| Small-molecule binding to the DNA minor groove is mediated by a conserved water cluster. | |
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MedLine Citation:
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PMID: 23276263 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
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High-resolution crystal structures of the DNA duplex sequence d(CGCGAATTCGCG)2 complexed with three minor-groove ligands, are reported. A highly-conserved cluster, of eleven linked water molecules, has been found in the native and all three ligand-bound structures, positioned at the boundary of the A/T and G/C regions where the minor groove widens. This cluster appears to play a key structural role in stabilizing non-covalently-binding small molecules in the AT region of the B-DNA minor groove. The cluster extends from the backbone phosphate groups along the mouth of the groove and links to DNA and ligands by a network of hydrogen bonds that help to maintain the ligands in position. This arrangement of water molecules is distinct from, but linked by hydrogen-bonding to the well-established spine of hydration, which is displaced by bound ligands. Features of the water cluster and observed differences in binding modes help to explain the measured binding affinities and thermodynamic characteristics of these ligands on binding to AT sites in DNA. |
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Authors:
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Dengguo Wei; W David Wilson; Stephen Neidle |
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Publication Detail:
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Type: JOURNAL ARTICLE Date: 2012-12-31 |
Journal Detail:
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Title: Journal of the American Chemical Society Volume: - ISSN: 1520-5126 ISO Abbreviation: J. Am. Chem. Soc. Publication Date: 2012 Dec |
Date Detail:
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Created Date: 2013-1-1 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 7503056 Medline TA: J Am Chem Soc Country: - |
Other Details:
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Languages: ENG Pagination: - Citation Subset: - |
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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