Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 345707
Title Local diffusive dynamics in DNA: A time-resolved fluorescence and molecular-dynamics study of dinucleotides with 2-aminopurine
Author(s) Somsen, O.J.G.; Trinkunas, G.; Keijzer, M.N. de; Hoek, A. van; Amerongen, H. van
Source Journal of Luminescence 119-120 (2006). - ISSN 0022-2313 - p. 100 - 104.
Department(s) Biophysics
Publication type Refereed Article in a scientific journal
Publication year 2006
Keyword(s) ultrafast transient-absorption - temperature - polymerase - hairpin
Abstract Fluorescent base analogues such as 2-aminopurine report DNA dynamics on the scale of single bases. We find that the time-dependent fluorescence of various 2-aminopurine-containing dinucleotides can be described by only two components: a fast (20 ps) exponential decay and a much slower (1 ns) stretched exponential. This is much simpler than previously proposed models. The fast component reflects quenching in the stacked equilibrium conformation. The slow stretched exponential indicates diffusive dynamics towards the equilibrium conformation. Depending on the dinucleotide, this migration effectively takes place in a one- or two-dimensional manifold. Molecular-dynamics simulations indicate that it involves twisting and sliding with parallel base planes. Our very simple representation of the data provides a powerful tool to study DNA fluorescence quenching and diffusive dynamics independently.
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