Supercoiling of DNA / DNA

Topology
 Open circular DNA
(ocDNA)/ relaxed form covalently closed,
circular DNA
(cccDNA)
covalently closed, circular Open circular DNA
DNA (ocDNA)/ relaxed form
(cccDNA)
 Supercoiling
• Supercoiling means coiling of duplex DNA
around its own axis is called supercoiling.

For example, a telephone cord is typically a coiled

wire.
DNA Supercoiling
• Circular B form DNA, has one helical turn every 10.5
bp, is said to be “relaxed”, as there is no net bending
of the DNA axis upon itself.
• If two points are twisted in opposite directions
supercoiling may be created
 Negative Supercoils Positive Supercoils

• Negative supercoils twist • Positive supercoils twist

the DNA about its axis in
the opposite direction from
the clockwise turns of the
right-handed (R-H) double
helix.
the DNA in the same
direction as the turns of the
R-H double helix.

• Negatively supercoiled • Positively supercoiled DNA

DNA is underwound (and is overwound (helix is
thus favors unwinding of wound more tightly).
duplex).

• Negatively supercoiled • Positively supercoiled DNA

DNA has R-H supercoil has L-H supercoil turns.
turns
SUPERCOILING INTRODUCES TORSIONAL
STRESS INTO DNA MOLECULES

• Since supercoiling induces serious torsional and bending

deformations into DNA, it is energetically unfavourable.

• Supercoiled DNA has a higher energy level than relaxed DNA

• For negative supercoiling, this energy makes it easier for

the DNA helix to be locally unwound or untwisted.

• Negative supercoiling may therefore facilitate processes

that require DNA unwinding, such as transcription,
replication and DNA repair.
 Positive Supercoils
• The only organisms that have been found to have positively supercoiled
DNA are certain thermophiles, microorganisms that live under conditions
of extreme high temperatures, such as in hot springs.

• In this case, the positive supercoils can be thought of as a store of free

energy that helps keep the DNA from denaturing at the elevated
temperatures.

• In sofar as positive supercoils can be converted into more twist (positively

supercoiled DNA can be thought of as being overwound), strand separation
requires more energy in thermophiles than in organisms whose DNA is
negatively supercoiled.
 Linking Number
• The basic parameter characterizing supercoiled DNA is the linking
number (L).

• This is number of times that one DNA strand winds about the others
strands.

• L cannot change provided both strands remain covalently intact.

• The number of times one strand would have to be passed through the other
strand in order for the two strands to be entirely separated from each other
is called the linking number,
Linking Number
 Linking Number
• When the molecule is relaxed, the linking number is
simply the number of base pairs divided by the
number of base pairs per turn, which is close to 10.5
– In a DNA duplex of 400 bp, L is 40 (assuming 10 bp per turn in
B-DNA).

• Linking number is always an integer.

• The linking number for relaxed DNA is usually taken as
the reference parameter and is written as L0
Linking Number
 Linking Number Is Composed of Twist and Writhe

• The linking number is the sum of two geometric components called the twist and the
writhe; Equation Lk = Tw +Wr

• L:linking number

– # of times that one DNA strand winds about the others strands, is always an integer

• T: twist

– Twist is simply the number of helical turns of one strand about the other.

• W: writhe

– the writhe is the number of times the double helix crosses over on itself (these are
the supercoils).

– by definition the measure of the degree of supercoiling

• Tw & Wr need not be integers.

 Twisting number

• T = Twisting number
• For B form DNA, it is + (# bp/10 bp per
twist)
• For A form DNA, it is + (# bp/11 bp per
twist)
• For Z DNA, it is - (# bp/12 bp per twist)
 Writhing Number
• W = Writhing Number is the turning of the
axis of the DNA duplex in space
• Relaxed molecule W=0
• Negative supercoils, W is negative
• Positive supercoils, W is positive
 THE LINKING NUMBER OF DNA - A TOPOLOGICAL PROPERTY

Linking number (Lk) is equal to the number of times a strand of DNA winds in the
right hand around the helix axis when the axis is constrained to lie in a plane

5’ 3’
3’ 5’

260 bp bp

B-DNA contains 10.5 residues

per turn

For a 260 bp piece of DNA:

Number turns = 260/10.5 = 25

The Lk = 25

The Lk of circular DNA can be changed only by cutting one or both strands of DNA, altering
The number of turns in the DNA helix and rejoining the DNA
POSITIVE AND NEGATIVE SUPERCOILING

If the twisting is in the same direction as the double helix (right

handed for B-DNA) the supercoiling formed is POSITIVE

If the twisting is in the opposite direction as the double helix (left

handed for B-DNA) the supercoiling formed is NEGATIVE

Lk0 is the linking number of the relaxed circular DNA molecule

Linking number can be broken down into 2 structural components
called writhe (Wr) and twist (Tw)

Writhe may be thought as a measure of the coiling of the helix

axis.

Twist determine the local twisting or spatial arrangement of

neighbouring base pairs.

Lk = Tw + Wr

Tw & Wr need not be integers.

 The level of supercoiling may be quantified in terms of supercoiling
density (

 Lk - Lk0) / Lk0

DNA isolated from cells is commonly negatively supercoiled by
6 turns per 100 turns of helix

Therefore:  = (94 - 100) / 100 = -0.06

The degree of underwinding in cellular DNAs generally falls in

the range of 5% to 7%; that is, -0.05to-0.07.
 Writhe can take two forms
• One form is the interwound or plectonemic writhe, in which
the long axis is twisted around itself.

• The other form of writhe is a toroid or spiral in which the

long axis is wound in a cylindrical manner, as often occurs
when DNA wraps around protein.

• Both are interconvertible.

 Topoisomerases Can Relax Supercoiled DNA

• The linking number can only be changed by breaking

one or both strands of the DNA, winding them tighter
or looser, and rejoining the ends.

• Enzymes capable of carrying out such reactions are

called topoisomerases because they change the
topological state of DNA.

• Topoisomerase falls into two basic classes, I and II.

 Topoisomerases of the I type cut one strand of a DNA
double helix, pass the other strand through, and then rejoin
the cut ends changing the linking number in steps of ±1.

 Topoisomerase II enzymes cut both strands of a dsDNA,

pass a region of the DNA duplex between the cut ends, and
then rejoin the ends changing the linking number in steps of
±2.
• Type II topoisomerases require the energy of ATP hydrolysis for
their action unlike Type I

• Topoisomerases are important players in DNA replication.

• DNA Gyrase: introduce the negative supercoiling (resolving the

positive one and using the energy from ATP hydrolysis.
(Prokaryotes)