Question

The Stability of the DNA double helix depends significantly on:

I. Hydrogen bonds between phosphate groups

II. Stacking interactions

III. Hydrophobic exclusion

IV. Calcium Ions

A) I, II, III, IV

B) II, IV

C) I, III

D) II, III

Please explain the reasoning behind the answer

Answer 1

The stability of DNA double helix depend significantly on ii) stacking interaction and iii) hydrophobic exclusion

A hydrogen bond between the bases and not between phosphate groups is able to stabilize the double helix because of the large number present in DNA molecules, contributes to the specificity for base pairing in a double helix but it does not affect the overall stability of that helix. The explanation for this, a high concentration of water surrounds the DNA and since water molecules are powerful hydrogen bond donor as well as acceptor they may replace the hydrogen bonding between bases and cause hydrogen bond formation between unpaired bases and water molecules when the DNA is single-stranded. The main factor that stabilizes the double helix is the stacking interaction between bases that is the layering of bases on the top of each other. Base stacking is hydrophobic and electrostatic in nature. In a double helix, stacking interaction is energetically favourable due to hydrophobic effect as the bases are buried in the interior of helix away from water. Although the stability of DNA double helix also increases with increasing salt concentration. The size, charge and concentration of cation such as Calcium ion, magnesium ion influence the stability of DNA. Cations can shield the negative charge of the phosphate in the double helix.