Function
One or more DNA-binding domains are often part of a larger protein consisting of additional domains with differing function. The additional domains often regulate the activity of the DNA-binding domain. The function of DNA binding is either structural or involving transcription regulation, with the two roles sometimes overlapping.
DNA-binding domains with functions involving DNA structure have biological roles in the replication, repair, storage, and modification of DNA, such as methylation.
Many proteins involved in the regulation of gene expression contain DNA-binding domains. For example, proteins that regulate transcription by binding DNA are called transcription factors. The final output of most cellular signaling cascades is gene regulation.
The DBD interacts with the nucleotides of DNA in a DNA sequence-specific or non-sequence-specific manner, but even non-sequence-specific recognition involves some sort of molecular complementarity between protein and DNA. DNA recognition by the DBD can occur at the major or minor groove of DNA, or at the sugar-phosphate DNA backbone (see the structure of DNA). Each specific type of DNA recognition is tailored to the protein's function. For example, the DNA-cutting enzyme DNAse I cuts DNA almost randomly and so must bind to DNA in a non-sequence-specific manner. But, even so, DNAse I recognizes a certain 3-D DNA structure, yielding a somewhat specific DNA cleavage pattern that can be useful for studying DNA recognition by a technique called DNA footprinting.
Many DNA-binding domains must recognize specific DNA sequences, such as DBDs of transcription factors that activate specific genes, or those of enzymes that modify DNA at specific sites, like restriction enzymes and telomerase. The hydrogen bonding pattern in the DNA major groove is less degenerate than that of the DNA minor groove, providing a more attractive site for sequence-specific DNA recognition.
The specificity of DNA-binding proteins can be studied using many biochemical and biophysical techniques, such as gel electrophoresis, analytical ultracentrifugation, calorimetry, DNA mutation, protein structure mutation or modification, nuclear magnetic resonance, x-ray crystallography, surface plasmon resonance, electron paramagnetic resonance, cross-linking and Microscale Thermophoresis (MST).
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