Detailed notes on Nucleic acids

1. Nucleic acid chemistry,
Properties of nucleic acids,
Watson and Crick model of
DNA
Dr Jimtha John C
Assistant Professor
St Mary's College
Thrissur

2. • polymers of monomers called nucleotides
• DNA and RNA
• act as genetic material in all life forms on
earth
• Freidreich Miescher discovered nucleic
acids in 1869 in the nuclei of pus cells
• In 1953, James Watson and Francis Crick
determined the structure of DNA
NUCLEIC ACIDS

4. NUCLEOTIDES
 Itconsists of a 5 carbon sugar to which a phosphate
group is esterified at the 5' position of the sugar ring
and one nitrogenous base is attached at the 1' site.
 By virtue of the sugars present in them, RNA is said
to be composed of ribonucleotides and DNA is said
to be a polymer of deoxyribonucleotides.
 Molecule with the sugar and the base alone without
the phosphate group is called nucleoside. E.g.:
Adenosine, deoxyadenosine, cytidine, deoxycytidine
etc.
 Adding a phosphate (or more than one phosphate)
group to a nucleoside creates a nucleotide. E.g.
adenylate, deoxyadenylate, cytidylate,

5. • The pentose in RNA is the D-ribose
sugar
• The sugar in DNA is called 2'- deoxy-D-
ribose because there is no hydroxyl group
at position 2' (just 2 hydrogen atoms).
• The absence of the reactive hydroxyl
group at the 2' position in DNA makes it
more stable than RNA.
• In nucleotides, both types of pentoses are
in their β-furanose, closed 5 membered
PENTOSE

7. • Derivatives of two parent compounds,
pyrimidines and purines.
• Purines are nine membered double ring
structures consisting of both the pyrimidine
and imidazole rings.
• Pyrimidines are six membered single ring
structures.
• Both DNA and RNA contain two major
purine bases, adenine (A) and guanine
(G), and two major pyrimidines. In both
NITROGEN BASES

9. • The purine and pyrimidine bases are
hydrophobic and relatively insoluble in water
at near-neutral ph.
• At acidic or alkaline pH the bases become
charged and their solubility in water increases.
• Purines and pyrimidines are highly conjugated
molecules . Resonance among atoms in the
ring gives most of the bonds partial double
bond character. As a result of resonance, all
nucleotide bases absorb UV light, and nucleic
acids are characterized by a strong absorption
at wavelengths roughly near 260 nm

10. • Each base pair of DNA is twisted (displaced) from
the previous one by an angle of about 36 degree.
• Free pyrimidine and purine bases may exist in two
or more tautomeric forms depending on the pH.
Uracil, for example, occurs in lactam, lactim, and
double lactim forms. The tautomeric states are in
equilibrium with each other.
The nitrogen atoms attached to the purine and
pyrimidine rings are in the amino configuration and
only rarely take the imino configuration.
Likewise, the oxygen atoms are in the keto
configuration and only rarely assume the enol
configuration.The capacity to form tautomer is a
frequent source of errors during DNA synthesis

12. • Each base pair of DNA is twisted
(displaced) from the previous one by an
angle of about 36 degree.
• The base of a nucleotide is joined
covalently (at N-1 of pyrimidines and N-9
of purines) in an N- glycosyl bond to the 1'
carbon of the pentose, and the phosphate
is esterified to the 5' carbon.
• Rotation about the N- glycosidic bond
gives rise to anti and syn conformations. In
B DNA, rotation about this bond is usually
restricted, thus, the anti conformation is
favored partly on steric grounds.
• Successive nucleotides of both DNA and

13. • The covalent backbones of nucleic acids
consist of alternating phosphate and
pentose residues, and the nitrogenous
bases may be regarded as side groups
joined to the backbone at regular intervals.
• The Phosphodiester bond-
The chemical linkage between adjacent
nucleotides , the phosphodiesterbond,
actually consist of two phosphoester
bonds, one on the 5' side of the phosphate
and another on the 3' side. The
phosphodiester linkages impart an
inherent polarity to the DNA chain. The 5'

14. Illustration of a phosphodiester bond.

15. • DNA has a double helical structure. It is
made up of two polynucleotide chains
wound around each other in a right
handed fashion. Backbone is made up of
sugar- phosphate and bases project
inside.
• The two chains have anti-parallel polarity
i.e; the two strands run in opposite
direction. If one strand has the polarity 5'->
WATSON AND CRICK MODEL OF
DNA

16. • The bases in the two strands are paired through
hydrogen bonds.
• Usually, Adenine (A) always forms two hydrogen
bonds with Thymine (T) on the opposite strand
and vice versa
Guanine (G) forms three hydrogen bonds with
Cytosine (C) on the opposite strand and vice
versa
• Associations between a smaller pyrimidine and
a larger purine are called Watson-Crick base
pairs (A:T and G:C base-pairs).
• Such pairing generates approximately uniform
distance between the 2 strands throughout the
length of the helix.

