The document discusses the concept of DNA supercoiling, explaining how DNA molecules can exist in various forms, including relaxed and supercoiled states, and the impact of twisting on DNA structure and energy. It highlights the roles of topoisomerases in managing supercoils, with Type I enzymes relaxing supercoiled DNA and Type II enzymes capable of introducing negative supercoils using ATP. Supercoiling is crucial for processes like DNA replication and transcription, with negative supercoiling being particularly prevalent in prokaryotes and eukaryotes, as it facilitates strand separation.

1. ASSIGNMENT ON
SUPERCOILING OF DNA
SUBMITTED TO:
SIR DR. M. WASIM
SUBMITTED BY:
AMINA ILYAS
2016-BC-004

2. SUPERCOILING IN DNA
Normally, DNA occurs as a helical, double-stranded molecule in which
the two strands are antiparallel; the classical B-type helix is the structure
first solved by Watson and Crick in 1953.B-form of DNA is a configuration of
minimum energy, any bending or twisting of the DNA molecule will
increase its free energy. In addition to varying secondary structures,the
DNA helix can wind in three-dimensional space to form further helices of
higher order. DNA in this conformation is termed supercoiled and
changes to this tertiary structure of a DNA molecule have dramatic
consequences for the free energy and biology of the molecule.
When the DNA helix has the normal number of base pairs per helical turn
it is in the relaxed state. Changing this normal amount of twist can be
demonstrated by grasping both ends of a short linear model (one to two
complete turns) and twisting the ends in opposite directions. 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.
“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. Supercoiling occurs when the molecule relieves the
helical stress by twisting around itself.”

3. As the two strands of double helix are separated a problem is
encountered, namely the appearance of positive supercoils in the region
of DNA ahead of the replication fork as a result of overwinding and
negative supercoils in the region behind the fork. The accumulating
positive supercoils interfere with further unwinding of the double helix.
Supercoiling can be demonstrated by tightly grasping one end of a helical
telephone cord while twisting the other end.
If the cord is twisted in the direction of tightening the coils, the cord will
wrap around itself in space to form positive supercoils. Positive
supercoiling is the right-handed
If the cord is twisted in the direction of loosening the coils, the cord will
wrap around itself in the opposite direction to form negative supercoils.
Negative supercoiling is the left-handed.
Although the helix is underwound and has low twisting stress, negative
supercoil's knot has high twisting stress. Prokaryotes and Eukaryotes
usually have negative supercoiled DNA. Negative supercoiling is naturally
prevalent because negative supercoiling prepares the molecule for
processes that require separation of the DNA strands. For example,
negative supercoiling would be advantageous in replication because it is
easier to unwind whereas positive supercoiling is more condensed and
would make separation difficult. Because DNA is condensed into
supercoils in order to fit inside the cell, several different enzymes are
needed to open and relax the DNA before replication can start.

4. To solve the problem of supercoiling, there is a group of enzymes called
DNA topoisomerases, which is responsible for removing supercoils in the
helix by transiently cleaving one or both of the DNA strands.
TOPOISOMERASES
Topoisomerases are enzymes that are responsible for the introduction
and elimination of supercoils. Positive and negative supercoils require
two different topoisomerases. This prevents the distortion of DNA by the
specificity of the topoisomerases. The two classes of topoisomerases are
Type I and Type II. Type I stimulates the relaxation of supercoiled DNA
and Type II uses the energy from ATP hydrolysis to add negative
supercoils to DNA. Both of these classes of topoisomerases have
important roles in DNA transcription, DNA replication, and recombinant

5. DNA.Topoisomerase form loops (unwinded regions of the double helix)
of negative supercoils. If the DNA lacks superhelical tension, there is no
unwinding of supercoils.
TYPE I DNA TOPOISOMERASE
These enzymes reversibly cleave one strand of the double helix. They
have both strand-cutting and strand-resealing activities. They do not
require ATP, but rather appear to store energy from the phosphodiester
bond they cleave, reusing the energy to reseal the strand. Each time a
transient “nick” is created in one DNA strand, the intact DNA strand is
passed through the break before it is released, thus relieving (relaxing)
accumulated supercoils. Type 1 topoisomerases relax negative
supercoils (that is, those that contain fewer turns of the helix than
relaxed DNA) in E. coli and both negative and positive supercoils in many
prokaryotic cells (but not E. coli) and in eukaryotic cells.
TYPE II TOPOISOMERASE
These enzymes bind tightly to the DNA double helix and make transient
breaks in both strands. The enzyme then causes a second stretch of the
DNA double helix to pass through the break and, finally, reseals the
break.
As a result, both negative and positive supercoils can be relieved by this
ATP requiring process. DNA gyrase, a type II topoisomerase found in
bacteria and plants, has the unusual property of being able to introduce
negative supercoils in to circular DNA using energy from the hydrolysis
of ATP. This facilitates the replication of DNA because the negative
supercoils neutralizes the positive supercoils introduced during opening
of the double helix. It also aids in the transient strand separation
required during transcription.