4 pts a. During the course of class discussions, we covered several examples of the balance between favorable and favorable interactions in determining structures of nucleic acids. Pick one of these examples and BRIEFLY delineate how the "bad" conformation allows something "good" to happen (I will NOT read more than 4 sentences!).

2 pts b. BRIEFLYexplain the consequences of the differing positions of helix axes on the appearance of the major and minor grooves of A & B type helices (2 sentences).

4 pts c. There is a monoclonal antibody that specifically recognizes Z-DNA. In probing yeast cells, there is some specific binding of the antibody to DNA. How would you expect antibody binding to be affected in yeast cells that lack the gene for Topoisomerase I? Be sure to explain the reasoning behind your answer (4 sentences).

5 pts d. It has been thought that urea denatures DNA by disrupting H-bonds between the base pairs. However, it was found that tetramethylurea is a much better dentaurant than is the unsubstituted urea. Based on their differences in structure what does the relative difference in the strengths of these two dentaturants tell you about (i) how urea denatures DNA (ii) the forces that stabilize DNA double helices (3 sentences)?

7 pts a. Koo et al. measured the relative mobility of polymers of several oligonucleotides that contained varying lengths of A-tracts. They found that the relative mobility of these polymerized oligonucleotides increases and then decreases as the length of the A-tract increases (see below for data and sequences). Considering ONLY A-tracts of four or more and using your knowledge of the junction model of DNA bending, explain this observation (4 sentences).

8 pts b. Use the data given in Table 1 (below) from the Nelson, et al. to paper support the junction bend model and argue against the smooth bending model? Be sure to discuss the ideas that underlie each of the two bending models. (4 sentences).

8 pts a. Before adding the intercalator, the linear DNA had L_k = T_w =100.