Local diffusive dynamics in DNA: A time-resolved fluorescence and molecular-dynamics study of dinucleotides with 2-aminopurine

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.