Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Sequence-dependent Deformability of RNA Helical Regions. What We Have Learned So Far

A decade ago it was still not conceivable that knowledge-based potentials could be obtained for RNA helical regions due to the small amount of crystallographic data available. With the turn of the century and the successful elucidation of the structure of the large ribosomal subunit at 2.4-Å resolution (1 ), the number of high-resolution X-ray crystal structures of RNA has increased by two orders of magnitude, providing enough information to develop a dimeric model of double-helical RNA with the 21 unique base-pair steps formed by the canonical G·C and A·U Watson-Crick pairs and the wobble G·U base pair. Using information derived from a 3.5-Å parsed subset of the BPS (Base Pair Structure) database (2 ) and so-called "inverse harmonic analysis"(3 ), we have derived the elastic force constants for the 21 unique base-pair steps, and are using this simple scoring potential model to simulate the fluctuations of RNA helical structures.

References and Footnotes
  1. Ban, N., Nissen, P., Hansen, J., Moore, P.B., Steitz, T.A. Science 289: 905-920 (2000)
  2. The BPS database can be found at :http://bps..rutgers.edu
  3. Olson W.K., Gorin A.A., Lu X.J., Hock L.M., Zhurkin V.B. Proc. Natl. Acad. Sci. 95: 11163-11168 (1998)

Mauricio Esguerra
Wilma K. Olson

Department of Chemistry & Chemical Biology
BioMaPS Institute for Quantitative Biology
Rutgers, the State University of New Jersey
Piscataway, NJ 08854

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