DNAbinding

DNA binding refers to the interaction of proteins, peptides, or other molecules with DNA, enabling regulation of genetic processes. Binding can be sequence-specific, where proteins recognize particular DNA motifs, or non-specific, mainly via electrostatic contacts with the DNA backbone. It underpins processes such as transcription, replication, repair, recombination, and chromatin organization.

Proteins that bind DNA include transcription factors, architectural proteins, enzymes, and nucleoproteins. They often contain DNA-binding domains that facilitate recognition. Common domains include helix-turn-helix, zinc finger, leucine zipper/basic leucine zipper, homeodomain, and helix-loop-helix. Some domains read base pair identities in the major groove; others interact with the phosphate backbone in the minor groove or with nucleic-acid conformations.

Binding affinity and specificity are influenced by protein-DNA complementarity, dimerization, cooperative binding, ion conditions, and chromatin context. Specific binding can involve hydrogen bonds with edges of base pairs, while non-specific binding stabilizes through electrostatics with the DNA backbone. Binding modes can include sliding, hopping, and intersegment transfer along DNA.

Roles and examples: transcriptional regulation by factors such as p53; chromatin organization by histones; DNA repair by various repair proteins; restriction enzymes cleave DNA at specific sites. Structural studies reveal how proteins achieve recognition; biophysical methods measure affinity and kinetics, while genomic methods map binding sites in cells.

Research approaches: EMSA, DNase I footprinting, SELEX, ChIP-seq, and structural methods like X-ray crystallography, NMR, cryo-EM.