How do the concentrations calculated in questions 2 and 3 compare to the effecti

Question

How do the concentrations calculated in questions 2 and 3 compare to the effective concentrations expected for DNA looping (10 - 100 nM)? Give a rough estimate of the expected advantage in ligation probability for 2 ends connected by a loop vs 2 random ends in nuclei that have been 100% or 1% digested with Mbo1.

Below are questions 2 and 3:

2. If the nucleus fo the cell is 10 µm (10-5 meters). What is the volume of the nucleus? What is the concentration of a single DNA end in the Nucleus (moles/Liter).

3. The restriction enzyme Mbo1 https://www.neb.com/products/r0147-mboi cuts the sequence GATC.

a. If the digestion is complete how many fragments do you expect will be generated from the human genome of 3 billion base pairs?

b. If the digestion is only 1% complete - that is only 1/100 potential sites are cleaved, how many fragments do you expect will be generated from the humnan genome of 3 billion base pairs?

c. For each case a and b what is the concentration of the Mbo1 generated ends in the nucleus?

Explanation / Answer

2.

3. The expected number of fragments when cut with Mbo 1 in the human genome of 3 billion base pairs is 1.17 x 107. The length of the restriction site is 4 base pairs. Therefore, the site GATC is expected for every 44 = 256 base pairs. The total length of the human genome is given as 3 billion base pairs. Thus, there are 1.17 x 107 GATC sites in the human genome giving rise to fragments.

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