This contains DNA Supercoiling , relation between Linking no,Twist and Writhe and a brief explanation of Topoisomerase

1. DNA SUPERCOILING
By Subhranil Bhattacharjee

2. What is Supercoilimg
• The term "supercoiling" means literally the coiling of a coil.
• DNA supercoiling is generally a manifestation of structural
strain.
• Supercoiling occurs when the molecule relieves the helical
stress by twisting around itself. Overtwisting leads to postive
supercoiling, while undertwisting leads to negative
supercoiling.
• If DNA is in the form of a circular molecule, or if the ends are
rigidly held so that it forms a loop, then overtwisting or
undertwisting leads to the supercoiled state.
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3. 2

4. Positive and Negative Supercoiling
• When the DNA helix has the normal
number of base pairs per helical
turn it is in the relaxed state.
• If the helix is overtwisted so that it
becomes tighter, the edges of the
narrow groove move closer
together.
• If the helix is undertwisted, the
edges of the narrow groove move
further apart.
• Notice that changing the twist
from the relaxed state requires
adding energy and increases the
stress along the molecule
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5. Positive supercoiling
• Positive supercoiling is the
right-handed, double
helical form of DNA. It is
twisted tightly in a right
handed direction until the
helix creates knot.
• positive supercoiling is
more condensed as the
supercoil forms at the
direction of DNA helix
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6. • Negative supercoiling is
the left-handed, double
helical form of DNA.
• Prokaryotes and
Eukaryotes usually have
negative supercoiled DNA.
it is naturally prevalent as
it prepares the molecule
for processes that require
separation of the DNA
strands without the need
of additional energy.
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7. How Supercoils are formed ?
• During the process of cellular events like replication and
transcription ,the DNA strand needs to be separated from
each other
• Once the DNA strand needs to be separated from each
other at that location, the twist number gets reduced .This
creates tension in the DNA so the writhe is formed to
compansate for the tension in the strand .
• Some enzymes like topoisomarase can relieve the stress
thus reduceing the Linking number.
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8. Linking Number, Twist, and Writhe
• To study these loops, mathematicians have created three quantities that
describe the loops and their relationship to each other.
• Linking number--The number of times the two strands are
intertwined.it is also the number of cleaves necessary for
separating two DNA strands.It will be constant.
• Twist--It is most easily imagined as the number of times each of
the curves rotates around the central axis of the double helix.
• Writhe--the number of times the central axis C makes loops
about itself.
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9. Numerical expression for degree of supercoiling
Lk= Tw+Wr
where, Linking Number = Twist +Writhe
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10. Example
• lets say the Lk is 9, the Tw is the same in case of relax
state(no supercoil)
so,
L=9+0
L = 9
Wr can be of two types +ve(clock-wise) or -ve(anti-clock)
.The Tw should increase or decrease depending to this
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11. • Now if we have +1 Wr , to maintain the constant Lk of 9 the
Tw redusesd to 8
so,
Lk=8+1 =9
The DNA being right handed ,when supercoiled in clockwise
direction the twist value should decrease to compensate and
accommodate that writhe otherwise the DNA will break apar.this
is energy consumeing and forms strong supercoiling
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12. • Now if we have -1 Wr , to maintain the constant Lk of 9 the Tw
increced to 10
so,
Lk=10-1 =9
now ,as the DNA being right handed forms a left-handed writhe
that is anti-clockwise .It dewinds the DNA and makes a writhe
that is easier to remove and so the Tw is increased to
compansate the negetive writhe
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13. DNA Topoisomerases
• DNA topoisomerases are enzymes found in all cell types
.These enzymes act to regulate DNA supercoiling by
catalysing the winding and unwinding of DNA strands.
• They do this by making an incision that breaks the DNA
backbone, so they can then pass the DNA strands
through one another, swivelling and relaxing/coiling the
DNA before resealing the breaks.
• DNA topoisomerases can be divided into two groups
based on the number of strands that they break.
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14. Class I DNA Topoisomerases
Break one strand of a DNA helix.
• ATP independent (except for reverse gyrase).
• Mechanism involves rotating the broken strand around the
intact strand to relax (unwind) the strain on the DNA helix,
followed by resealing the ends of the broken strand.
• Play an important role in DNA replication and
transcription
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15. Class II DNA Topoisomerases• Break two strands of a DNA helix.
• ATP dependent.
• Mechanism involves passing an intact DNA helix through
the gap made by the broken DNA helix, then resealing the
strands
• Play an important role in chromosome condensation and
in the segregation of daughter chromosomes during cell
division
Class II Topoisomerase14

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