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

G. E. Sims
2003 Nucleic Acids Research  
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 multidimensional scaling method. The mapping of the conformational space reveals nine primary clusters which distinguish among the common A-, B-and Z-forms and their
more » ... arious substates, plus ®ve 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.
doi:10.1093/nar/gkg750 pmid:14500824 pmcid:PMC206451 fatcat:cqxdgtqoorattnjfdprllntbza