Visualization of planar drug intercalations in B-DNA
- 1 January 1975
- journal article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 2 (10), 1701-1718
- https://doi.org/10.1093/nar/2.10.1701
Abstract
A computerized linked-atom modeling system was developed to examine the stereochemical requirements for intercalation of planar drugs into DNA. All classes of conformational possibilities for extending the polynucleotide backbone were examined for their ability to accommodate insertion of a drug into a base-paired region of DNA compatible with adjacent regions of B-DNA while stacking interactions, steric strain and non-bonded interatomic contacts were optimised. One conformation was found which proved superior to all others in ability to satisfy these criteria: an extension of the backbone by characteristic changes in two torsion angles to trans values, plus a change in one sugar puckering to C3'-endo to relieve strain in an adjacent residue. The turn angle distributed over three polynucleotides for this most general mode of intercalation is 90 degrees, equivalent to a helical unwinding of -18 degrees for B-DNA.Keywords
This publication has 21 references indexed in Scilit:
- Hyaluronic acid: Molecular conformations and interactions in two sodium saltsJournal of Molecular Biology, 1975
- The degree of unwinding of the DNA helix by ethidiumJournal of Molecular Biology, 1974
- Structural details of a double-helix observed for DNAs containing alternating purine and pyrimidine sequencesJournal of Molecular Biology, 1974
- Structures for the polynucleotide complexes poly(dA) · poly(dT) and poly(dT) · poly(dA) · poly(dT)Journal of Molecular Biology, 1974
- Refinement of the structure of B-DNA and implications for the analysis of X-ray diffraction data from fibers of biopolymersJournal of Molecular Biology, 1973
- Stereochemistry of actinomycin binding to DNA: I. Refinement and further structural details of the actinomycin—deoxyguanosine crystalline complexJournal of Molecular Biology, 1972
- Stereochemistry of actinomycin binding to DNAJournal of Molecular Biology, 1972
- Resonance energy transfer between ethidium bromide molecules bound to nucleic acidsJournal of Molecular Biology, 1971
- The geometry of nucleic acidsProgress in Biophysics and Molecular Biology, 1970
- Structural considerations in the interaction of DNA and acridinesJournal of Molecular Biology, 1961