Question

Decreasing the concentration of sodium ions from double stranded DNA solution results in decrease in Tm. This happens because of increased

• A. repulsion of bases between two strands
• B. repulsion of phosphate groups between two strands
• C. stacking of bases in two strands
• D. repulsion of deoxyribose sugars between two strands

Hint:

Decreasing sodium ion concentration reduces the shielding effect on the negative charges of the phosphate backbone, leading to greater repulsion and a decrease in Tm.

Answer 1

The Correct Option is B

Step 1: Understanding Tm and the role of sodium ions.
Tm (melting temperature) is the temperature at which half of the DNA strands are in the double-stranded state and half are in the single-stranded state. The concentration of sodium ions affects the stability of the double helix. Sodium ions shield the negative charges on the phosphate backbone, stabilizing the DNA duplex.

Step 2: Analyzing the options.
(A)repulsion of bases between two strands: This is not the primary cause for the decrease in Tm when sodium ions are decreased.
(B)repulsion of phosphate groups between two strands: Correct — The phosphate backbone is negatively charged, and decreasing sodium ions reduces the shielding effect, leading to greater repulsion between the phosphate groups. This destabilizes the DNA and lowers Tm.
(C)stacking of bases in two strands: Base stacking contributes to DNA stability but is not the primary factor in the effect of sodium ions on Tm.
(D)repulsion of deoxyribose sugars between two strands: This is not a major contributor to the stability of the DNA duplex in the context of sodium ions.

Step 3: Conclusion.
The correct answer is (B)repulsion of phosphate groups between two strands, as decreased sodium ion concentration increases the electrostatic repulsion between the negatively charged phosphate groups, lowering Tm.