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Nucleic Acids Research, 2003, Vol. 31, No. 19 5607-5616
© 2003 Oxford University Press

Global mapping of nucleic acid conformational space: dinucleoside monophosphate conformations and transition pathways among conformational classes

Gregory E. Sims and Sung-Hou Kim*

Department of Chemistry, University of California at Berkeley and Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

*To whom correspondence should be addressed. Tel: +1 510 486 4333; Fax: +1 510 486 5272; Email: shkim{at}cchem.berkeley.edu

A global conformational space of 6253 dinucleoside monophosphate (DMP) units consisting of RNA and DNA (free and protein/drug-bound) was ‘mapped’ using high resolution crystal structures cataloged in the Nucleic Acid Database (NDB). The torsion angles of each DMP were clustered in a reduced three-dimensional space using a classical multi-dimensional scaling method. The mapping of the conformational space reveals nine primary clusters which distinguish among the common A-, B- and Z-forms and their various substates, plus five secondary clusters for kinked or bent structures. Conformational relationships and possible transitional pathways among the substates are also examined using the conformational states of DNA and RNA bound with proteins or drugs as potential pathway intermediates.


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