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BIO SCI 99 Study Guide - Midterm Guide: Linking Number, Dna Supercoil, Dna Replication

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Lecture 9 DNA Replication Part III
(Greyed-out text is meant only to be helpful and is optional)
1. Supercoiling
What does the term linking number define? Is it correct to say that the linking
number of relaxed DNA is zero? Why not?
Relaxed DNA is a right-handed double helix (coil)two strands of DNA that are
paired with each other along their length through hydrogen bonding between their
bases. The two strands in the helix coil around each other once per turn, therefore
each turn of the helix results in one intertwining, or link, between the two strands.
If you wanted to unlink the two strands and the two ends of the dsDNA were
anchored somehow and not permitted to turn relative to one another, you would be
forced to make cuts in the strands in order to unlink them. If you were limited to
removing one link per cut and cutting only one strand at a time, you would have to
make one cut per turn in the dsDNA.
The number of intertwinings (or links) between the two strands of dsDNA as they
wind around the helix is referred to as the linking number. Since there is one helical
turn per 10.5 base pairs in relaxed dsDNA, the linking number of relaxed dsDNA is
equal to the length of the dsDNA in base pairs divided by 10.5 base pairs. The activity
of topoisomerases can be described by how they change the linking number of a
dsDNA molecule relative to the relaxed state of the dsDNA. Note that linking
number is only defined when the dsDNA is circular, or, if linear, when the two ends
of the dsDNA are not free to rotate relative to one another.
The two strands of the dsDNA (in the most common B-form) coil around each other
in a clockwise direction as you move along the length of the helix. If you anchor one
end of the DNA double helix and twist the free end in the direction of the right-
handed coil (clockwise), would you be adding turns (or coils or links) or removing
them? In other words, would the linking number increase, decrease or remain the
same? What about if you twisted the free end of the anchored dsDNA in the
opposite direction?
Conversely, if, instead of twisting the free end of the anchored dsDNA, you cut one
of the strands in the middle, pass the unbroken strand through the cut and reseal
the cut. Would this change the number of times the two strands are intertwined or
linked? In other words, would the linking number of the dsDNA be changed? Would
the outcome depend on direction from which the unbroken strand was passed
through the cut?
Does it take energy to change the linking number of dsDNA that is completely
relaxed? Supercoiling describes what happens when you change the linking number
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