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A Structural Basis for Recognition of A·T and T·A Base Pairs in the Minor Groove of B-DNA

Kielkopf, Clara L. and White, Sarah and Szewczyk, Jason W. and Turner, James M. and Baird, Eldon E. and Dervan, Peter B. and Rees, Douglas C. (1998) A Structural Basis for Recognition of A·T and T·A Base Pairs in the Minor Groove of B-DNA. Science, 282 (5386). pp. 111-115. ISSN 0036-8075. doi:10.1126/science.282.5386.111.

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Polyamide dimers containing three types of aromatic rings—pyrrole, imidazole, and hydroxypyrrole—afford a small-molecule recognition code that discriminates among all four Watson-Crick base pairs in the minor groove. The crystal structure of a specific polyamide dimer-DNA complex establishes the structural basis for distinguishing T·A from A·T base pairs. Specificity for the T·A base pair is achieved by means of distinct hydrogen bonds between pairs of substituted pyrroles on the ligand and the O2 of thymine and N3 of adenine. In addition, shape-selective recognition of an asymmetric cleft between the thymine-O2 and the adenine-C2 was observed. Although hitherto similarities among the base pairs in the minor groove have been emphasized, the structure illustrates differences that allow specific minor groove recognition.

Item Type:Article
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URLURL TypeDescription
Dervan, Peter B.0000-0001-8852-7306
Rees, Douglas C.0000-0003-4073-1185
Additional Information:© 1998 American Association for the Advancement of Science. Received 26 June 1998; accepted 25 August 1998. We are grateful to the NIH for research support, to the NSF for a predoctoral fellowship to C.L.K., to J. Edward Richter for an undergraduate fellowship to J.M.T., and to the Howard Hughes Medical Institute for a predoctoral fellowship to E.E.B. We thank J. E. Wedekind, C. L. Drennan, T. M. Iverson, and M. Williamson for assistance with data collection and S. Horvath for oligonucleotide synthesis. The rotation camera facility at SSRL is supported by the U.S. Department of Energy and NIH. Coordinates have been deposited in the Nucleic Acid Database with accession numbers BDD002 (ImHpPyPy) and BDD003 (ImPyPyPy).
Funding AgencyGrant Number
NSF Predoctoral FellowshipUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Department of Energy (DOE)UNSPECIFIED
Issue or Number:5386
Record Number:CaltechAUTHORS:20141125-100839997
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Official Citation:A Structural Basis for Recognition of A·T and T·A Base Pairs in the Minor Groove of B-DNA Clara L. Kielkopf, Sarah White, Jason W. Szewczyk, James M. Turner, Eldon E. Baird, Peter B. Dervan, and Douglas C. Rees Science 2 October 1998: 282 (5386), 111-115. [DOI:10.1126/science.282.5386.111]
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:52137
Deposited By: Tony Diaz
Deposited On:25 Nov 2014 20:26
Last Modified:10 Nov 2021 19:21

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