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Characterization of protein-DNA complexes by affinity cleaving

Dervan, Peter B. (1991) Characterization of protein-DNA complexes by affinity cleaving. In: Protein 3- DNA Interactions. Methods in Enzymology. Vol.208. No.208. Academic Press , San Diego, CA, pp. 497-515. ISBN 978-0-12-182109-8.

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High-resolution crystallographic views of protein-DNA complexes reveal the structural complexity of protein-DNA interactions. The combination of direct protein-DNA contacts mediated by multiple hydrogen bonds and sequence-dependent DNA conformational effects limits our ability to make detailed structural predictions, even if a new DNA-binding protein can be assigned to a structural class such as helix-turn-helix, double-barreled helix, zinc-binding finger, or scissor grip-leucine zipper. In the absence of high-resolution crystallographic and nuclear magnetic resonance (NMR) data, solution methods such as affinity cleaving can be used to characterize the topology of protein-DNA complexes and correlate sequence similarities with known structural classes. The conversion of a sequence-specific DNA-binding protein into a sequence-specific DNA-cleaving protein by covalent attachment of the iron chelator, ethylenediaminetetraacetic acid (EDTA), to a specific amino acid residue creates a class of hybrid affinity-cleaving proteins that are available through chemical synthesis. Moreover, a structural domain consisting of naturally occurring amino acids that binds transition metals and oxidatively cleaves DNA extends this method to recombinant methods for protein synthesis.

Item Type:Book Section
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Dervan, Peter B.0000-0001-8852-7306
Additional Information:© 1991 Elsevier. This work was supported by grants from the DARPA University Research Initiative Program and the National Foundation for Cancer Research. I am indebted to my students and coworkers who made this work possible; in particular, J. P. Sluka, D. P. Mack, J. H. Griffin, K. Graham, J. A. Shin, and M. G. Oakley. We are grateful for helpful discussions and collaborations with the M. J. Simon research group and for generous technical advice from S. B. H. Kent and S. J. Horvath.
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Defense Advanced Research Projects Agency (DARPA)UNSPECIFIED
National Foundation for Cancer ResearchUNSPECIFIED
Series Name:Methods in Enzymology
Issue or Number:208
Record Number:CaltechAUTHORS:20160510-145812699
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Official Citation:Peter B. Dervan, [24] Characterization of protein—DNA complexes by affinity cleaving, Methods in Enzymology, Academic Press, 1991, Volume 208, Pages 497-515, ISSN 0076-6879, ISBN 9780121821098, (
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66955
Deposited By: Victoria Brennan
Deposited On:19 May 2016 21:40
Last Modified:11 Nov 2021 00:24

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