DNA footprint protection (described in Research Technique 8.1) is...

Question

DNA footprint protection (described in Research Technique 8.1) 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 400-bp segment of cloned DNA is thought to contain a promoter. The cloned DNA is analyzed by DNA footprinting to help determine if it has the capacity to act as a promoter sequence. The accompanying gel has two lanes, each containing the cloned 400-bp DNA fragment treated with DNase I to randomly cleave unprotected DNA. Lane 1 is cloned DNA that was mixed with RNA polymerase II and several TFII transcription factors before exposure to DNase I. Lane 2 contains cloned DNA that was exposed only to DNase I. RNA pol II and TFIIs were not mixed with that DNA before adding DNase I.

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

Accepted Answer

Hey, everyone. Let's take a look at this question together in double stranded DNA, eco R one recognizes the base sequence which runs from the five N to the three N and contains the following nucleotides and cuts between the guanine and the adenine resulting in DNA fragments with single stranded free ends on either strand of the double stranded DNA. These single stranded free ends are referred to as what are they answer choice. A free ends, answer choice B blunt ends, answer choice, C palindromic ends or answer choice D sticky ends. Let's work this problem out together to try to figure out which of the following answer choices is the correct answer. So we know that ECO R one is a restriction enzyme that recognizes that base sequence that runs from the five end to the three end and contains the following nucleotides. So this is our base sequence recognized by eco R one. And then we have the anti parallel DNA strand. And this combination of that base sequence and the anti parallel strand are what is referred to as palindromic sequences. So it cannot be answer choice C since this is before the restriction enzyme cuts between the guanine and the adenine. So we can eliminate answer choice C. And then we can see where eco R one makes that cut between that guanine and the adenine in both palindromic sequences. And we can also see that we have the same nucleotide at each end as well as these four base pair sequences, which these or base single stranded sequences that result after the cutting between the guanine and the adenine in both strands is referred to as sticky ends. Making answer choice d the correct answer since we note that the term is called sticky ends, since they can stick to a complementary base pair sequence by hydrogen bonding. And we note that it is not answer choice, a free ends. Since we note that the cut results in those DNA fragments having those free ends on either side of that double stranded DNA. And it is not blunt ends since a blunt N involves no overhang of the sequence. And in the case of eco R one, we can see that we do have that overhang. So it cannot be blunt ends. And answer choice. D sticky ends is the correct answer. I hope you found this video to be helpful. Thank you and goodbye.

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