A Binding Mode of A-[tris(1,10-phenanthroline)ruthenium(II)]2+ Exhibiting Preference for Purine-3′,5′-Pyrimidine Sites of DNA

Ian S Haworth; Adrian E Elcock; Alison Rodger; W. Graham Richards

doi:10.1080/07391102.1991.10507936

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A Binding Mode of A-[tris(1,10-phenanthroline)ruthenium(II)]2+ Exhibiting Preference for Purine-3′,5′-Pyrimidine Sites of DNA

Journal article

Peer reviewed

A Binding Mode of A-[tris(1,10-phenanthroline)ruthenium(II)]2+ Exhibiting Preference for Purine-3′,5′-Pyrimidine Sites of DNA

Ian S Haworth, Adrian E Elcock, Alison Rodger and W. Graham Richards

Journal of biomolecular structure & dynamics, Vol.9(3), pp.553-569

12/1991

DOI: 10.1080/07391102.1991.10507936

PMID: 1815643

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Abstract

Molecular mechanics calculations and molecular dynamics simulations have been used to study the binding of the partially inserted major groove complex of Lambda-[Ru(1,10-phenanthroline)3]2+ with DNA. Energy refinements of this complex showed a clear preference for binding at purine-3',5'-pyrimidine sites over pyrimidine-3',5'-purine sites. The basis for this difference is shown to be a slight change in the binding orientation induced by interchanging the purine and pyrimidine bases. This in turn provides for a better secondary interaction with the helix backbone at a point beyond the immediate binding site. It is this secondary interaction that provides the additional energetic stabilisation for complexes formed at purine-3',5'-pyrimidine sites. Molecular dynamics simulations including explicit representation of solvent support these conclusions and provide an insight into the positional stability of the ligand at a particular site. Repuckering of specific deoxyribose rings to the C3'-endo conformation seems to be an important feature of the DNA/ligand complex.

Thermodynamics

Ligands

DNA - chemistry

Ruthenium

Phenanthrolines - chemistry

Base Sequence

Computer Simulation

Models, Molecular

Molecular Sequence Data

Organometallic Compounds - chemistry

Nucleic Acid Conformation

Binding Sites

Details

Title: Subtitle: A Binding Mode of A-[tris(1,10-phenanthroline)ruthenium(II)]2+ Exhibiting Preference for Purine-3′,5′-Pyrimidine Sites of DNA
Creators: Ian S Haworth - Physical Chemistry Laboratory, Oxford, England
Adrian E Elcock
Alison Rodger
W. Graham Richards
Resource Type: Journal article
Publication Details: Journal of biomolecular structure & dynamics, Vol.9(3), pp.553-569
Publisher: England
DOI: 10.1080/07391102.1991.10507936
PMID: 1815643
ISSN: 0739-1102
eISSN: 1538-0254
Language: English
Date published: 12/1991
Academic Unit: Physics and Astronomy; Biochemistry and Molecular Biology
Record Identifier: 9984025252202771

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