Journal Article

PreJuSER-22673

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Strikingly Different Effects of Hydrogen Bonding on the Photodynamics of Individual Nucleobases in DNA: Comparison of Guanine and Cytosine

Zeleny, T. ; Ruckenbauer, M. ; Aquino, A. J. A. ; Müller, T.FZJ* ; Lankas, F. ; Drsata, T. ; Hase, W. L. ; Nachtigallova, D. ; Lischka, H.

2012
American Chemical Society Washington, DC

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Please use a persistent id in citations: doi:10.1021/ja3028845

Abstract: Ab initio surface hopping dynamics calculations were performed to study the photophysical behavior of cytosine and guanine embedded in DNA using a quantum mechanical/molecular mechanics (QM/MM) approach. It was found that the decay rates of photo excited cytosine and guanine were affected in a completely different way by the hydrogen bonding to the DNA environment. In case of cytosine, the geometrical restrictions exerted by the hydrogen bonds did not influence the relaxation time of cytosine significantly due to the generally small cytosine ring puckering required to access the crossing region between excited and ground state. On the contrary, the presence of hydrogen bonds significantly altered the photodynamics of guanine. The analysis of the dynamics indicates that the major contribution to the lifetime changes comes from the interstrand hydrogen bonds. These bonds considerably restricted the out-of-plane motions of the NH(2) group of guanine which are necessary for the ultrafast decay to the ground state. As a result, only a negligible amount of trajectories decayed into the ground state for guanine embedded in DNA within the simulation time of 0.5 ps, while for comparison, the isolated guanine relaxed to the ground state with a lifetime of about 0.22 ps. These examples show that, in addition to phenomena related to electronic interactions between nucleobases, there also exist relatively simple mechanisms in DNA by which the lifetime of a nucleobase is significantly enhanced as compared to the gas phase.

Keyword(s): J

Note: This work has been supported by the Austrian Science Fund within the framework of the Special Research Program and F41 Vienna Computational Materials Laboratory (ViCoM). This work was also performed as part of research supported by the National Science Foundation Partnership in International Research and Education (PIRE) Grant No. OISE-730114; support was provided by the Robert A. Welch Foundation under Grant No. D-0005. The calculations were performed in part at the Vienna Scientific Cluster (project nos. 70019 and 70151). The research at IOCB was part of the project RVO:61388963. This work was also supported by the grants of the Grant Agency of the Czech Republic (P208/12/1318 and GACR 203/09/H046), the grant of the Czech Ministry of Education, Youth and Sport (LH11021) and Operational Program Research and Development for Innovations - European Regional Development Fund (project CZ.1.05/2.1.00/03.0058 of the Ministry of Education, Youth and Sports of the Czech Republic). F.L. acknowledges the support by the J. E. Purkyne Fellowship provided by the Academy of Sciences of the Czech Republic.

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Contributing Institute(s):

1. Jülich Supercomputing Centre (JSC)

Research Program(s):

1. Scientific Computing (FUEK411) (FUEK411)
2. 411 - Computational Science and Mathematical Methods (POF2-411) (POF2-411)

Appears in the scientific report 2012

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Database coverage:
; BIOSIS Previews ; Current Contents - Life Sciences ; Current Contents - Physical, Chemical and Earth Sciences ; JCR ; NCBI Molecular Biology Database ; Nationallizenz ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Thomson Reuters Master Journal List ; Web of Science Core Collection

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