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Review
. 2014 Feb;42(4):2099-111.
doi: 10.1093/nar/gkt1112. Epub 2013 Nov 16.

Protein-DNA Binding: Complexities and Multi-Protein Codes

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Free PMC article
Review

Protein-DNA Binding: Complexities and Multi-Protein Codes

Trevor Siggers et al. Nucleic Acids Res. .
Free PMC article

Abstract

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.

Figures

Figure 1.
Figure 1.
Multiple modes of DNA binding. Schematized are examples illustrating four mechanistic categories by which proteins recognize different DNA sites via distinct structural modes.
Figure 2.
Figure 2.
Multi-protein recognition codes. Schematized are examples illustrating four mechanistic categories by which targeting of proteins to distinct DNA sites involves the assembly of multi-protein complexes.

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References

    1. Seeman NC, Rosenberg JM, Rich A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl Acad. Sci. USA. 1976;73:804–808. - PMC - PubMed
    1. Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS. Origins of specificity in protein-DNA recognition. Annu. Rev. Biochem. 2010;79:233–269. - PMC - PubMed
    1. Garvie CW, Wolberger C. Recognition of specific DNA sequences. Mol. Cell. 2001;8:937–946. - PubMed
    1. Jayaram B, Jain T. The role of water in protein-DNA recognition. Annu. Rev. Biophys. Biomol. Struct. 2004;33:343–361. - PubMed
    1. Reddy CK, Das A, Jayaram B. Do water molecules mediate protein-DNA recognition? J. Mol. Biol. 2001;314:619–632. - PubMed

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