title: The Role of Hydrogen Bonds in the Stabilization of Silver-Mediated Cytosine Tetramers.
abstract: 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.
authors.affiliation: COMP Centre of Excellence, Department of Applied Physics, Aalto University , P.O. Box 11100, 00076 Aalto, Finland.
authors.forename: Leonardo Andrés
authors.initials: LA
authors.lastname: Espinosa Leal
authors.affiliation: COMP Centre of Excellence, Department of Applied Physics, Aalto University , P.O. Box 11100, 00076 Aalto, Finland.
authors.forename: Alexander
authors.initials: A
authors.lastname: Karpenko
authors.affiliation: Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States.
authors.forename: Steven
authors.initials: S
authors.lastname: Swasey
authors.affiliation: Department of Physics, University of California , Santa Barbara, California 93106-9510, United States.
authors.forename: Elisabeth G
authors.initials: EG
authors.lastname: Gwinn
authors.affiliation: Departament de Química Orgànica & Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona , Martí I Franquès 1, 08208 Barcelona, Spain.
authors.forename: Victor
authors.initials: V
authors.lastname: Rojas-Cervellera
authors.affiliation: Departament de Química Orgànica & Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona , Martí I Franquès 1, 08208 Barcelona, Spain.
authors.forename: Carme
authors.initials: C
authors.lastname: Rovira
authors.affiliation: COMP Centre of Excellence, Department of Applied Physics, Aalto University , P.O. Box 11100, 00076 Aalto, Finland.
authors.forename: Olga
authors.initials: O
authors.lastname: Lopez-Acevedo
mesh_terms: D002942:Circular Dichroism; D003596:Cytosine / Q000737:chemistry*; D005740:Gases / Q000737:chemistry; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011789:Quantum Theory; D012834:Silver / Q000737:chemistry*
chemical_list: D005740:Gases; D012834:Silver; D003596:Cytosine
keywords: DNA; argentophilic; circular dichroism; density functional theory; metal−organic; silver cation