The presentation covers all details of the DNA structure for an easy understanding of Molecular biology students. It covers the details of DNA structure, its bonds as well as the different conformations.

1. DNA Structure
Dr. Riddhi Datta
Department of Botany
Dr. A.P.J. Abdul Kalam Government
College
West Bengal State University
cbcs Botany Core viii

2. Let’s make a DNA molecule!
© Dr. Riddhi Datta
https://www.youtube.com/watch?v=pB0FMshudqE

3. • DNA:A polymer of deoxyribonucleotides
• Self-replicating
• Encodes genetic information in all living organisms
and some viruses
• Found in chromosomes, mitochondria, chloroplast in
case of eukaryotes and in nucleoid in case of
prokaryotes
• Gene: DNA segments that encodes a functional
protein
• Non-coding regions of DNA have structural and
regulatory roles
© Dr. Riddhi Datta
Deoxyribo nucleic acid (DNA)

4. Nucleotides and Nucleosides
• Nucleotides are the building blocks of nucleic acids.
• Nucleotides have three characteristic components:
– a nitrogenous base
– a pentose
– a phosphate
• The molecule without the phosphate group is called a
nucleoside.
• The nitrogenous bases are derivatives of two parent
compounds- pyrimidine and purine.
© Dr. Riddhi Datta

5. © Dr. Riddhi Datta
Nucleotides and Nucleosides

6. © Dr. Riddhi Datta
Nucleotides and Nucleosides
• Ester bond:
– Between phosphate
and sugar
• Glycosidic bond:
– Between sugar and
base

7. © Dr. Riddhi Datta
Nitrogenous bases

8. Base Nucleoside Nucleotide Nucleic acid
Purines
Adenine Adenosine Adenylate RNA
Deoxyadenosine Deoxyadenylate DNA
Guanine Guanosine Guanylate RNA
Deoxyguanosine Deoxyguanylate DNA
Pyrimidines
Cytosine Cytidine Cytidylate RNA
Deoxycytidine Deoxycytidylate DNA
Thymine Thymidine (deoxy) Thymidylate (deoxy) DNA
Uracil Uridine Uridylate RNA
© Dr. Riddhi Datta
Nomenclature of nucleic acid components

9. • DNA consists of two long polymers
of deoxyribonucleotides.
• The backbone is formed by
deoxyribose (sugar) and phosphate
groups linked by phosphodiester
bonds.
• Attached to each sugar is one of the
four nitrogeneous bases- adenine,
guanine, thymine and cytosine.
• Traditionally, DNA is drawn from 5’
to 3’ direction.
© Dr. Riddhi Datta
Primary structure of DNA
5’
3’

10. • DNA is a double helical structure.
• The two strands wound around the same
axis.
• The two stands are anti-parallel, i.e. their
5’ 3’ phosphodiester bonds run in
opposite directions.
• The two strands are complementary to
each other.
• The sugar-phosphate backbone forms the
periphery while the bases are stacked in the
core.
© Dr. Riddhi Datta
Secondary structure of DNA

11. • The two strands are held together by hydrogen
bonds between two nucleotides in the opposite
strands.
• Adenosine forms two hydrogen bonds with
thymidine.
• Guanosine forms three hydrogen bonds with
cytidine.
• The bases are stacked inside the helix at right
angles to the helix axis.
• The hydrophobic interaction and van der Waals
force between stacked bases are also important to
maintain the double helical structure. © Dr. Riddhi Datta
Secondary structure of DNA

12. © Dr. Riddhi Datta

13. • As the DNA strands wind around each
other they leave gaps between each set of
phosphate backbone. These grooves are
of two types:
– Major groove (22 Å wide)
– Minor groove (12 Å wide)
• The edges of the bases are more
accessible in the major groove where
proteins (like transcription factors) can
interact.
© Dr. Riddhi Datta
Secondary structure of DNA

14. • The angle at which two sugars protrude from the base pair
(i.e. angle between the glycosidic bond) is around 120°.
• As the bases stack on each other, the narrow angle between
the sugars on one edge of the bases generates minor groove
while the large angle on the other edge generates major
groove.
• Edges of each base is exposed at the major and minor
groove, creating a pattern of hydrogen bond acceptors and
donors and of van der Waals surface that identifies the base
pair.
• These patterns help proteins to specifically recognize DNA
sequence without unwinding the double helix. © Dr. Riddhi Datta
Secondary structure of DNA

