Book of Abstracts: Albany 2005
Exploring the Flexibility of Nucleic Acids from Molecular Dynamics Simulations
Nucleic acids are largely polymorphic and flexible molecules, whose conformations change very quickly as a response to external stimulus. Very little could be understood on nucleic acids functionality without considering their flexibility and deformability.
Molecular dynamics on nucleic acids has a short history, since the first simulations were published only 20 years ago. However, the technique has reached maturity, becoming a very powerful tool to describe nucleic acids structure and reactivity, and obviously the ideal approach to represent nucleic acid flexibility. During my presentation I will summarize recent advances in the field showing extended MD simulations of unperturbed and perturbed nucleic acids, including for the first time some unfolding simulations. I will also comment how data-mining techniques can extract useful information on nucleic acids flexibility from trajectories approaching Tb size. The power of such techniques coupled to molecular dynamics simulations will be proved in the analysis of DNA·DNA, RNA·RNA and DNA·RNA hybrids.