title: Drug-nucleic acid interactions: conformational flexibility at the intercalation site.
abstract: The conformational features of the intercalation site in polynucleotides were examined. We found that, for all the crystal structures of drug-dinucleoside complexes studied thus far, two torsion angles differ from those found in A RNA (phi and chi) and that alternate sugar puckering is not a prerequisite for intercalation. This intercalation geometry, which is the basis of helix axis displacement in a polymer, would necessitate conformational changes in the adjacent nucleotides. The base-turn angle is less sensitive to the conformation of the backbone than it is to small alterations in the base-pairing geometry. We postulate that this angle is dependent on the nature of the intercalating drug.
mesh_terms: D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids; D004364:Pharmaceutical Preparations
chemical_list: D009696:Nucleic Acids; D004364:Pharmaceutical Preparations
references.citation: J Mol Biol. 1961 Feb;3:18-30
references.pmid: 13761054
references.citation: J Mol Biol. 1977 Aug 15;114(3):333-65
references.pmid: 71352
references.citation: Nucleic Acids Res. 1977 Nov;4(11):3855-61
references.pmid: 593890
references.citation: J Mol Biol. 1977 Aug 15;114(3):317-31
references.pmid: 909091
references.citation: J Mol Biol. 1977 Aug 15;114(3):301-15
references.pmid: 909090
references.citation: Nature. 1977 Sep 22;269(5626):304-7
references.pmid: 904684
references.citation: Nucleic Acids Res. 1975 Oct;2(10):1701-17
references.pmid: 1187341
references.citation: Prog Nucleic Acid Res Mol Biol. 1970;10:183-265
references.pmid: 4910304
references.citation: J Mol Biol. 1976 Jun 14;104(1):145-67
references.pmid: 957430
references.citation: J Mol Biol. 1976 Jun 14;104(1):109-44
references.pmid: 957429
references.citation: Proc Natl Acad Sci U S A. 1975 Feb;72(2):628-32
references.pmid: 1054844
references.citation: Proc Natl Acad Sci U S A. 1975 Dec;72(12):4825-9
references.pmid: 1061071