Basic Amino Acid Residue Binding Mechanism to DNA?

Question

I understand that many protein DNA binding domains bind to DNA via basic residues such as Arginine and Lysine. But what is the mechanism used to bind to DNA and where on the DNA would these residues bind?

Answer 1

At the basic level, it is hydrogen bonding, such as that attraction between the Lysine and the negatively charged phosphate backbone of DNA, and hydrophobic interactions, which causes similarly charged molecules to repel and assist in the stabilization of the structure. As far as mechanisms, this is one of the active areas of research where there are many hypothesis with substantial supportive evidence. I will include an article that has a good introduction of this in the comments.