DNA Topology
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DNA Topology


It is a well-known fact that
double-stranded DNA forms a double helix structure, but
the double helix itself can twist and turn into
different conformations. So, how does DNA
change its shape, and why is this
behavior important to our cellular functions? This video will use a
physical model of DNA to help explain the
significance of DNA topology and simulate how specific
enzymes modify the conformation of double-stranded DNA. The unstrained, or
relaxed, DNA structure has 10.4 base pairs
per turn of the helix. One way to describe the
structure of a DNA double helix is by a combination of its twist
and writhe, the sum of which is called the linking number. The twist is described as the
number of helical turns of one strand about the other
and can be measured by counting how many times
one strand wraps completely around the other. For example, this
relaxed linear DNA has a twist of one, two, three. There is 0 writhe
in this example. The writhe is described as how
many times the double helix crosses over itself and
is positive or negative depending on the orientation. For example, this circular
DNA has a writhe of -1 because it follows
the right hand rule and the upper strand
travels left to right. And this DNA has a writhe of 1. Both of these examples
also have twist. Realistically, long DNA
molecules like these can have linking numbers
in the thousands. For this video,
we’re going to look at a physical model
of circular DNA with covalently linked ends. Unlike linear DNA, this shape
is topologically constrained, meaning you can’t change the
linking number of the DNA without breaking one
or both of the strands. But what would physically
happen to this DNA if you added or removed twists
or writhe in the double helix? Overwound DNA has fewer
than 10.4 base pairs per turn of the helix. Thus, overwound DNA is more
tightly wound than relaxed DNA and has a greater
number of twists and a higher linking
number than relaxed DNA. When DNA is overwound and has
an increased linking number, the DNA becomes
positively supercoiled, and the double-stranded
structure begins wrapping around itself
and creating positive writhe. Regardless of these visible
changes in conformation, remember that positively
supercoiled DNA will have a higher linking
number than relaxed DNA, and the two strands of
the double-stranded DNA are more difficult to separate. Underwound DNA has greater
than 10.4 base pairs per turn of the helix. Thus, underwound DNA is less
tightly wound than relaxed DNA and has a fewer number of
twists and a lower linking number than relaxed DNA. When DNA is underwound and has
a decreased linking number, the DNA becomes
negatively supercoiled and the double-stranded
structure begins wrapping around itself
in the opposite direction as positive supercoiling,
creating negative writhe. Regardless of these visible
changes in conformation, remember that negatively
supercoiled DNA will have a lower linking
number than relaxed DNA, and the two strands of
the double-strand DNA can be separated more easily. But if DNA is least strained
in the relaxed form, how does the double helix change
from being relaxed to overwound or underwound? And how does positively
or negatively supercoiled DNA return
to a relaxed state? Topoisomerases are
a class of enzyme that usually restores
DNA to its relaxed state. This means that topoisomerases
unwind overwound DNA strands, reducing the linking number
back to the preferred 10.4 base pairs per turn, or rewind
underwound DNA strands, increasing the
linking number back to 10.4 base pairs per turn. Topoisomerases work by
breaking one or two DNA strands and passing the same number of
DNA strands through the break. This change results in
an increase or decrease in the linking number of our
topologically constrained circular DNA. There are two main categories
of topoisomerase, Type I and Type II. Type I topoisomerase breaks
one of the two DNA strands and passes the other
strand through the gap. This increases or decreases
the linking number by 1. Here, the top DNA double
helix represents the structure before the topoisomerase
added a twist, and the bottom DNA double helix
is after the enzyme completes the reaction. Type I topoisomerase
reactions do not require additional energy. Type II topoisomerase breaks
both of the two DNA strands and passes the entire double
helix through the gap. This increases or decreases
the linking number by 2. Here, the top DNA double
helix represents the structure before the topoisomerase acts,
and the bottom DNA double helix is after the enzyme
completes the reaction. In this case, the result is
that the writhe of the molecule increases by 2. To make this idea
clear, this diagram shows what this
change would look like if you added one
positive writhe at a time instead of using Type
II topoisomerase. Type II topoisomerase reactions
require some form of energy, such as ATP or NADH. Bacteria also have a special
form of Type II topoisomerases called gyrase. Gyrase enzymes use energy
to negatively supercoil DNA rather than restoring
DNA to the relaxed state. Certain thermophiles
also have topoisomerases that use energy to
positively supercoil DNA rather than restoring
DNA to the relaxed state. Because it acts
oppositely to gyrase, these enzymes are
called reverse gyrase. But if DNA is unstrained
in its relaxed state, why would organisms have enzymes
that intentionally supercoil their DNA either
positively or negatively? Thermophiles and
hyperthermophiles thrive at relatively
high temperatures, ranging from 45 to over
100 degrees Celsius. Positive supercoiling
in thermophile DNA adds additional twists or
writhe to the double helix, thus increasing
the linking number. These changes stabilize
the structure, preventing the DNA
from denaturing as easily at high temperature. Wanting stable DNA structures
makes evolutionary sense, but what about the
organisms with negatively supercoiled DNA? In fact, the DNA
of most organisms is negatively supercoiled. Negatively supercoiled DNA
provides a store of free energy that helps with
cellular processes that require strand separation
of the double helix, like DNA replication
and transcription. Underwound DNA has a tendency
to partially separate, so strand separation is
easier than in a relaxed DNA structure, with more twists
holding the double helix together. In short, negatively
supercoiled, or underwound, DNA makes it easier to
separate the double helix into two single strands. As you separate the double helix
and negatively supercoiled DNA, you are creating more twists
in the rest of the DNA, causing rewinding of
the underwound strands. Rather than putting strain
on the DNA topology, the DNA that is
still base paired is returned to the
ideal relaxed state. Plus, you have a portion of
separated single DNA strands that can be used in cellular
processes like replication and transcription. If you tried to separate the
double helix of relaxed DNA, you would introduce
more twists in the DNA and end up overwinding, or
positively supercoiling, the double helix, which is
energetically unfavorable. This video modeled
how DNA topology extends beyond the
double helix structure and how topology is critical
to our cell’s ability to function smoothly by
replicating or transcribing DNA more efficiently. Now, are you able to model
overwound and underwound DNA and tell the difference
between Type I and Type II topoisomerases and
their functions? And can you explain
what role DNA topology plays in cellular
processes and function? Thanks for watching.

39 thoughts on “DNA Topology

  1. Question : why would any organism use Type 2 topoisomerase when using type one twice yields the same result ? one consumes ATP and the other Doesn't

  2. 4:53 (By the way, I learned a ton from this video). In Voet&Voet, Gyrase is described a restoring a positive supercoiled DNA to the relaxed state. You say "rather than the relaxed state" which is not the same as the textbook. However, maybe you're right. Just sayin'

  3. I can't understand why in the overwound DNA the number of bp/turn decreases c.c
    I mean, when we use the ethidium bromide, the number of bp/turn increases and the Wr tends to become positive.

    Could someone explain me this?
    Thanks

    PS: The video is awesome

  4. Hi
    what is RNA ?
    How many types of RNA?
    The structure of RNA
    what is Amino Acids ?
    The structure of Amino acids ?
    What is Genes ?
    what is Chromosome?
    can you share information of list of systems of the Human body ?

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