DNA, RNA and Hybrid

By running MD simulations over short DNA and RNA duplexes, I showed that the pattern of flexibility of DNA and RNA duplexes is different. In the first case there are many possible deformations of low energetic cost, while for RNA there are a few very soft deformations, but the others are very stiff. Entropy and stiffness analysis suggest that overall the DNA duplex is more disordered and can fluctuate more than the RNA one. However, this greater flexibility of DNA is mostly local and due to backbone fluctuations that do not introduce large global changes in the helix (Noy et al. JMB 2004).

entropy   entropyeigcondifferences

The structure of the hybrid duplex DNA:RNA is intermediate between A and B forms but, in general, closer to the canonical A-type helix. The molecular recognition pattern of the DNA‚RNA hybrid is a unique combination of those of normal DNA and RNA duplexes. Results obtained from essential dynamics and stiffness analysis demonstrate the large and very asymmetric flexibility of the hybrid and the strong predilection that each strand (DNA or RNA) has on the nature of their intrinsic motions in the corresponding homoduplexes (Noy et al. JACS, 2005)