<P> DNA - binding proteins include transcription factors which modulate the process of transcription, various polymerases, nucleases which cleave DNA molecules, and histones which are involved in chromosome packaging and transcription in the cell nucleus . DNA - binding proteins can incorporate such domains as the zinc finger, the helix - turn - helix, and the leucine zipper (among many others) that facilitate binding to nucleic acid . There are also more unusual examples such as transcription activator like effectors . </P> <P> Structural proteins that bind DNA are well - understood examples of non-specific DNA - protein interactions . Within chromosomes, DNA is held in complexes with structural proteins . These proteins organize the DNA into a compact structure called chromatin . In eukaryotes, this structure involves DNA binding to a complex of small basic proteins called histones . In prokaryotes, multiple types of proteins are involved . The histones form a disk - shaped complex called a nucleosome, which contains two complete turns of double - stranded DNA wrapped around its surface . These non-specific interactions are formed through basic residues in the histones making ionic bonds to the acidic sugar - phosphate backbone of the DNA, and are therefore largely independent of the base sequence . Chemical modifications of these basic amino acid residues include methylation, phosphorylation and acetylation . These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription . Other non-specific DNA - binding proteins in chromatin include the high - mobility group (HMG) proteins, which bind to bent or distorted DNA . Biophysical studies show that these architectural HMG proteins bind, bend and loop DNA to perform its biological functions . These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that form chromosomes . </P> <P> A distinct group of DNA - binding proteins are the DNA - binding proteins that specifically bind single - stranded DNA . In humans, replication protein A is the best - understood member of this family and is used in processes where the double helix is separated, including DNA replication, recombination and DNA repair . These binding proteins seem to stabilize single - stranded DNA and protect it from forming stem - loops or being degraded by nucleases . </P> <P> In contrast, other proteins have evolved to bind to specific DNA sequences . The most intensively studied of these are the various transcription factors, which are proteins that regulate transcription . Each transcription factor binds to one specific set of DNA sequences and activates or inhibits the transcription of genes that have these sequences near their promoters . The transcription factors do this in two ways . Firstly, they can bind the RNA polymerase responsible for transcription, either directly or through other mediator proteins; this locates the polymerase at the promoter and allows it to begin transcription . Alternatively, transcription factors can bind enzymes that modify the histones at the promoter . This alters the accessibility of the DNA template to the polymerase . </P>

Main access site for proteins that recognize specific dna sequences