SUNY at Albany
June 19-23, 2001
Structure an dynamics of the water shell in the (CG)n duplexes in a view of stabilization of 2Õ-O-methylated RNA.
RNA duplexes containing alternating CG base pairs are able to form left-handed Z-RNA double helices. Its A=>Z-RNA conformational transition might be promoted by high salt conditions and high pressure. It has been shown recently that Z_ domain of human dsRNA adenosine deaminase (ADAR1) also induces a slow A=>Z-RNA transition in duplex r(CG)6 with a high activation energy (1).
In contrast, 2Õ-O-methylated RNA duplex does not undergo helicity reversal under similar experimental conditions and remains in the right-handed form. The 2Õ-O-methyl modification of (CG)3 duplex increase significantly its stability (the melting temperature Tm rises from 68 to 76oC). Recently it has been suggested that the naturally occurring 2Õ-O-methylation of an RNA genome may have provided a chemically simple stepping stone from RNA to DNA in genome evolution (2).
The crystal structure of 2Õ-O-Me(CG)3 duplex has been determined using synchrotron radiation (3), whereas the extensive attempts to get diffracting monocrystals of native r(CG)3 duplex have been unsuccessful. There are 44 water molecules and two hydrated Mg 2+ ions in the crystal structure of 2Õ-O-Me(CG)3 duplex. The water solution structures of native and methylated r(CG)3 duplexes have been determined by NMR spectroscopy under low salt conditions (4). NMR studies have shown that both structures in water are similar with an average rmsd of 1.0? and that solution and crystal structures of 2Õ-O-Me(CG)3 duplex remain close to each other with rmsd value of 1.7?. All these structures form right-handed helixes with certain deviations from the canonical A-RNA structure. The deviation is lower in the crystal structure (rmsd 1.3?) than in solution (rmsd 1.8 ?).
The crystallographic structure of 2Õ-O-Me(CG)3 duplex was used as starting point for Molecular Dynamics computer simulations of both native and 2Õ-O-methylated RNA duplexes in explicit water solutions. MD simulations confirm the previous NMR observations that 2Õ-O-methylation has a minor effect on the global structure of the r(CG)3 duplex and reproduce the hydration pattern of 2Õ-O-Me(CG)3 duplex in the crystal. The 2Õ-O-methyl groups point towards the minor groove leading to its narrowing and trapping a single row of water molecules bridging either two self-parallel cytosines or two self-parallel guanines by a pair of hydrogen bonds. The interactions of these water molecules with other water molecules are quite limited. The 2Õ-OH groups of native r(CG)3 duplex point outside the minor groove making it broader and facilitating its accessibility for water. A string of water molecules links 2Õ-OH groups lying on the edges of the minor groove.
This work was supported by grant from the State Committee for Scientific Research , Republic of Poland (8 T11F002 19).References and Footnotes
K.Kulinska*, T.Kulinski, A.Lyubartsev, A.Laaksonen and R.W.Adamiak
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14,
61-704 Pozna_, Poland; phone: +(48) 61 8528503 ext. 158; fax: +(48) 61 8520532;