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In simple terms proteins have specific structures to bind DNA, these have specific Amino Acids that give specificity for certain DNA sequences. As far as I am aware the main binding force is Hydrogen bonds between the Amino Acids and the DNA bases.

More specifically there are three well known of DNA binding motifs that proteins have. These are:

Homeodomains (Helix-Turn-Helix)

This class has three alpha helices, the 3 helix sits in the major groove of DNA and interacts with it in a base specific manor via Hydrogen bonding. Helix 1 and 2 sit above the DNA strand to stabilise the binding and the N terminal tail interacts in the minor groove.

Zinc Fingers

Form a special structure around a zinc atom (held by interaction with Cysteine and Histidine residues) to stabilise them (the protein motif is too small to have a hydrophobic core). To bind DNA the alpha helix (where the Histidine residues are found) of the domain again typically iteracts with the major groove of the target DNA.

Basic Leucine Zippers

These consist of two long alpha helices bound together by interactions between leucine residues found every 7 amino acids on each chain. The ends of the helices have a basic region that is responsible for binding DNA, again in the major groove.

That is all I can remember off the top of my head, hope it helps.

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Related Questions

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