This question is regarding the paper at this link it is free

This question is regarding the paper at this link: (it is free!) https://www.ncbi.nlm.nih.gov/pubmed/9565591

Question 3

a) The researchers talk about how the DNase I mutants could either nick or cut a DNA segment. What is the difference between a nick and a cut?

b) Imagine you have circular DNA that is supercoiled. What would the effect of a nick be? How about a cut? (Assume that the nick and cut are permanent)

c) According to Fig 3, which of the mutants gave you a nick? Which produced a cut? Explain how you determined your answer.

d) Which type of activity (nick or cut) were the researchers looking for and why?

Solution

A. Nick is a type of cut only. Restriction enzyme are known to produce this cut or Nick. In Nick only one phosphodiesterase bond breaks and nucleotides remain intact. When Nick in both the strand are at same site it produces blunt end whereas when it happens at different sites staggered ends are produced.

B. When a Nick is introduced in the supercoiled DNA it releases the superhelical tension and a cut in the DNA results in a linearised form. When run on agarose gel electrophoresis, these three forms move in the following sequence:

1. Supercoiled DNA

2. Linearised form

3. Nicked supercoiled form.

C and D : We are not supposed to provide you answer when the link is given. However, I have answered the general questions which does not require the link.