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Published 1991 | public
Book Section - Chapter

Characterization of protein-DNA complexes by affinity cleaving

Abstract

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.

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.

Additional details

Created:
August 19, 2023
Modified:
January 13, 2024