15. • COVALENT BONDS:
– Ester bond (phosphodiester bond):
• Between phosphate and sugar
– Glycosidic bond:
• Between sugar and base
• HYDROGEN BOND:
– Between the base pairs
© Dr. Riddhi Datta
Types of bonds present in DNA Bonds affecting DNA stability
• HYDROGEN BOND: stabilize
– Relatively weak but additive and facilitates base stacking
– Hydrogen bond also forms due to formation of a water
spine in minor groove
• HYDROPHOBIC INTERACTION: stabilize
– Hydrophilic groups are oriented outside while hydrophobic
groups are outside
• STACKING INTERACTION: stabilize
– Relatively weak but additive and van derWaals force
– The π-π between bases in the helical stacks greatly
stabilize the double helix
• ELECTROSTATIC INTERACTION: destabilize
– Contributed primarily by phosphate groups
– Affects intra- and inter-strand interactions
– This repulsive forces can be neutralized by positively
charged proteins and Na+ ions
VAN DER WAALS INTERACTIONS (not within
DNA structure)
Between major and minor grooves and
interacting proteins

16. UV radiation:
• DNA absorbs UV rays at 260 nm. When
DNA is denatured from double stranded to
single stranded form, its UV absorbance
increases cooperatively.
• The absorption pattern also increases with
increase in GC content.
• This is called hyperchromatic shift.
• For RNA, increase in absorbance pattern is
gradual and irregular.
• DNA absorbs UV due to the aromatic bases.
© Dr. Riddhi Datta
Properties of DNA

17. UV radiation:
• The A260 value of same amount of DNA (e.g
50μg) will differ for single stranded and
double stranded forms.
– Double stranded DNA:A260 = 1.00
– Single stranded DNA:A260 = 1.37
– Free bases:A260 = 1.60
• Purity of nucleic acids can be estimated by
A260 / A280 values:
– Pure DNA:A260 / A280 = 1.80
– Pure RNA:A260 / A280 = 2.00
© Dr. Riddhi Datta
Properties of DNA

18. Denaturation:
• If double stranded DNA is treated with strong alkali or high temperature, the two strands
unwinds and separates.This is known as denaturation.
• The temperature at which the two strands separates is called the melting temperature (Tm)
and the process is called melting of DNA.
Renaturation:
• The process by which two separated DNA strands form a double helix again is called
renaturation.
• This is done by lowering the temperature to 25°C or below.
• R.T. Britten and D.E. Kohne (1970) obtained renatured DNA by lowering temperature and
determined its C0t value.
• C0=primary density; t=interval of time in seconds
© Dr. Riddhi Datta
Properties of DNA

19. C0t curve analysis:
• It is a technique to determine complexity of genome (DNA).
• The technique is based on the principles of DNA reassociation kinetics,
• It measures how much repetitive DNA is present in a DNA sample
• The technique was developed by R.T. Britten and D.E. Kohne (1970)
• Principle:
– The rate of DNA renaturation is directly proportional to the
number of times the sequences are present in the genome.
– Given enough time, all denatured DNA will eventually renature.
– The more the repetitive sequence, the lesser the time required for
renaturation.
– Renaturation also depends on DNA concentration, reassociation
temperature,cation concentration and viscosity.
• C0t=DNA conc. (moles/L) x renaturation time (s) x
buffer factor (constant for buffer composition and
accounts for the effect of cations)
• Low C0t value: more repetitive sequences; High C0t value: more
unique and less repetitive sequences
© Dr. Riddhi Datta
Properties of DNA

20. C0t curve analysis:
• Application:
– Used for determining genomic complexity in different organisms
– It can detect the repetitive DNA sequence present in the sample that dominates eukaryotic
genomes
– This allows DNA sequencing to concentrate on the parts of the genome that are most informative
and interesting, which will speed up the discovery of new genes and make the process more
efficient.
© Dr. Riddhi Datta
Properties of DNA

21. C0t curve analysis:
• Example:
– Bacterial genome: 99.7% Single copy
– Calf genome: 17% High repeat, 23% Intermediate repeat, 60% Single copy
© Dr. Riddhi Datta
Properties of DNA
Pink: High repeat
Brown: Intermediate repeat
Blue: Single copy

22. Buoyant density:
• DNA has a buoyant density similar to CsCl. Hence DNA can be mixed with CsCl and separated by centrifugation.
DNA is acidic:
• Though nitrogen bases are present in DNA, it is called nucleic acid. This is because these bases are stacked inside
the double helix and are not available for interactions. The backbone is formed by sugar-phosphate where the
phosphate is negatively charged and has acidic hydroxyl groups.This makes DNA acidic.
• At high ionic concentration, cations shield the negative charge and stabilize the DNA double helix.
Ionic induction:
• As DNA is acidic, it is negatively charged. During agarose gel electrophoresis it moves towards anode (+). By this
process DNA can be separated according to their weight.
G:C bond:
• G:C bonds are more stable as they form 3 H-bonds and more favorable stacking interactions. So, higher the GC
content, more stable is the DNA molecule.
Enzymatic hydrolysis:
• DNA can be hydrolysed by enzymes called DNases. Enzyme that can hydrolyse DNA sequentially from ends is
called exonuclease (Ex: Exonuclease I). Enzyme that can hydrolyse phosphodiester bonds in DNA internally is
called endonuclease (Ex: DNase I).
© Dr. Riddhi Datta
Properties of DNA

