Q.47 An analysis of DNA-protein interactions was carried out using all DNA-protein complexes
in the protein data bank (PDB). The frequency distribution of four amino acid residues,
represented as P, Q, R and S, occurring in non-covalent interactions between the protein and
DNA backbone is shown below.
Which one of the following is correct?
(A) P-Lys, Q-Arg, R-Gln, S-Glu (B) P-Gln, Q-Glu, R-Lys, S-Arg
(C) P-Asn, Q-Asp, R-Arg, S-Lys (D) P-His, Q-Glu, R-Gln, S-Lys

Question Overview

A study of all DNA–protein complexes in the Protein Data Bank (PDB) analyzed which amino acids make non-covalent interactions with the DNA backbone.

A bar graph shows the frequency of four residues:

• P ≈ 30%

• Q ≈ 55%

• R ≈ 10%

• S ≈ 5%

We must match P, Q, R, S with the correct amino acids.

Concept Reminder

DNA backbone is negatively charged due to phosphate groups.
Therefore, amino acids that commonly bind DNA are:

• Positively charged residues

  • Lysine (Lys, K)

  • Arginine (Arg, R)

• Polar but uncharged residues

  • Glutamine (Gln, Q)

  • Asparagine (Asn, N)

Least frequent:

• Acidic or negative residues (Asp, Glu)

Correct Answer: (A)

P–Lys, Q–Arg, R–Gln, S–Glu

Why Option (A) is Correct

Q has the highest frequency (~55%) → Arginine

Arginine interacts strongly with DNA due to multiple positive charges, enabling stable ionic interactions.

P is second (~30%) → Lysine

Another positively charged residue, Lysine, commonly binds to the negatively charged DNA phosphate backbone.

R is moderate (~10%) → Glutamine

Glutamine participates in hydrogen bonding, but less frequently than Lys/Arg.

S is minimal (~5%) → Glutamate

Glutamate is negatively charged, causing repulsion with DNA, explaining its low frequency.

Why Other Options Are Incorrect

(B) P–Gln, Q–Glu, R–Lys, S–Arg

• Q cannot be Glu because Glutamate rarely binds DNA

• S cannot be Arg because Arginine is the most frequent

(C) P–Asn, Q–Asp, R–Arg, S–Lys

• Q as Asp is incorrect: Asp (negative) rarely binds DNA

• R cannot be Arg because arginine should be highest

(D) P–His, Q–Glu, R–Gln, S–Lys

• Glu again incorrectly placed at highest frequency

• Lysine can’t be lowest (S)

Conclusion

The pattern of interaction frequency strongly favors positively charged residues, followed by polar, with acidic residues lowest.

Final Correct Answer: (A)
P–Lys, Q–Arg, R–Gln, S–Glu