2) Imagine a 500 bp double-stranded piece of closed circular DNA. The path of th

Question

2) Imagine a 500 bp double-stranded piece of closed circular DNA. The path of the DNA backbone is shown in the figure on the right. The DNA lies nearly flat and therefore the directional writhing number (Wn) is a good approximation of the true writhing number (w). a) The average helical twist angle is 34. What is your best estimate of the linking number of this DNA? Show your calculation. Recall that L T+ W. You should round your answer off to the nearest integer since L has to be an integer Why does L have to be an integer? Why didn't your calculation automatically yield an integral value for L? b) Imagine that the illustrated DNA contains a 22 bp segment of alternating purine/pyrimidine residues. In the DNA as illustrated, this segment has an average helical twist angle of 34°. Estimate the writhe of the DNA after the 22 bp segment flips into the Z conformation (helical twist angle =-30°.) The DNA backbone remains intact throughout the transition. Show your calculation. c) Would the B to Z transition in this piece of closed circular DNA be topologically favored or topologically disfavored.

Explanation / Answer

linking number = total base pair / 10 (base pair per turun) = 10.5 is actual number give non-integer

500/10= 50

L=50

L=T+W

W=0 ( there is "0" superhelix)

50=T+0

T=50 (50 twist)

linking number always should be in integer number because it represents number of times that one strand winds to other.

C) B to Z is unfavorable because topologically B is most stable.

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