Effect of temperature on DNA double helix: An insight from molecular dynamics simulation.

The three-dimensional structure of DNA contains various sequence-dependent structural information, which control many cellular processes in life, such as replication, transcription, DNA repair, etc. For the above functions, DNA double helices need to unwind or melt locally, which is different from terminal melting, as often seen in molecular dynamics (MD) simulations or even in many DNA crystal structures. We have carried out detailed MD simulations of DNA double helices of regular oligonucleotide fragments as well as in polymeric constructs with water and charge-neutralizing counter-ions at several different temperatures. We wanted to eliminate the end-effect or terminal melting propensity by employing MD simulation of DNA oligonucleotides in such a manner that gives rise to properties of polymeric DNA of infinite length. The polymeric construct is expected to allow us to see local melting at elevated temperatures. Comparative structural analysis of oligonucleotides and its corresponding virtual polymer at various temperatures ranging from 300 K to 400 K is discussed. The general behaviour, such as volume expansion coefficients of both the simulations show high similarity, indicating polymeric construct, does not give many artificial constraints. Local melting of a polymer, even at elevated temperature, may need a high nucleation energy that was not available in the short (7 ns) simulations. We expected to observe such nucleation followed by cooperative melting of the polymers in longer MD runs. Such simulations of different polymeric sequences would facilitate us to predict probable melting origins in a polymeric DNA.

Structural implications of electric-field induced dichroism of nucleic acids: Studies of alternating purine-pyrimidines.

Transient and steady-state electric dichroism measurements of double helical poly(dG-dC) and its 5-methyl guanosine analogue and transient electric dichroism measurements of double helical poly(dA-dT) are shown to give the following information on the structural and dynamical properties of these molecular systems: (i) the Z form structure of the alternating guanosine-cytidine moieties has the same inter base-pair separation in solution as it does in the fibre and crystalline forms; (ii) the mean normal to the base pairs (and thus their average tilt and twist) of the B and Z forms of the guanosine-cytidine moieties is very nearly the same despite the large difference in their secondary structure; (iii) the alternating adenosinethymidine nucleic acid is at least twice as flexible as random-sequence DNA.