SUNY at Albany
June 19-23, 2001
Molecular dynamics studies of RNA loop stabilization by U-turn motif
Recent studies reveal the important role of RNA loop structures in the recognition and formation of functional RNA-RNA and RNA-protein complexes. In vivo and in vitro experiments show that an adenosine rich loop in HIV RNA mediates complex formation between tRNA and viral RNA during initiation of reverse transcription. The NMR data indicate a compact fold of this A-rich loop in the solution . To investigate the conformational dynamics and interactions stabilizing the structure in solution we have performed extensive molecular dynamics calculations of model hairpin. The initial structures of the sequence GGUGUAAAAAUC (loop nucleotides marked in bold) were based on NMR data . Several MD runs of the 1 ns length in explicit water box containing sodium ions with different initial structures and conditions produced dynamically stable trajectories.
The 6 nucleotide loop structure is stabilized by a non canonical G-A pair and U-turn motif , in which uridine5 N3 forms a hydrogen bond with the oxygen of the adenine 7 phosphate group and 2ÕOH of uridine5 forms a hydrogen bond with N7 of adenine7. The dynamic stacking of adenines at the 3Õ side of the loop is conserved during MD trajectories. Such prestacked structure seems to be important in respect to the RNA interactions because the formation of duplex interactions with other RNA is enhanced over duplex formation by disordered loop region.
Acknowledgments. This work was supported by grant from the State Committee for Scientific Research , Republic of Poland (8 T11F002 19).References and Footnotes
T.Kulinski, K.Kulinska, J.Sarzynska
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14,
61-704 Poznan, Poland ,