17. Hydrogen bond between
exocyclic amino group at
C6 of adenine;another
between N1 of Adenine
and N3 of Thymine.
Exocyclic NH2 at C2 on
Guanine forms hydrogen
bond with carbonyl
group at C2 on Cytosine.
Another hydrogen bond
forms between N1 of
Guanine and N3 of
Cytosine. A third one
forms between the
carbonyl at C6 of Guanine
and the exocyclic NH2 at
C4 of Cytosine

18. • Since A:T and G:C, the nucleotide
sequences of the 2 strands are fixed
relative to one another. Thus, the 2 chains
are complementary to one another; i.e; if
one strand has the sequence 5'ATGC3'
then the other strand has complementary
sequence 3'TACG5'.
• DNA is a right handed helix. The pitch of
the helix is about 3.4 nm (34 Ȧ or 35.7 Ȧ
precisely) and there are roughly 10 base
pairs (10.5 base pairs to be precise) in
each turn. Thus, distance between 2 base
pairs in a helix is about 0.34 nm (or about

19. • Backbone of DNA (and RNA) is hydrophilic; the
hydroxyl groups of the sugar residues form
hydrogen bonds with water.
• Phosphate groups are completely ionized and
negatively charged at pH 7, this gives the
molecule a negative charge.
• Negative charges are generally neutralized by
ionic interactions with positive charges on
proteins like histones , metal ions etc.
• The bases are flat, relatively water insoluble
molecules

20. • Bases tend to stack above each other roughly
perpendicular to the direction of the helical
axis.
• Hydrophobic interactions and van der Waals
forces between the stacked, planar bases
(base stacking interactions) provide stability
for the entire DNA molecule.
• The helical turns and planar base pairs cause
the molecule to resemble a spiral staircase.

21. • The two strands are held together by
hydrogen bonds between bases of opposite
strands.
• Because individual hydrogen bonds are weak
and easily broken, the DNA strands can
become separated during various activities.
• But the strengths of hydrogen bonds are
additive, and the large number of hydrogen
bonds holding the strands together make the
double helix a thermodynamically stable
structure.

22. • The spaces between adjacent turns of the
helix form 2 grooves of different width- a
wider major groove and a narrower minor
groove.
• The major and minor grooves are a simple
consequence of the geometry of the base
pair.
• The angle at which the 2 sugars protrude
from the base pairs (i.e.; the angle
between the glycosidic bonds) is about
120 degree (for the narrow angle) or 240
degree (for the wide angle).

23.  Edges of each base pair
are exposed in the
major and minor
grooves.
 Proteins that bind to
DNA often contain
domains that fit into the
major and minor
grooves.
 A protein bound in a
groove is able to read
the sequence of
nucleotides along the
DNA without having to
separate the strands.

24. DNA can undergo reversible strand separation or
denaturation. When DNA solution is subjected to
extreme pH or to temperatures above 80 degree
Celsius, its strands separate.
• Heat and extreme pH denature or melt double-
helical DNA. Disruption of hydrogen bonds between
paired bases and of base stacking interactions
causes unwinding of the double helix to form two
single strands.
• Organic solvents and detergents interfere with
hydrophobic interactions and also cause DNA
denaturation.
• No covalent bonds in the DNA are broken.
NUCLEIC ACID CHEMISTRY

25. • Each species of DNA has a characteristic
denaturation temperature, or melting point (tm)
• Melting point of a DNA duplex is also affected by a
number of factors-
a) G•C content- the higher its content of G•C base
pairs, the higher the melting point of the DNA. G•C
base pairs, with three hydrogen bonds, require
more heat energy to dissociate than A•T base pairs
b) Salt concentration -monovalent cations like
sodium (Na+) and potassium (K+) stabilize double
helices by partially neutralizing the negative charge
along the phosphodiester backbone. Thus, higher
salt concentration will also increase the Tm of a
given polynucleotide duplex.

