Structural fluctuations and excitation transfer between adenine and 2-aminopurine in single-stranded deoxytrinucleotides.

Steady-state fluorescence measurements on the deoxytrinucleotides (5')dTp2APpA(3') and (5')dAp2APpA(3') show a temperature-dependence and a viscosity-dependence for energy transfer that qualitatively differ from those seen in our previous study of charge transfer (CT) in these systems. Time-resolved anisotropy studies and molecular dynamics simulations are presented that provide a detailed characterization of the structural dynamics of these systems and how these fluctuations modulate the electronic interaction between 2AP and its neighbors. To gain quantitative insight into the interplay of conformational fluctuations and stacking-induced energy transfer, we present results from a new hybrid quantum-classical simulation method for computing the A --> 2AP energy transfer rate that makes use of the full three-dimensional nature of the donor and acceptor transition densities. Analysis of the results shows that the standard transition dipole-transition dipole approximation for the Coulombic coupling substantially overestimates the transfer rate and that the nearest neighbor energy transfer from adenine to 2AP occurs on a much faster time scale than that for CT. This suggests that, unlike the CT dynamics where conformational "gating" plays a critical role, the large amplitude fluctuations that modulate the process are largely "frozen" out on the energy transfer time scale.

Stacking-unstacking dynamics of oligodeoxynucleotide trimers.

The structure and dynamics of DNA trimers are experimentally assessed using the fluorescent purine analogue 2-aminopurine (2AP), incorporating 2AP between purine and pyrimidine bases to form 5'dXp2APpY3' molecules. Circular dichroism and fluorescence quenching of the 2AP show that the bases are stacked; at the same time, fluorescence decay lifetimes are heterogeneous, indicative of conformational sampling. 2AP does not exhibit the long fluorescence decay time characteristic of the free nucleoside, suggesting that its motions in the trimers bring it into proximity of the neighboring bases, resulting in efficient charge transfer and average fluorescence lifetimes on the order of 1-2 ns.

2-Aminopurine electronic structure and fluorescence properties in DNA.

2-Aminopurine (2AP) fluorescence intensity and decay lifetimes have been used as indicators of nucleic acid geometry and dynamics. To characterize 2AP photophysics in the context of a DNA strand, time-dependent density functional theory is applied to 2AP stacked with two flanking nucleobases. Calculations show that 2AP in the trimers suffers a reduction in the oscillator strength of its low-lying pi-pi* 2AP-like allowed transition, manifested in a reduction of its radiative rate. Trimers also exhibit two or three lower-energy excited states (charge transfer states) that are predicted to facilitate nonradiative transitions from the fluorescent excited state.