1. Name the forces that are the underlying cause of stacking (2 sentences). Explain the physical and/or thermodynamic origin of each of these forces (4 sentences). Explain why methylation of the compound involved in stacking would affect stacking. Please comment on the weak force which would be affected by modification and why this affects stacking ability.
 
 

2. A plot depicting the free energy of helix formation is given in your class lecture notes (Figure 17). Explain why the free energy of forming the first 3-4 base pairs is unfavorable, but formation of the subsequent pairs is favorable (3-4 sentences).
 
 

3. The following two facts form a paradox; Fact 1: Calculations of melting temperature (T_M) of nucleic acid double helices, based on quantum mechanical principles, indicate that T_M should be sequence dependent. Fact 2: Experimental measurements indicate that T_M of nucleic acid double helices increase linearly with G/C content; i.e., T_M is composition dependent. (i) Define the paradox (2 sentences). (ii) What observation(s) resolve(s) this paradox (3 sentences).
 
 

4. (i) What are the preferred puckering modes of the sugars in A & B DNA. (ii) Under conditions of lowered water activity (low relative humidity) some DNA sequences will undergo a transition from B®A form. The changes in backbone configuration are accompanied by alterations in at least three helical parameters. Name and explain the helical parameters that change (3-6 sentences). (iii) Explain how the change in backbone configuration in B®A transition drive the alteration in helical parameters (4 sentences).
 
 

5. Draw the c vs d plot for Z-DNA. With reference to your knowledge of Z-DNA structure, why does this plot have a characteristic two 'domain' appearance (4 sentences).