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

Gregory E. Sims | Zendy

Open Access

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

Author(s) -

Gregory E. Sims

Publication year - 2003

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkg750

Subject(s) - nucleic acid , biology , dna , rna , crystallography , transfer rna , nucleotide , conformational change , bent molecular geometry , biophysics , biochemistry , chemistry , gene , organic chemistry

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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