26. c) The presence of mismatched bases in a
duplex will generally have a destabilizing
effect and decrease Tm.
d) Agents that destabilize the hydrogen
bonds like urea or formamide also lower
the Tm
e) Longer duplexes are more stable and
therefore will have higher Tm.
• RNA duplexes are more stable than DNA
duplexes to denaturation. At neutral pH,
denaturation of a double helical RNA

27. HYPERCHROMIC AND
HYPOCHROMIC EFFECTS
 Close interaction between stacked bases in a nucleic
acid decreases its absorption of UV light relative to
that of a solution with the same concentration of free
nucleotides
 Absorption at 260 nm is decreased further when two
complementary nucleic acids strands are paired.
This is called the hypochromic effect
 Denaturation of a double stranded nucleic acid
produces the opposite result: an increase in
absorption at 260 nm called the hyperchromic
effect.
 The transition from double-stranded DNA to the

29. RENATURATION
Renaturation of a DNA molecule is a rapid
one-step process, when a double-helical
segment of a dozen or more residues still
unites the two strands. When the temperature
or pH is returned to the range in which most
organisms live, the unwound segments of the
two strands spontaneously rewind, or anneal,
to yield the intact duplex.
• If the two strands are completely separated,
renaturation occurs in two steps. In the first,
relatively slow step, the two strands
recognize each other by random collisions
and form a short segment of complementary
double helix. The second step is much faster:

30. Nucleic acids from different species can form
hybrids
• Different organisms generally have some
proteins and RNAs with similar functions and
similar structures. Mostly, DNA encoding these
proteins and RNAs have similar sequences.
• The closer the evolutionary relationship
between two species, the more extensively their
DNAs will hybridize. For example, human DNA
hybridizes much more extensively with mouse
DNA than with DNA from yeast.
 Some bases in DNA strands are methylated.

31. • Adenine and cytosine are methylated more often
than guanine and thymine
• Methylation - acts as a defense mechanism ; it is
involved in the repair of mismatched base pairs
;it also suppresses the migration of transposons.
Nucleotides and nucleic acids undergo
nonenzymatic transformations. Alterations in
DNA structure that produce permanent changes
in the genetic information encoded are called
mutations.

32. PROPERTIES OF NUCLEIC ACIDS
Effect of pH and temperature on nucleic acids
Nucleic acids are stable between a pH range of
5-9. Beyond this range, they undergo
denaturation spontaneously. At low or acidic
pH, the bases become protonated and thus
positively charged, repelling each other. At
high or alkaline pH, the bases lose protons and
become negatively charged, again repelling
each other because of the similar charge.

33. • As the temperature increases, the
resulting increase in molecular motion
eventually breaks the hydrogen bonds and
other forces that stabilize the double helix;
the strands then separate, driven apart by
the electrostatic repulsion of the negatively
charged deoxyribose-phosphate backbone
of each strand. Near the denaturation
temperature, a small increase in
temperature causes a rapid, near
simultaneous loss of the multiple weak
interactions holding the strands together

34. Properties that get altered upon
Denaturation:
• Absorbance At 260 nm-
Absorbance at 260 nm is roughly as follows -
Nucleotides > ss DNA > ds DNA
RNA > DNA
Purines > Pyrimidines
Adenine > Guanine > Thymine = Cytosine
• Viscosity decreases upon denaturation
• Optical Rotation becomes more negative upon
denaturation as the plane polarized light shifts
slightly towards left

35. • Density of nucleic acids increases upon
denaturation
Effect of acids and alkali on nucleic acids:
Both DNA and RNA undergo acid hydrolysis. RNA
readily undergoes alkali hydrolysis but DNA is
relatively more stable than RNA to alkali hydrolysis
due to the absence of 2'-OH groups in the sugar of
DNA.
 Effect of bisulfite and nitrous acid:
Bisulfite and nitrous acid promote deamination or
removal of an amino group from cytosine, resulting
in conversion of cytosine to uracil. In DNA, cytosine
deamination will ultimately lead to conversion of a
G-C base pair to an A-T base pair if left
uncorrected.

36. Effect of Ionizing radiations and Oxidizing
agents:
These nonspecifically damage DNA by
breaking the phosphodiester backbone and
producing polynucleotide fragments with
different 5’and 3’ terminal products. They also
directly attack and alter the chemical
composition of bases in nucleic acid.
• Many DNA molecules are circular-
DNA in eukaryotes exists in the linear form.
Many prokaryotic and viral DNA are circular
molecules. Circular DNA molecules are also
found in the mitochondria and chloroplasts

37. Supercoiling affects the structure of DNA :
The double helix winds around itself to change
the topology of the DNA molecule in space. This
process creates tension in the DNA and is called
supercoiling. It can only occur if the DNA has no
free ends or in linear DNA if it is anchored to a
protein scaffold. Simplest example of a DNA
molecule with no free ends is a circular molecule.

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