DNA–protein interaction is the reversible molecular association of a protein with DNA through noncovalent contacts that recognize nucleotide sequence, local DNA shape, helical geometry, chemical modifications, or higher-order nucleic-acid structures. The interaction is formed by combinations of electrostatic attraction between basic protein residues and the DNA phosphate backbone, hydrogen bonds, van der Waals contacts, water-mediated interactions, and contacts with exposed base edges in the major or minor groove [1][2]. DNA-binding proteins may engage DNA in sequence-selective or structure-selective binding modes and can recognize local conformational properties such as groove width, base-pair geometry, bending propensity, or single-stranded and noncanonical DNA structures [2][3]. Binding affinity, specificity, stoichiometry, cooperativity, residence time, and protein-induced conformational changes define the molecular properties of an individual DNA–protein complex [1][4]. Such interactions comprise the direct physical associations through which proteins access, organize, replicate, transcribe, repair, recombine, or package DNA [3][4].
- molecular recognition
- sequence specificity
- DNA shape readout
- DNA-binding proteins
🔵 DNA and Nucleic Acid Chemistry • 🟣 Molecular Biology • 🟡 Biochemistry, Genetics and Molecular Biology • 🔴 Life Sciences
References
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- Nicholas M Luscombe; Susan E Austin; Helen M Berman; Janet M Thornton; An Overview of the Structures of Protein-DNA Complexes. Genome Biol. 2000, 1, REVIEWS001, 10.1186/gb-2000-1-1-reviews001.
- Remo Rohs; Xiangshu Jin; Sean M. West; Rohit Joshi; Barry Honig; Richard S. Mann; Origins of Specificity in Protein-DNA Recognition. Annu. Rev. Biochem. 2010, 79, 233-269, 10.1146/annurev-biochem-060408-091030.
- Malwina Hyjek-Składanowska; Brooke A Anderson; Vitaliy Mykhaylyk; Christian Orr; Armin Wagner; Jarosław T Poznański; Krzysztof Skowronek; Punit Seth; Marcin Nowotny; Structures of Annexin A2-PS DNA Complexes Show Dominance of Hydrophobic Interactions in Phosphorothioate Binding. Nucleic Acids Res. 2022, 51, 1409-1423, 10.1093/nar/gkac774.