Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)

RNASTEPS, An Online Database of Sequence-dependent Deformability of RNA Helical Regions

The RNASTEPS database, located at http://rnasteps.rutgers.edu, is a repository of the base-pair steps found in the double-helical regions of 656 RNA crystal structures of 3.5 Å or better resolution. The database includes a variety of structural parameters and molecular images, computed with the 3DNA software package [1,2] and known to be useful for characterizing and understanding the sequence-dependent spatial arrangements of the DNA and RNA base pairs and base-pair steps. The data can be accessed by searches of Leontis-Westhof base-pair patterns and Protein Data Bank and Nucleic Acid Database structure identifiers. The site also includes a repository of the average values and covariance of the rigid-body parameters characterizing well represented base-pair steps, the knowledge-based elastic potentials derived from these data [3], and other measures of RNA step deformability, such as the conformational volume, base-pair overlap, and root-mean-square deviation of atomic coordinates. The collective information provides a useful benchmark for RNA force-field development. The cumulative data account for the measured persistence length of double-stranded RNA [4] in simulations using the approach of Czapla et al. [5]. An example of the distributions and ‘energies’ extracted from the roll and twist angles of 1274 GG·CC steps and the corresponding molecular superposition of these steps is shown below:


  1. X-L. Lu and W. K. Olson, Nucleic Acids Research, 31, 5108-5121 (2003)
  2. X-L. Lu and W. K. Olson, Nature Protocols, 3, 1213-1227 (2008)
  3. W. K. Olson and A. A. Gorin and X-J. Lu and L. M. Hock and V. B. Zhurkin, Proc. Natl. Acad. Sci., 95, 11163-11168 (1998)
  4. J. A. Abels and F. Moreno-Herrero and T. van der Heijden and C. Dekker and N. H. Dekker, Biophysical Journal, 88, 2737-2744 (2005)
  5. L. Czapla and D. Swigon and W. K. Olson, Journal of Chemical Theory and Computation, 2, 685–695 (2006)

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 USA

ph: (732) 445-3993
fx: (732) 445-5958
mauricio.esguerra@ki.se wilma.olson@rutgers.edu