DNA binding site

DNA binding sites are a type of binding site found in DNA where other molecules may bind. DNA binding sites are distinct from other binding sites in that (1) they are part of a DNA sequence (e.g. a genome) and (2) they are bound by DNA-binding proteins. DNA binding sites are often associated with specialized proteins known as transcription factors, and are thus linked to transcriptional regulation. The sum of DNA binding sites of a specific transcription factor is referred to as its cistrome. DNA binding sites also encompasses the targets of other proteins, like restriction enzymes, site-specific recombinases (see site-specific recombination) and methyltransferases.

DNA binding sites can be thus defined as short DNA sequences (typically 4 to 30 base pairs long, but up to 200 bp for recombination sites) that are specifically bound by one or more DNA-binding proteins or protein complexes. It has been reported that some binding sites have potential to undergo fast evolutionary change.

DNA binding sites can be categorized according to their biological function. Thus, we can distinguish between transcription factor-binding sites, restriction sites and recombination sites. Some authors have proposed that binding sites could also be classified according to their most convenient mode of representation. On the one hand, restriction sites can be generally represented by consensus sequences. This is because they target mostly identical sequences and restriction efficiency decreases abruptly for less similar sequences. On the other hand, DNA binding sites for a given transcription factor are usually all different, with varying degrees of affinity of the transcription factor for the different binding sites. This makes it difficult to accurately represent transcription factor binding sites using consensus sequences, and they are typically represented using position specific frequency matrices (PSFM), which are often graphically depicted using sequence logos. This argument, however, is partly arbitrary. Restriction enzymes, like transcription factors, yield a gradual, though sharp, range of affinities for different sites and are thus also best represented by PSFM. Likewise, site-specific recombinases also show a varied range of affinities for different target sites.

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