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NUCLEIC ACIDS an Overview
Three important Components
• Bases
• Sugar
• Phosphate group
The bases of DNA and RNA are heterocyclic (carbon- and nitrogen-containing) aromatic
rings, with a variety of substituents
. Adenine (A) and guanine (G) are purines, bicyclic structures (two fused rings),
cytosine (C), thymine (T) and uracil (U) are monocyclic pyrimidines.
In RNA, the thymine base is replaced by uracil. Thymine differs from uracil only in
having a methyl group at the 5-position, that is thymine is 5-methyluracil.
Sugars
In RNA, the sugar is ribose, and in DNA, it is 2-deoxyribose, in which the

hydroxyl group at the 2-position is replaced by a hydrogen.
Nucleosides
In nucleic acids, the bases are covalently attached to the 1-position of a pentose sugar ring, to
form a nucleoside .
The point of attachment to the base is the 1-position (N-1) of the pyrimidines and the 9-position
(N-9) of the purines
The bond between the bases and the sugars is the glycosylic (or glycosidic) bond.
If the sugar is ribose, the nucleosides (technically ribonucleosides) are adenosine, guanosine,
cytidine and uridine.
If the sugar is deoxyribose (as in DNA), the nucleosides (2-deoxyribonucleosides) are

deoxyadenosine, etc. Thymidine and deoxythymidine may be used interchangeably.
Nucleotides
A nucleotide is a nucleoside with one or more phosphate groups bound covalently
to the 3-, 5- or (in ribonucleotides only) the 2-position. If the sugar is deoxyribose, then
the compounds are termed deoxynucleotides .
Chemically,
the compounds are phosphate esters. In the case of the 5-position, up to three
phosphates may be attached, to form, for example, adenosine 5-triphosphate, or
deoxyguanosine 5-triphosphate, commonly abbreviated to ATP and dGTP respectively.
In the same way, we have dCTP, UTP and dTTP (equivalent to TTP).
.
Nucleoside 5-triphosphates (NTPs), or deoxynucleoside 5-triphosphates (dNTPs) are the
building blocks of the polymeric nucleic acids. In the course of DNA or RNA synthesis,
two phosphates are split off as pyrophosphate to leave one phosphate per nucleotide
incorporated into the nucleic acid chain.
Phosphodiester bonds
In a DNA or RNA molecule, deoxyribonucleotides or ribonucleotides respectively are joined into
a polymer by the covalent linkage of a phosphate group between the 5-hydroxyl of one ribose
and the 3-hydroxyl of the next .
This kind of bond or linkage is called a phosphodiester bond, since the phosphate is
chemically in the form of a diester. A nucleic acid chain can hence be seen to have a direction.
Any nucleic acid chain, of whatever length has a free 5-end, which may or may not have any
attached phosphate groups, and a free 3-end, which is most likely to be a free
hydroxyl group. At neutral pH, each phosphate group has a single negative charge. This is why
nucleic acids are termed acids; they are the anions of strong acids. Nucleic acids are thus highly
charged polymers.
DNA/RNA Sequence
Conventionally, the repeating monomers of DNA or RNA are represented by

their single letters A, T, G, C or U.
In addition, there is a convention to write the sequences with the 5-end at the left.
Hence a stretch of DNA sequence might be written
5-ATAAGCTC-3, or even just ATAAGCTC.
An RNA sequence might be 5-AUAGCUUGA-3.
* directionality of the chain means that, for example, ATAAG is not the same as
GAATA.
DNA Double helix
DNA most commonly occurs in nature as the well-known ‘double helix’. The basic features
of this structure were deduced by James Watson and Francis Crick in 1953.
Two separate chains of DNA are wound around each other, each following a helical (coiling)
path, resulting in a right-handed double helix.
The negatively charged sugar–phosphate backbones of
the molecules are on the outside, and the planar bases
of each strand stack one above the other in the center of
the helix .
Between the backbone strands run the major and minor

grooves, which also follow a helical path.
The strands are joined noncovalently by hydrogen

bonding between the bases on opposite strands, to form
base pairs. There are around 10 base pairs per turn in
the DNA double helix.
The two strands are oriented in opposite directions

