Conformational flexibility influences degree of hydration of nucleic acid hybrids.

Smritimoy Pramanik, Satoru Nagatoishi, Sarika Saxena, Jhimli Bhattacharyya, Naoki Sugimoto

Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan.

The journal of physical chemistry. B 2011 Dec 1

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Four nucleic acid duplexes-DNA/RNA hybrid, RNA/DNA hybrid, RNA duplex, and DNA duplex-were studied under molecular crowding conditions of osmolytes. Destabilization of duplexes (ΔΔG°(25)) indicated that the ΔΔG°(25) values of hybrids were intermediate between those of DNA and RNA duplexes. In the presence of polyethylene glycol 200, the ΔΔG°(25) values were estimated to be +3.0, +3.5, +3.5, and +4.1 kcal mol(-1) for the DNA duplex, DNA/RNA hybrid, RNA/DNA hybrid, and RNA duplex, respectively. Differences in the number of water molecules taken up (-Δn(w)) upon duplex formations between 0 and 37 °C (Δ(-Δn(w))) were estimated to be 44.8 and 59.7 per duplex structure for the DNA/RNA and RNA/DNA hybrids, respectively. While the Δ(-Δn(w)) value for the DNA/RNA hybrid was intermediate between those of the DNA (26.1) and RNA (59.2) duplexes, the value for RNA/DNA hybrid was close to that of RNA duplex. These differences in the thermodynamic parameters and hydration are probably a consequence of the enhanced global flexibility of the RNA/DNA hybrid structure relative to the DNA/RNA hybrid structure observed in molecular dynamics simulations. This molecular crowding study provides information not only on hydration but also on the flexibility of the conformation of nucleic acid duplexes. © 2011 American Chemical Society

Citation

Smritimoy Pramanik, Satoru Nagatoishi, Sarika Saxena, Jhimli Bhattacharyya, Naoki Sugimoto. Conformational flexibility influences degree of hydration of nucleic acid hybrids. The journal of physical chemistry. B. 2011 Dec 1;115(47):13862-72