Time-resolved Stokes shifts in a dye-containing oligonucleotide have been observed over the entire time range from 40 fs to 40 ns. The dynamics fit to a power law with a small exponent of 0.15. Similar relaxation has been seen in proteins but has not been anticipated in DNA. Distinct relaxation components due to specific subcomponents of the system, bulk water, bound water, counterions, backbone, bases, and so on, are not found. The various subcomponents may be so strongly coupled that their motions cannot be treated separately.

The dynamics of the electric fields in the interior of DNA are measured by using oligonucleotides in which a native base pair is replaced by a dye molecule (coumarin 102) whose emission spectrum is sensitive to the local electric field. Time-resolved measurements of the emission spectrum have been extended to a six decade time range (40 fs to 40 ns) by combining results from time-correlated photon counting, fluorescence up-conversion and transient absorption. Recent results showed that when the reporter is placed in the center of the oligonucleotide, the dynamics are very broadly distributed over this entire time range and do not show specific time constants associated with individual processes [J. Am. Chem. Soc. 2005, 127, 7270]. This paper examines an oligonucleotide with the reporter near its end. The broadly distributed relaxation seen before remains with little attenuation. In addition, a new relaxation with a well defined relaxation time of 5 ps appears. This process is assigned to the rapid component of "fraying" at the end of the helix.

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.