(antiparallel) in terms of their 5→3 direction and, most
crucially, the two strands are complementary in terms of
sequence.
This last feature arises because the structures of the bases and the constraints of the DNA
backbone dictate that the bases hydrogen-bond to each other as purine–pyrimidine pairs
which have very similar geometry and dimensions .
Guanine pairs with cytosine (three H-bonds) and adenine pairs with thymine (two H-
bonds). Hence, any sequence can be accommodated within a regular double-stranded
DNA structure. The sequence of one strand uniquely specifies the sequence of the
other, with all that that implies for the mechanism of copying (replication) of DNA and
the transcription of DNA sequence into RNA .
CHEMICAL AND PHYSICAL PROPERTIES OF NUCLEIC ACIDS
Stability of Nucleic Acids :
Double helices of DNA and RNA secondary structure are stabilized by the hydrogen
bonding between base pairs.
As in proteins, the presence of H-bonds within a structure does not normally confer
stability. This is because the difference in energy between, in the case of DNA, the
single-stranded random coil state, and the double-stranded conformation.
H-bonds between base pairs in double-stranded DNA merely replace what would be
equally strong and energetically favorable H-bonds with water molecules in
free solution, if the DNA were single-stranded.
Hydrogen bonding contributes to the specificity required for base pairing in a double
helix ,but it does not contribute to the overall stability of that helix.
The root of this stability lies elsewhere, in the stacking interactions between the
base pairs .
The surfaces of the bases have few polarized bonds; consequently, base surfaces are
hydrophobic. As a result, the most energetically favoured conformation is attained by
reducing exposure of the base surfaces to the aqueous environment, which is achieved
by the bases moving closer together. In this conformation, the backbone is ‘tilted’ by an
angle of 30° from horizontal. Tilting the backbone in this way brings the planar rings of
adjacent base pairs to a position where they lie vertically one above the other, an
arrangement that maximises hydrophobic interactions and in addition, maximises van
der Waals attractive forces between them.
Effect of acid
In strong acid and at elevated temperatures, for example perchloric acid (HClO4)
at more than 100°C, nucleic acids are hydrolyzed completely to their
constituents: bases, ribose or deoxyribose and phosphate.
In more dilute mineral acid, for example at pH 3–4, the most easily hydrolyzed
bonds are selectively broken. These are the glycosylic bonds attaching the purine
bases to the ribose ring, and hence the nucleic acid becomes apurinic .
Effect of alkali
DNA
Increasing pH above the physiological range (pH 7–8) has more subtle effects
on DNA structure.
Tautomers are isomers (structural isomers) of organic compounds that readily

interconvert by a chemical reaction called tautomerization. This reaction commonly
results in the formal migration of a hydrogen atom or proton, accompanied by a
switch of a single bond and adjacent double bond. The concept of tautomerizations is
called tautomerism. Because of the rapid interconversion, tautomers are generally
considered to be the same chemical compound. Tautomerism is a special case of
structural isomerism and can play an important role in non-canonical base pairing in
DNA and especially RNA molecules
In the same way, the structure of guanine is also shifted to the enolate form at high pH,
and analogous shifts take place in the structures of the other bases. This affects the
specific hydrogen bonding between the base pairs, with the result that the
doublestranded structure of the DNA breaks down; that is the DNA becomes
denatured .
Chemical Denaturation:
A number of chemical agents can cause the denaturation of DNA or RNA at

denaturation neutral pH, the best known examples being urea (H2NCONH2) and
formamide (HCONH2). A relatively high concentration of these agents (several molar)
has the effect of disrupting the hydrogen bonding of the bulk water solution. This
means that the energetic stabilization of the nucleic acid secondary structure, caused
by the exclusion of water from between the stacked hydrophobic bases, is lessened and
the strands become denatured.
Viscosity
Cellular DNA is very long and thin; technically, it has a high axial ratio. DNA is around
2 nm in diameter, and may have a length of micrometers, millimeters or even several
centimeters in the case of eukaryotic chromosomes.
if DNA had the same diameter as spaghetti, then the E. colichromosome (4.6
million base pairs) would have a length of around 1 km. In addition, DNA is a
relatively stiff molecule; its stiffness would be similar to that of partly cooked
spaghetti, using the same analogy.
A consequence of this is that DNA solutions have a high viscosity. Furthermore, long
DNA molecules can easily be damaged by shearing forces, or by sonication (high-
intensity ultrasound), with a concomitant reduction in viscosity.
Buoyant density
Analysis and purification of DNA can be carried out according to its
density.
In solutions containing high concentrations of a high molecular

weight salt, for example 8 M cesium chloride (CsCl), DNA has a
similar density to the bulk solution, around 1.7 g cm–3.
If the solution is centrifuged at very high speed, the dense cesium salt
tends to migrate down the tube, setting up a density gradient .
Eventually the DNA sample will migrate to a sharp band at a
position in the gradient corresponding to its own buoyant density.
This technique is known as equilibrium density gradient
centrifugation or isopycnic centrifugation .
Since, under these conditions, RNA pellets at the bottom of the tube
and protein floats, this can be an effective way of purifying DNA
away from these two contaminants.

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NUCLEIC ACIDS an Overview

Three important Components

In RNA, the sugar is ribose, and in DNA, it is 2-deoxyribose, in which the

If the sugar is deoxyribose (as in DNA), the nucleosides (2-deoxyribonucleosides) are

Conventionally, the repeating monomers of DNA or RNA are represented by

5-ATAAGCTC-3, or even just ATAAGCTC.

An RNA sequence might be 5-AUAGCUUGA-3.

Between the backbone strands run the major and minor

The strands are joined noncovalently by hydrogen

The two strands are oriented in opposite directions

Stability of Nucleic Acids :

Tautomers are isomers (structural isomers) of organic compounds that readily

A number of chemical agents can cause the denaturation of DNA or RNA at

In solutions containing high concentrations of a high molecular

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