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Conformational Flexibility of B-DNA at 0.74 Å Resolution: d(CCAGTACTGG)_2

Kielkopf, Clara L. and Ding, Sheng and Kuhn, Peter and Rees, Douglas C. (2000) Conformational Flexibility of B-DNA at 0.74 Å Resolution: d(CCAGTACTGG)_2. Journal of Molecular Biology, 296 (3). pp. 787-801. ISSN 0022-2836. doi:10.1006/jmbi.1999.3478.

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The affinity and specificity of a ligand for its DNA site is a function of the conformational changes between the isolated and complexed states. Although the structures of a hydroxypyrrole-imidazole-pyrrole polyamide dimer with 5′-CCAGTACTGG-3′ and the trp repressor recognizing the sequence 5′-GTACT-3′ are known, the baseline conformation of the DNA site would contribute to our understanding of DNA recognition by these ligands. The 0.74 Å resolution structure of a B-DNA double helix, 5′-CCAGTACTGG-3′, has been determined by X-ray crystallography. Six of the nine phosphates, two of four bound calcium ions and networks of water molecules hydrating the oligonucleotide have alternate conformations. By contrast, nine of the ten bases have a single, unique conformation with hydrogen atoms visible in most cases. The polyamide molecules alter the geometry of the phosphodiester backbone, and the water molecules mediating contacts in the trp repressor/operator complex are conserved in the unliganded DNA. Furthermore, the multiple conformational states, ions and hydration revealed by this ultrahigh resolution structure of a B-form oligonucleotide are potentially general considerations for understanding DNA-binding affinity and specificity by ligands.

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URLURL TypeDescription DOIArticle
Rees, Douglas C.0000-0003-4073-1185
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Additional Information:© 2000 Academic Press. Received 1 November 1999; received in revised form 17 December 1999; accepted 18 December 1999. We are grateful to the NIH for research support and to the NSF and NIH for predoctoral fellowships to C.L.K. We thank R. Bau for assistance with the refinement, S. Horvath for oligonucleotide synthesis, Leemor Joshua-Tor, Eldon Baird and members of the Dervan and Barton groups for discussions. This work is based in part on research conducted at the Stanford Synchrotron Radiation Laboratory, which is funded by the Department of Energy (BES, OBER) and the National Institutes of Health (NCRR, NIGMS).
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Department of Energy (DOE)UNSPECIFIED
Subject Keywords:B-DNA; DNA structure; ultrahigh resolution; nucleic acid structure; calcium binding
Issue or Number:3
Record Number:CaltechAUTHORS:20150108-154955030
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Official Citation:Clara L Kielkopf, Sheng Ding, Peter Kuhn, Douglas C Rees, Conformational flexibility of B-DNA at 0.74 å resolution: d(CCAGTACTGG)2, Journal of Molecular Biology, Volume 296, Issue 3, 25 February 2000, Pages 787-801, ISSN 0022-2836, (
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ID Code:53417
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Deposited On:14 Jan 2015 07:24
Last Modified:10 Nov 2021 20:01

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