A Structural Basis for Recognition of A·T and T·A Base Pairs in the Minor Groove of B-DNA
Abstract
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.
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).Additional details
- Eprint ID
- 52137
- Resolver ID
- CaltechAUTHORS:20141125-100839997
- NIH
- NSF Predoctoral Fellowship
- Howard Hughes Medical Institute (HHMI)
- Department of Energy (DOE)
- Created
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2014-11-25Created from EPrint's datestamp field
- Updated
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2021-11-10Created from EPrint's last_modified field