Chapter 8, Problem 26P

DNA footprint protection (described in Research Technique $\text{8}\text{.1}$) is a method that determines whether proteins bind to a specific sample of DNA and thus protect part of the DNA from random enzymatic cleavage by DNase I. A $\text{400-bp}$ segment of cloned DNA is thought to contain a promoter. The cloned DNA is analyzed by DNA foot printing to determine if it has the capacity to act as a promoter sequence. The gel shown below has two lanes, each containing the cloned $\text{400-bp}$ DNA fragment treated with DNase I to randomly cleave unprotected DNA. Lane $\text{1}$ is cloned DNA that was mixed with RNA polymerase II and several TFII transcription factors before exposure toDNase I. Lane $\text{2}$ contains cloned DNA that was exposed only to DNase I. RNA pol II and TFIIs were not mixed with DNA before adding DNase I.

a. Explain why this gel provides evidence that the cloned DNA may act as a promoter sequence.

b. Approximately what length is the DNA region protected by RNA pol II and TFIIs?

c. What additional genetic experiments would you suggest to verify that this region of cloned DNA contains a functional promoter?