Journal
NUCLEIC ACIDS RESEARCH
Volume 42, Issue 4, Pages 2099-2111Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkt1112
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Funding
- NIH [K22AI093793]
- PhRMA Foundation Research Starter Grant
- Basil O'Connor Research Award from March of Dimes Foundation [5-FY13-212]
- Oxford University Press
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Binding of proteins to particular DNA sites across the genome is a primary determinant of specificity in genome maintenance and gene regulation. DNA-binding specificity is encoded at multiple levels, from the detailed biophysical interactions between proteins and DNA, to the assembly of multi-protein complexes. At each level, variation in the mechanisms used to achieve specificity has led to difficulties in constructing and applying simple models of DNA binding. We review the complexities in protein-DNA binding found at multiple levels and discuss how they confound the idea of simple recognition codes. We discuss the impact of new high-throughput technologies for the characterization of protein-DNA binding, and how these technologies are uncovering new complexities in protein-DNA recognition. Finally, we review the concept of multi-protein recognition codes in which new DNA-binding specificities are achieved by the assembly of multi-protein complexes.
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