Dynamics of Water and Ions Near DNA: Comparison of Simulation to Time-Resolved Stokes-Shift Experiments

Abstract

Time-resolved Stokes-shift experiments measure the dynamics of biomolecules and of the perturbed solvent near them on subnanosecond time scales, but molecular dynamics simulations are needed to provide a clear interpretation of the results. Here we show that simulations using standard methods quantitatively reproduce the main features of TRSS experiments in DNA and provide a molecular assignment for the dynamics. The simulations reproduce the magnitude and unusual power-law dynamics of the Stokes shift seen in recent experiments [D. Andreatta, et al., J. Am. Chem. Soc. 127, 7270 (2005)]. A polarization model is introduced to eliminate cross correlations between the different components contributing to the signal. Using this model, well-defined contributions of the DNA, water and counterion to the experimental signal are extracted. Water is found to have the largest contribution and to be responsible for the power-law dynamics. The counterions have a smaller, but non-negligible contribution with a time constant of 220 ps. The contribution to the signal of the DNA itself is minor and fits a 30 ps stretched exponential. Both time-averaged and dynamic distributions are calculated. They show a small subset of ions with a different coupling, but no other evidence of substates or dynamic heterogeneity.

Anomalous power law decay in solvation dynamics of DNA: a mode coupling theory analysis of ion contribution

“…The short time contribution is dominated by ion-water coupling and the decay time constant is less than 10 ps or so. [30,[22][23][24][25] If groove water is involved, even then the slow decay is not easily expected to (a) make a dominant contribution beyond 100 ps, (b) give rise to a power law with such a small power as observed by Berg and co-workers. [22][23][24][25] Thus, water does not provide an easy explanation of the power law decay.…”

“…The origin of this power law decay component has remained ill-understood, although it has been attributed tentatively to the relaxation of ions in and around DNA. [22][23][24][25] As already mentioned the experiments of Zewail, Pal and co-workers did not find evidence of any slow decay where they used amino purine as a substitute base to probe the solvation dynamics around DNA. [29] Computer simulations [30] conformations is expected to introduce a slow quasi-exponential decay unless it is coupled to solvent (water molecules) and ions to involve a range of timescales.…”

“…While short time response of the medium will involve contributions from both solvent and ions, the long time contributions (those measuring beyond 100ps) are expected to be dominated by such experiments were carried out by several groups [22][23][24][25][26][27][28], with mixed success. One important limitation of some of the earlier studies was that the measurements were limited to relatively shorter time scales.…”

“…[29] In another approach a fluorescent probe is intercalated to one of the grooves of the DNA. [22][23][24][25][26][27][28] While these two approaches do not give identical results, some common features have been detected. Prominent among them is the existence of an apparently universal power law decay component, first reported by Berg and co-workers.…”

“…Prominent among them is the existence of an apparently universal power law decay component, first reported by Berg and co-workers. [22][23][24][25] However, when probed with ultrafast time resolution (of the order of ps) or in computer simulation studies with run time of the order of 1 ns or so, the power law decay is not observable. It seems to appear in the longer time.…”