Protein–deoxyribonucleic acid (DNA) interactions play a central role in directing the flow of genetic information and in the control of life itself. Research has demonstrated that many DNA-binding proteins belong to distinct families containing common structural motifs. In this article, several important motifs are introduced and their interactions with DNA are discussed. Interestingly, these motifs show great variability in their DNA-binding modes. In some cases, a simple structural element, such as a single helix or ribbon, accounts for the most critical interactions, whereas in other protein–DNA complexes, more complicated structural scaffolds are required. In addition, the efficiency and specificity of protein–DNA interactions depend on the nature of bonding, the induced fit of macromolecules and the oligomerisation of protein motifs.

Key Concepts:

• DNA-binding motifs are prototypic structural elements, each representing a group of DNA-binding proteins.
  
• The stability of protein–DNA complexes is attributed to both sequence-specific and nonsequence-specific interactions, whereas the specificity only depends on the former.
  
• Conformational change is often observed in protein–DNA complexes, which facilitates the complex formation and/or the following biological function.
  
• In addition to promoting extreme conformational change in DNA, oligomerisation of DNA-binding proteins may also enable regulation of protein–DNA complexes.