Q.31 Amino acid residues predominantly involved in protein-DNA interactions are
(A) alanines
(B) negatively charged
(C) prolines
(D) positively charged

The correct answer is: (D) positively charged amino acid residues are predominantly involved in protein–DNA interactions, because they interact electrostatically with the negatively charged DNA backbone.​

Correct Answer Explained

DNA carries a strong negative charge due to its phosphate backbone, so amino acids that interact most effectively with DNA are usually positively charged. These positively charged side chains form electrostatic attractions and hydrogen bonds with the DNA backbone and bases, stabilizing protein–DNA complexes.​

Therefore, the correct option is:

• (D) positively charged

Typical positively charged amino acids involved in DNA binding include lysine and arginine in many DNA-binding proteins and histones.​

Option (A) Alanines

Alanine has a small, non‑polar methyl side chain that is chemically neutral.​

• It does not provide strong electrostatic attraction to the negatively charged DNA backbone.

• Alanine is more important for maintaining protein structure and packing than for specific DNA recognition or binding.​

So, alanines are not predominantly involved in protein–DNA interactions, making option (A) incorrect.​

Option (B) Negatively Charged

Negatively charged amino acids include aspartate and glutamate, which carry a negative charge on their side chains at physiological pH.​

• Since DNA is also negatively charged, direct electrostatic interaction between DNA and negatively charged residues is generally unfavorable and can be repulsive.​

• Such residues may appear in interfaces for fine‑tuning specificity or orientation, but they are less frequent and are not the predominant contributors to protein–DNA attraction.​

Thus, negatively charged residues are not the main players in protein–DNA interactions, so option (B) is incorrect.​

Option (C) Prolines

Proline is a unique amino acid with a cyclic structure that introduces kinks or bends in polypeptide chains.​

• It primarily affects protein conformation rather than directly binding to DNA through charge-based interactions.

• Proline can be present in DNA-binding domains to help position other residues correctly, but it is not the predominant residue making contact with DNA.​

Therefore, option (C) is also incorrect.

Option (D) Positively Charged (Correct)

Positively charged (basic) amino acids, mainly lysine and arginine, are strongly enriched in protein–DNA binding regions.​

• They form favorable electrostatic interactions with the negatively charged phosphate backbone of DNA.

• They can also establish hydrogen bonds with DNA bases, contributing to both binding strength and sequence specificity.​

Hence, option (D) positively charged amino acid residues is the correct answer for amino acids predominantly involved in protein–DNA interactions.​