physical chemistry letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.563
H-Index - 203
ISSN - 1948-7185
DOI - 10.1021/acs.jpclett.5b01864
Subject(s) - hydrogen bond , chemistry , nucleobase , cytosine , crystallography , tetramer , chemical physics , circular dichroism , dna , metal , computational chemistry , molecule , organic chemistry , biochemistry , enzyme
DNA oligomers can form silver-mediated duplexes, stable in gas phase and solution, with potential for novel biomedical and technological applications. The nucleobase-metal bond primarily drives duplex formation, but hydrogen (H-) bonds may also be important for structure selection and stability. To elucidate the role of H-bonding, we conducted theoretical and experimental studies of a duplex formed by silver-mediated cytosine homopobase DNA strands, two bases long. This silver-mediated cytosine tetramer is small enough to permit accurate, realistic modeling by DFT-based quantum mechanics/molecular mechanics methods. In gas phase, our calculations found two energetically favorable configurations distinguished by H-bonding, one with a novel interplane H-bond, and the other with planar H-bonding of silver-bridged bases. Adding solvent favored silver-mediated tetramers with interplane H-bonding. Overall agreement of electronic circular dichroism spectra for the final calculated structure and experiment validates these findings. Our results can guide use of these stabilization mechanisms for devising novel metal-mediated DNA structures.