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Sequence-Specific Recognition of DNA by Phenanthrenequinone Diimine Complexes of Rhodium(III): Importance of Steric and van der Waals Interactions

Sitlani, Ayesha and Barton, Jacqueline K. (1994) Sequence-Specific Recognition of DNA by Phenanthrenequinone Diimine Complexes of Rhodium(III): Importance of Steric and van der Waals Interactions. Biochemistry, 33 (40). pp. 12100-12108. ISSN 0006-2960. https://resolver.caltech.edu/CaltechAUTHORS:20160406-085310442

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Abstract

The importance of steric and van der Waals interactions in the sequence-specific recognition of DNA by [Rh(phi)]^(3+) complexes has been explored through the synthesis and application of a series of Rh(phi)^(3+) (phi: 9,10-phenanthrenequinone diimine) derivatives. [Rh(phi)]^(3+) complexes intercalate in the major groove of DNA via the phi ligand and promote strand scission in the presence of UV light. The complexes reported here are derivatives of the parent molecules [Rh(phi)_2bpy]^(3+)and [Rh(bpy)_2phi]^(3+)(bpy:2,2'-bipyridyl). The [Rh(phi)]^(3+) complexes have comparable photoefficiencies; therefore, their different photocleavage patterns on ^(32)P-end-labeled DNA fragments reflect their unique sequence-specific recognition characteristics. The shapes of the [Rh(phi)]^(3+) complexes are found to govern DNA recognition and reaction. Importantly and generally, the more sterically bulky complexes, containing methyl or phenyl groups on the ancillary ligands, cleave DNA at a subset of sequences recognized by their parent molecules. [Rh(diphenylbpy)_2phi]^(3+) specifically targets the site 5'-CTCTAGAG-3'. Furthermore, chiral discrimination in site selectivity is observed; the different isomers target different sites. Δ- and Λ-[Rh(5,5'-dimethylbpy)_2phi]^(3+) cleave specifically at sites that are defined by the consensus sequences 5'-C-T-N-G-3' and 5'-A-C/G-T-C/G-3', respectively. The sequence selectivities may be understood on the basis of both negative steric clashes and positive van der Waals interactions between methyl groups on the metal complex and thymine methyl groups in the DNA major groove.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1021/bi00206a013DOIArticle
http://pubs.acs.org/doi/abs/10.1021/bi00206a013PublisherArticle
ORCID:
AuthorORCID
Barton, Jacqueline K.0000-0001-9883-1600
Additional Information:© 1994 American Chemical Society. Received May 27, 1994; Revised Manuscript Received July 20, 1994. Publication Date: October 1994. We are grateful to the National Institute of General Medical Sciences (GM33309) for financial support of this research. We thank A. M. Pyle for her syntheses of several Rh(phi)_2^(3+) complexes.
Funders:
Funding AgencyGrant Number
National Institute of General Medical SciencesGM33309
Issue or Number:40
Record Number:CaltechAUTHORS:20160406-085310442
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20160406-085310442
Official Citation:Sequence-Specific Recognition of DNA by Phenanthrenequinone Diimine Complexes of Rhodium(III): Importance of Steric and van der Waals Interactions Ayesha Sitlani and Jacqueline K. Barton Biochemistry 1994 33 (40), 12100-12108 DOI: 10.1021/bi00206a013
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:65954
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:06 Apr 2016 18:03
Last Modified:03 Oct 2019 09:52

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