23. • Several structural variants of DNA are possible:
– B-DNA (most prevalent conformation in physiological conditions)
– A-DNA
– Z-DNA
© Dr. Riddhi Datta
Conformations of DNA

24. Z-DNA:
• Z-DNA is a left handed double helical structure with a zig-zag pattern.
• Biologically active but transient structure induced by biological activity.
• The major and minor grooves show little difference in width.
• Conditions for Z-DNA:
– Alternating purine-pyrimidine
– Negative DNA super coiling
– Low salt and cation concentration
– Physiological temperature 37 °C and pH 7.3 – 7.4
• Significance:
– Provides torsional strain relief (supercoiling) while DNA transcription occurs.
– Potentiality to form Z-DNA also correlates with regions of active transcription
© Dr. Riddhi Datta
Conformations of DNA

25. A-DNA:
• A-DNA is a right handed double helical structure fairly similar to B-
DNA.
• Biologically active but transient structure induced by biological activity.
• The structure is shorter and more compact.
• Major grooves are deeper and minor grooves shallower than B-DNA.
• Conditions for Z-DNA:
– Dehydrated samples of DNA (ex: samples for crystallographic studies)
– Found in DNA-RNA hybrids and double stranded RNA.
© Dr. Riddhi Datta
Conformations of DNA

26. Geometry attributes A-DNA B-DNA Z-DNA
Helix sense Right-handed Right-handed Left-handed
Repeating units 1 base pair (bp) 1 bp 2 bp
Rotation/bp +33.6° +36° -30°
Mean bp/turn 11 10 12
Inclination of bp to axis +19° -1.2° -9°
Rise/bp along axis 2.3Å 3.4Å 3.8Å
Rise/turn of helix 24.6Å 34Å 45.6Å
Mean propeller twist +18° +16° 0°
Glycosyl angle anti anti Pyrimidine: anti; Purine: syn
Sugar pucker C3’ endo C2’ endo C: C2’ endo; G: C2’ exo
Helix diameter 26Å 20Å 18Å
© Dr. Riddhi Datta
Conformations of DNA
B-DNA

27. © Dr. Riddhi Datta
anti and syn glycosyl angle
The bond joining the 1′-carbon of the deoxyribose sugar to the heterocyclic base is the N-glycosidic
bond. Rotation about this bond gives rise to syn and anti conformations. Rotation about this bond is
restricted and the anti conformation is generally favored, partly on steric grounds.

28. • The bases in a base pair are usually not coplanar; they instead are twisted about the
hydrogen bonds that connect them, like the blades of a propeller.
• The dihedral angle that defines the non-coplanarity is called the propellor twist angle.
© Dr. Riddhi Datta
Propeller twist

29. • The pentose sugar ring in DNA is not planar.This non-planarity is called sugar puckering.
• Sugar puckering can influence both nucleotide incorporation and extension by polymerases.
• RNA polymerases preferentially incorporate nucleotides having C3’-endo pucker while DNA
polymerases prefer C2’-endo pucker.
• If the puckered C atom is displaced towards the C5 atom, then that twisted form is called endo. If it
is displaced away from the C5 atom, the form is called exo.
• For example, if C3 is twisted towards the C5, it is called C3’-endo.
© Dr. Riddhi Datta
Sugar pucker

30. © Dr. Riddhi Datta
NonWatson-Crick base pairing
Watson-Crick base pairing:
• Planar base-pairing
• A::T and G:::C
• Dimensions of both base pairs are similar, i.e. C1-C1 distances are nearly equal
• β-glycosidic bonds attached to same edge of the base pair which defines major and minor grooves
• There is potential for further H-bonding which is important for sequence specific protein binding
Watson-Crick base pairing:
• A-T pairs use N1 of adenine as H-
bond acceptor. This geomerty is
more stable for double helices.
Hoogsteen base pairing:
• A-T pairs use N7 of adenine as H-
bond acceptor. Seen in crystals of
monomeric A-T base pairs.
• Co-crystallized monomeric G-C
pairs always follow Watson-Crick
base pairing.

31. © Dr. Riddhi Datta