1. DNA is a macromolecule that carries genetic information in the form of nucleotides joined by phosphodiester bonds in a double helix structure. 2. The nucleotides consist of a pentose sugar, a nitrogenous base, and phosphate groups. Adenine pairs with thymine and guanine pairs with cytosine through hydrogen bonds. 3. Watson and Crick discovered that DNA has a double helix structure with the bases pointing inward and the sugar-phosphate backbones on the outside. The two anti-parallel strands are held together by hydrogen bonds between complementary nucleotide base pairs.

1. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
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DNA & Its Topology
Deoxyribonucleic acid, simply known as DNA, is a large molecule that carries genetic
information. The DNA is a macromolecule. It is a polymer, composed of building blocks
called deoxyribonucleotides (or also known as deoxyribotids). The
deoxyribonucleotide is a nucleotide that consists of three major components:
1) A pentose sugar (2 – deoxyribose)
2) A nitrogenous base (pyrimidine or purine)
3) Phosphate groups (one to three)
Deoxyribose Sugar
The deoxyribose sugar (2 – deoxyribose) is a pentose sugar (5 carbons) and is very
similar to the ribose sugar. The only difference is that deoxyribose sugar has one less
oxygen atom at C2 (Carbon# 2).
Figure: Deoxyribose sugar has one less oxygen atom than ribose sugar at C2.
Nitrogenous Bases
The nitrogenous bases are cyclic compounds that contain nitrogen. They are of two
types: Pyrimidines and Purines. The pyrimidines have only one cyclic ring, i.e.
Cytosine (C) and Thymine (T). The purines have a double-ringed structure (two
rings), i.e. Adenine (A) and Guanine (G).

2. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
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Figure: Cytosine and Thymine are single ringed pyrimidines that are present in the DNA
molecules. Another single ringed pyrimidine is uracil, but it is not present in DNA, rather
it is a part of the RNA molecules.
Figure: Adenine and Guanine are double-ringed purines that are present in the DNA
molecules.
Phosphate Groups
The phosphate groups are derived from phosphoric acid. Up to three phosphate groups
can be present in a nucleotide. If one group is present, we call it a monophosphate, if
two are present, we call it a diphosphate and if three are present, we call it a
triphosphate. The nucleotides present in a DNA molecule have only one phosphate
group attached to them (monophosphate) but the nucleotides present in the cytoplasm
have three phosphates (triphosphate).
Nucleotides & Nucleosides
A nucleotide is formed when a pentose sugar (Deoxyribose, in case of a
deoxyribonucleotide), nitrogenous base (Adenine, Guanine, Cytosine or Thymine in
case of deoxyribonucleotide), and phosphate groups attached.

3. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
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The part of a nucleotide that contains a nitrogenous base and a pentose sugar is called
a nucleoside. In the case of DNA, it is a deoxyribonucleoside. The nucleosides have
the suffix “ine” at the end of their names, i.e. Deoxyadenosine, Deoxyguanosine,
Deoxycytidine, and Deoxythymidine.
When phosphate groups are attached to these nucleosides, they become nucleotides,
i.e. Deoxyadenosine monophosphate (dAMP), Deoxyguanosine monophosphate
(dGMP), Deoxycytidine monophosphate (dCMP), and Deoxythymidine
monophosphate (dTMP). The nucleotides present in the DNA molecules are in the
form of monophosphates but those in the cytoplasm are in the form of triphosphates, i.e.
Deoxyadenosine triphosphate (dATP), Deoxyguanosine triphosphate (dGTP),
Deoxycytidine triphosphate (dCTP), and Deoxythymidine triphosphate (dTTP).
This is because the DNA polymerase enzyme can only act upon triphosphates of
deoxyribonucleotides.
Figure: Structure of a nucleotide – Deoxyadenosine monophosphate (dAMP)
The phosphate on the carbon 5 of deoxyribose of one nucleotide forms a bond with the
hydroxyl group on carbon 3 of deoxyribose of another nucleotide. This bond is called a
phosphodiester bond. Nucleotides in a chain of DNA are connected due to this bond.

4. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
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Figure: Carbon 5 of one nucleotide and carbon 3 of another are linked together by a
phosphodiester bond/linkage.
The Equivalence Rule
In 1950, Erwin Chargaff gave the equivalence rule. He said that the four nucleotide
bases are not present in equal proportions in a DNA molecule. Instead, he proposed
that the total number of purines was equal to the total number of pyrimidines:
A+G = T+C
The amount of adenine and thymine is equal (A=T) and the amount of guanine and
cytosine is equal (G=C). This is because adenine forms a base pair with thymine, and
guanine forms a base pair with cytosine.
Physical Structure of DNA
The physical structure of DNA was first understood when Rosalind Franklin obtained an
X-ray diffraction photograph of DNA which demonstrated that DNA was a helical
structure with a diameter of 20 Aº and a pitch (one round) of about 34 Aº. Based on
Rosalind’s findings and Chargaff’s equivalence rule, Watson and Crick presented their
model of DNA commonly known as the Watson and Crick model of DNA.

5. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
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According to this model, in a DNA molecule, the adjacent deoxyribonucleotides are
joined in a chain by phosphodiester bonds which link the 5' carbon of the deoxyribose of
one mononucleotide unit with the 3' carbon of the deoxyribose of the next
mononucleotide unit. According to Watson and Crick, DNA molecule consists of two
polynucleotide chains wrapped helically around each other, with the sugar-phosphate
chain on the outside (forming the ribbon-like backbone of double helix) and purines and
pyrimidines on the inside of the helix. The two polynucleotide strands are held together
by hydrogen bonds between specific pairs of purines and pyrimidines.
Figure 1: Structure of DNA, according to Watson and Crick
The hydrogen bonds between purines and pyrimidines are such that adenine can bond
only with thymine by two hydrogen bonds, and guanine can bond only with cytosine by
three hydrogen bonds. For every adenine in one chain, there will be thymine in the other
and for every guanine in the first chain, there will be a cytosine in the other. Thus, the
two chains are complementary to each other; that is, the sequence of nucleotides in
one chain dictates the sequence of nucleotides in the other. The two strands run anti-
parallel, i.e. in opposite directions. One strand has phosphodiester linkage in 3'→ 5'
direction, while the other strand has phosphodiester linkage in just reverse or 5'→3'
direction.

6. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
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Both polynucleotides strands remain separated by 20 Aº distance. Ten mononucleotides
occur per complete turn of DNA helix. The helix has two external grooves, a deep wide
one, called major groove, and a shallow narrow one, called minor groove. Both of
these grooves are large enough to allow protein molecules to come in contact with the
bases.
Forms of DNA
There are three major forms of DNA, namely A, B, and Z DNA. They differ in the relation
between their bases and the helical axis.
B-DNA: It is right-handed DNA. It is the structure of fully hydrated DNA. It is the most
common form of DNA encountered in vivo (inside a living system/cell). Its diameter is
20Ao and there are 10 nucleotides per one completer turn of 360o (meaning that the
angle of twist of each nucleotide is 36o). The major groove is wide while the minor
groove is narrow.
A-DNA: It is also a right-handed DNA. This form of DNA is acquired when B-DNA is
dehydrated, i.e. it is the dehydrated form of B-DNA. As a result of dehydration, the
angle of twist of nucleotides increases. The diameter increases to 26Ao and the number
of base pairs per 360o turn becomes 11.6. The major groove becomes narrow and deep
while the minor groove becomes wide and shallow. The structural transformation of B-
DNA to A-DNA (due to dehydration) is reversible.
Z-DNA: It is a left-handed form of DNA. Z-DNA is so-called because of the zig-zag
structure of its phosphate backbone. It has a diameter of 18Ao. There are 12 base pairs
in a complete 360o turn. The minor groove is narrow and deep whereas the major
groove is flat. Another important feature of Z-DNA is that adjacent nucleotides have
opposite orientation, i.e. they form dinucleotides.
Topology of DNA
Topology is a branch of mathematics that deals with the study of the properties of
geometric forms (shapes) that remain unchanged under certain transformations, as
bending or stretching.

7. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
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The ideal or relaxed state of DNA is the B form, a right-handed structure with a diameter
of 20Ao. This is because this is the structure of minimum energy. Any deviation from this
relaxed state causes an increase in energy, this problem is solved by the supercoiling
of DNA, i.e. DNA curves itself into a coil. This minimizes the excess energy that builds
up in the DNA molecule when it is deformed.
1. Linking Number
The number of times that one strand wraps around the other remains fixed, it is known
as the linking number. Linking number (denoted as Lk) is a measure of the total
number of complete revolutions that either strand makes about the other. As long as the
strands remain intact, Lk is a fixed quantity. The linking number cannot be changed
unless a bond is broken.
2. Topoisomerases
Topoisomerases are special enzymes that change the topology of DNA by changing its
linking number by introducing a nick/cut in the DNA. There are two types of
topoisomerases: Topoisomerase I and Topoisomerase II.
Topoisomerase I changes Lk in units of one by breaking a single strand of DNA and
allowing the duplex to unwind. Whereas, Topoisomerase II changes Lk by units of two
by breaking both strands, creating a gate through which a second segment of helix is
passed.