Chapter 11

X-ray diffraction studies indicate the existence of a novel doublestranded DNA helical conformation in which \(\Delta Z\) (the rise per base pair \()=0.32 \mathrm{nm}\) and \(P(\text { the pitch })=3.36 \mathrm{nm} .\) What are the other parameters of this novel helix: (a) the number of base pairs per turn, (b) \(\Delta \phi(\text { the mean rotation per base pair }),\) and (c) \(c(\) the true repeat)?

If \(80 \%\) of the base pairs in a duplex DNA molecule \((12.5 \mathrm{kbp})\) are in the B-conformation and \(20 \%\) are in the Z-conformation, what is the length of the molecule?

A "relaxed," circular, double-stranded DNA molecule \((1600 \mathrm{bp})\) is in a solution where conditions favor 10 bp per turn. What is the value of \(L_{0}\) for this DNA molecule? Suppose DNA gyrase introduces 12 negative supercoils into this molecule. What are the values of \(L\) \(W,\) and \(T\) now? What is the superhelical density, \(\sigma\) ?

At \(0.2 M \mathrm{Na}^{+},\) the melting temperature of double-stranded DNA is given by the formula, \(T_{m}=69.3+0.41(\% \mathrm{G}+\mathrm{C}) .\) The DNAs from mice and rats have \((\mathrm{G}+\mathrm{C})\) contents of \(44 \%\) and \(40 \%,\) respectively. Calculate the \(T_{\mathrm{m}}\) s for these DNAs in \(0.2 \mathrm{M}\) NaCl. If samples of these DNAs were inadvertently mixed, how might they be separated from one another?

Online resources provide ready access to detailed information about the human genome. Go the National Center for Biotechnology Information (NCBI) genome database at http://www.ncbi.nlm.nih.gov/ Genomes/index.html and click on Homo sapiens in the Map Viewer genome annotation updates list to access the chromosome map and organization of the human genome. Next, go to http://www.ncbi .nlm.nih.gov/genome/. In the "Search For" box, type in the following diseases to discover the chromosomal location of the affected gene and, by exploring links highlighted by the search results, discover the name of the protein affected by the disease: a. Sickle cell anemia b. Tay Sachs disease c. Leprechaunism d. Hartnup disorder

(Integrates with Chapter \(10 .\) ) Erwin Chargaff did not have any DNA samples from thermoacidophilic bacteria such as those that thrive in the geothermal springs of Yellowstone National Park. (Such bacteria had not been isolated by 1951 when Chargaff reported his results.) If he had obtained such a sample, what do you think its relative \(G: C\) content might have been? Why?

Think about the structure of DNA in its most common B-form double helical conformation and then list its most important structural features (deciding what is "important" from the biological role of DNA as the material of heredity . Arrange your answer with the most significant features first.