DYNAMICS AND RELATIVE STABILITIES OF PARALLEL-STRANDED AND ANTIPARALLEL-STRANDED DNA DUPLEXES

The dynamics and stability of four DNA duplexes are studied by means o f molecular dynamics simulations. The four molecules studied are combi nations of 4, 15 bases long, single-stranded oligomers, Fl, F2, F3, an d F4. The sequence of these single strand oligomers are chosen such th at F1-F2 and F3-F4 form parallel (ps) DNA double helices, whereas F1-F 4 and F2-F3 form antiparallel-stranded (aps) DNA double helices. Simul ations were done at low (100 K) and room (300 K) temperatures. At low temperatures the dynamics are quasi-harmonic and the analysis of the t rajectories gives good estimates of the low frequency vibrational mode s and density of states. These are used to estimate the linear (harmon ic) contribution of local fluctuations to the configurational entropy of the systems. Estimates of the differences in enthalpy between ps an d aps duplexes show that aps double helices are more stable than the c orresponding ps duplexes, in agreement with experiments. At higher tem peratures, the distribution of the fluctuations around the average str uctures are multimodal and estimates of the configurational entropy ca nnot be obtained. The multi-basin, nonlinear character of the dynamics at 300 K is established using a novel method which extracts large amp litude nonlinear motions from the molecular dynamics trajectories. Our analysis shows that both ps DNA exhibit much larger fluctuations than the two aps DNA. The large fluctuations of ps DNA are explained in te rms of correlated transitions in the beta, epsilon, and zeta backbone dihedral angles.