Question

Suppose you are a research assistant in a lab studying dna-binding proteins. you have been given the amino acid sequences of all the proteins encoded by the genome of a certain species and have been asked to find candidate proteins that could bind dna. what type of amino acids would you expect to see in the dna-binding regions of such proteins?

Answer 1

DNA is a negatively charged component so the amino acids most probably to combine with the DNA are going to exhibit a positive charge at pH 7. Thus, the likely amino acids would be Arginine, Histidine, and Lysine.  

There are three amino acids, which possess basic side chains at neutral pH. These are lysine, arginine, and histidine. Their side chains comprise nitrogen and bear a resemblance to ammonia that is a base. Their pKa values are high enough that they seem to combine with protons, thus, attaining a positive charge in the process.