Kinetic consequences of covalent linkage of DNA binding polyamides
Abstract
Polyamides composed of N-methylpyrrole (Py) and N-methylimidazole (Im) subunits can bind in the minor groove of DNA at predetermined sequences with subnanomolar affinity and high specificity. Covalent linkage of polymer subunits using a gamma-aminobutyric acid linker has been shown to increase both the affinity and specificity of polyamides. Using a fluorescence detected stopped-flow assay, we have studied the differences in association and dissociation kinetics of a series of polyamides representing unlinked, hairpin and cyclic analogues of the four ring polyamide ImPyPyPy-beta-Dp. Whereas the large differences seen in the equilibrium association constants between the unlinked and covalently linked polyamides are primarily due to higher association rate constants, discrimination between matched and mismatched sites by each polyamide can be ascribed in large part to differences in their dissociation rate constants. The consequences of this kinetic behavior for future design are discussed.
Additional Information
© 2001 American Chemical Society. Received September 22, 2000. Publication Date (Web): December 7, 2000. We would like to thank Professors Axel Brunger, Alanna Schepartz, and Andrew Hamilton for allowing use of their instruments, NIH for funding this work (GM 21966 and GM 27681), and GeneSoft Inc. for salary support to R.B. in the laboratory of D.M.C.Attached Files
Supplemental Material - bi0022339_s.pdf
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Additional details
- Eprint ID
- 66843
- Resolver ID
- CaltechAUTHORS:20160510-091104816
- NIH
- NIH
- GeneSoft Inc.
- Created
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2016-05-18Created from EPrint's datestamp field
- Updated
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2021-11-11Created from EPrint's last_modified field