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 SupercoilingCircular 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

Toroidal

Interwound

THE LINKING NUMBER OF DNA - A TOPOLOGICAL PROPERTY

5’

5’

3’3’

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

260 bp bp

B-DNA contains 10.5 residuesper 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, alteringThe 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 (righthanded for B-DNA) the supercoiling formed is POSITIVE

If the twisting is in the opposite direction as the double helix (lefthanded for B-DNA) the supercoiling formed is NEGATIVE

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

Lk0 is the linking number of the relaxed circular DNA molecule

Lk - Lk0) / Lk0

DNA isolated from cells is commonly negatively supercoiled by6 turns per 100 turns of helix

Therefore: = (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°

34.3°

30.9°<

>37.7°

Essential Cell Biology, 2/e

The degree of underwinding in cellular DNAs generally falls in the range of 5% to 7%; that is, –

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.

Relaxed

Negative

Positive

Lk=Tw+Wr

Sinder, DNA Structure & Function

SUPERCOILING INTRODUCES TORSIONALSTRESS 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 tobe locally unwound or untwisted.

Negative supercoiling may therefore facilitate processes that require DNAunwinding, such as transcription, replication and DNA repair.

HAIRPIN AND CRUCIFORM DNA STRUCTURES

T T A G C A C G T G C T A A A A T C G T G C A C G A T T

5’ 3’

3’ 5’

Palindromes are inverted repeats of DNA

Palindrome DNA sequences are self-complementary andtherefore have the ability to base-pair with each other

Base pairing of palindrome sequences can result inhairpin 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

Hairpin formation

Cruciform formation

When only a single DNA(or RNA) strand is involved.

When both strands of a duplex DNA are involved.

Secondary Structure of Nucleic Acids

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

Triple Helix

From H. Lodish et al., Molecular Cell Biology, 4th ed., Freeman, New York (2000).

From

C. K

. Mathew

s et al., Biochem

istry, 3rd ed.B

enjamin/C

umm

ings, San F

rancisco (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.

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.

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