Book of Abstracts: Albany 2007
June 19-23 2007
Conformational Equilibrium of RNA
In aqueous solution, double-stranded RNA oligonucleotides favor an A-form structure while DNA oligonucleotides with the same sequence favor a B-form structure. This alteration in global conformational equilibrium of nucleic acids is examined through free energy calculations using explicit solvent molecular dynamics on a CG-rich DNA and RNA oligonucleotide. The consequences of the 2' hydroxyl group and the detailed differences in dynamical behavior between the RNA and DNA oligonucleotides are characterized. The implications of these differences in the context of the biological behavior of RNA are discussed.