Question

Isolated naked bacterial DNA from which proteins are removed is supercoiled. DNA in bacterial chromosomes is also supercoiled. When naked DNA is nicked, supercoiling is abolished. In contrast nickling chromosomal DNA does not abolish supercoiling. Why?

Answer 1

• Supercoiling is basic property of both chromosomal or naked DNA.
• Supercoiling is mediated by enzymes Topoisomerase and Polymerase.
• Based on coiling or twist (Tw)- rotation around the helical axis:

a. If supercoiling is in the same direction of the helix, it is positive supercoiling

b. If supercoiling is in the opposite direction of the helix, it is negative supercoiling

• Supercoiling is also based on writhe (Wr)- path traced by helical axis in space:

Constrained or unconstrained writhe depends on association or type of wrapping with DNA binding proteins.

• Supercoiling also is related to the linking number (Lk):

Lk = Wr + Tw.

When a nick is incroduced in a DNA, there is a discontinuity in the structure, and the DNA gains a relaxed state. This will be absolute, if supercoiling was dependent on only Tw.

But since the supercoiling is also related with to writhe, and liking number, the association of the chromosomes with proteins, determines its level of supercoiling.

Since naked DNA is ot associated with proteins, it readily abolishes the supercoiling, while chromosomal DNA being wrapped around Various DNA binding proteins, does not abolish supercoiling with the nick.