Raina Jain,

M.Sc. Biotechnology,
Navsari Agricultural University,
Navsari
 Supercoiling
Supercoiling means coiling of a coil.
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

Relaxed DNA Supercoiled DNA

Types of Supercoiling
Toroid
al

Interwoun
d
 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

The level of supercoiling may be quantified in terms of supercoiling density (σ )

σ = ( Lk - Lk0) / Lk0
Lk0 is the linking number of the relaxed circular DNA molecule

DNA isolated from cells is commonly negatively supercoiled by

6 turns per 100 turns of helix

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

If the DNA is wound so that there are fewer bases
per turn <9 bp, it is overwound creating positive
supercoiling
The angle of twist increases from 34.3° to 37.7°

If there are more bases per turn >11 bp, it is

underwound creating negative supercoiling
The angle of twist decreases from 34.3° to 30.9°

30.9° >37.7
< °
34.3
°
Essential Cell Biology, 2/e
The degree of underwinding in cellular DNAs generally falls in
the range of 5% to 7%; that is, σ = −0.05 τ ο 0.07.

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.

 Relaxe
d

Negativ Positiv
e e

Lk=Tw+Wr

Sinder, DNA Structure & Function

SUPERCOILING INTRODUCES TORSIONAL
STRESS INTO DNA MOLECULES

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.
HAIRPIN AND CRUCIFORM DNA STRUCTURES
Palindromes are inverted repeats of DNA

5’ TTAGCACGTGCTAA 3’
3’ AATCGTGCACGATT 5’

Palindrome DNA sequences are self-complementary and

therefore have the ability to base-pair with each other

Base pairing of palindrome sequences can result in

hairpin or cruciform DNA structures

Palindromic sequences are self complementary within each

strand and therefore have potential to form Hairpin or
Cruciform (cross-shaped) structures.
HAIRPIN AND CRUCIFORM DNA STRUCTURES

Cruciform formation
Hairpin formation

When only a single DNA(or RNA) When both strands of a duplex

strand is involved. DNA are involved.
 Secondary Structure of Nucleic Acids

Triple Helix
A triple-stranded structure can also exist at least in the test tube, and
possibly during recombination and DNA repair.

From H. Lodish et al., Molecular Cell Biology, 4th ed., Freeman, New York (2000).
Triple-helical structures involve, in addition to the normal Watson-Crick
base pairing, the Hoogsteen base pairing. For example,
the first triple helix discovered, poly(U)·poly(A)·poly(U), has an
all-purine strand (Pur) paired with two all-pyrimidine strands
(Pyr). This type of triple-base bonding is of
biological importance. For instance, it helps
stabilize structures of tRNAs.

Benjamin/Cummings, San Francisco (2000).

From C. K. Mathews et al., Biochemistry, 3rd ed.
In the so-called H-DNA, a portion of the Pyr·Pur duplex denature and loops back
to form triple helix, leaving one of the strands from the denatured portion
unpaired.
The loss of Watson-Crick pairs must have been over-compensated by the
formation of Hoogsteen base pairs.
In fact, cocrystallization of monomeric adenine and thymine derivatives invariably
leads to Hoogsteen pairs, suggesting that Hoogsteen base pairing is more stable
for A·T pairs than is Watson-Crick base pairing.
THANK
YOU