Chapter 4, Problem 14P

The gel electrophoresis pattern in Figure 4.23 was determined by soaking the gel in a solution of ethidium bromide (EtBr). This is a fluorescent molecule with a planar structure:

The flat molecule intercalates, or fits directly between two adjacent base pairs in a double helix. In doing so, it unwinds the double helix by 26^o for each ethidium molecule bound.
a. If EtBr was added to relaxed, closed circular DNA, would you expect positive or negative supercoiling to occur? Explain.
b. If the circular DNA were nicked (had a single-stranded break) on one strand, what would be the effect on supercoiling?
c. If negatively supercoiled DNA is titrated with EtBr, the electrophoretic mobility decreases at first but then increases at higher EtBr concentrations. Explain.