1. Why is DNA more stable than RNA? What is the physiologic significance of this

Question

1. Why is DNA more stable than RNA? What is the physiologic significance of this variability in stability?

2. What forces drive the formation of double helical DNA? What forces stabilize the final structure? What forces drive the formation of complex structures in RNA? What forces stabilize the final structures?

3. Briefly describe the process of DNA melting. What is the hyperchromic effect and how is it used to determine the state (native or denatured) of DNA?

4.List the general differences between A-DNA, B-DNA, and Z-DNA with regard to: a) properties of the central cavity. b) the characteristics of the major and minor grooves. c) the puckering of the ribofuranose ring.

5.When are A-, B-, and Z-DNA thought to occur in vivo?

6. Explain why a 3’-OH group is essential for polymerization of nucleotides. Why is a NTP also essential for this reaction to occur?

7. How does the structure of cytosine differ from that of cytidine. How does the structure of cytidine differ from that of cytidylate?

Explanation / Answer

1) RNA has a 2'OH,due to which under basic conditions, the hydroxyl group may be deprotonated and may act as an nucleophile and hydrolyze the phosphate bond.DNA forms hydrogen bonds and is double stranded which makes it more stable.

2)Hydrogen bond formation.RNA gets stabilised by stem loop/hairpin loop formation.

3) DNA denaturation, also called DNA melting, is the process by which double-stranded deoxyribonucleic acid unwinds and separates into single-stranded strands through the breaking of hydrophobic stacking attractions between the bases.DNA absorbs very strongly at wavelengths close to UV light (~260 nm). A single stranded DNA will absorb more UV light than that of double-stranded DNA.

4) Central Cavity:
A-DNA: base pairs stack a little off-centre creating a gap along the helix axis
B-DNA: no gap along the helix axis
Z-DNA: no gap along the axis

Groove:
A-DNA: narrow major groove, wide minor groove
B-DNA: wide major groove, narrow minor groove
Z-DNA: flat major groove, narrow minor groove

Puckering:
A-DNA: C3' endo
B-DNA: C2' endo
Z-DNA: C2' and C3' endo

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