1.
DNA
and
Forces Stabilizes DNA Structure
Prepared by-
Dr. Sanjeev Kumar (M.V.SC at DGCN, COVAS, CSKHPKV, Palampur
India)
Dr. Kritika Dhial (M.V.SC at DGCN,COVAS, CSKHPKV, Palampur
India)

2.
Historical facts about DNA

3.
DNA ?
• DNA Stands for “DeoxyriboNcleic Acid”.
• Term DNA was given by Zaccharis
• DNA is biopolymer consist of nucleotide as monomeric unit.
• DNA is double helical strcture in eukaryote and prokaryote, but in virus it
may be double stranded or single stranded and presented as monopartite
or multipartite.
• In eukaryotes, DNA is presented in nucleus surrounded by nuclear
membrane
• In prokaryotes, DNA is presented in nucleoid region of Cytoplasm without
nuclear membrane
• In virus, DNA is presented in the core of virus surrounded by Protein layer
(called as capsid).

4.
DNA ?
• Cell perform various functions in specific way as per directed by DNA
contained by it.
• DNA contains all biological information of a cell/individual like
functioning, development, growth, life span etc. .
• The biological information transferred from one generation to the next
generation in the chemical form as DNA, so it is called as hereditary
material.
• DNA can be measured by the unit picogram
• DNA can be synthesized in vitro (in the laboratory).

5.
Composition of DNA ?
• DNA is a biopolymer consist of repeated units called as nucleotides.
• Nucleotide= Nitrogen base + Sugar+ Phosphate group.
• Nitrogen bases are two types- 1. Purines, 2. Pyrimidine.
• Sugar present in DNA is 2-Deoxyribose.
• Purines are heterocyclic double ring molecules and contain nitogen
atoms at 1,3,7, and 9 positions.
• Purines are two types Adenine and Guanine.
• Pyrimidines are hterocyclic single ring molecule contain nitrogen
atoms at 1, and 3 positions.
• Pyrimidine are thee type thymine, cytosine, and uracil ( present in
RNA).

6.
Composition of DNA ?

7.
Watson and Crick model of DNA
In 1953, J.D. Watson (an American biologist) and
F.H.C. Crick (a British Physicist) proposed the
three-dimensional model of physiological DNA (i. e
B-DNA) on the basis of X-ray diffraction data of
DNA obtained by Franklin and Wilkins.
The important features of Watson – Crick Model
or double helix model of DNA are as follows:
1. The DNA molecule consists of two
polynucleotide chains or strands that spirally
twisted around each other and coiled around a
common axis to form a right-handed double-helix.
2. The two strands are antiparallel i.e. they ran in
opposite directions so that the 3′ end of one chain
facing the 5′ end of the other.
3. The sugar-phosphate backbones remain on the
outside, while the core of the helix contains the
purine and pyrimidine bases.

8.
Watson and Crick model of DNA
4.The two strands are held together by hydrogen bonds between the
purine and pyrimidine bases of the opposite strands.
5. Adenine (A) always pairs with thymine (T) by two hydrogen bonds
and guanine (G) always pairs with cytosine (C) by three hydrogen
bonds. This complimentarily is known as the base pairing rule.
Thus, the two stands are complementary to one another.
6. The base sequence along a polynucleotide chain is variable and a
specific sequence of bases carries the genetic information.
7. The base compositions of DNA obey Chargaff s rules (E.E. Chargaff,
1950) according to which A=T and G=C; as a corollary ∑ purines
(A+G) = 2 pyrimidines (C+T); also (A+C) = (G+T). It also states that
ratio of (A+T) and (G+C) is constant for a species (range 0.4 to
1.9)

9.
Watson and Crick model of DNA
8. The diameter of DNA is 2nm or 20
A. Adjacent bases are separated
0.34 nm or by 3.4 A along the
axis. The length of a complete
turn of helix is 3.4 nm or 34 A i.e.
there are 10bp per turn. (B- DNA-
Watson rick DNA)
9. The DNA helix has a shallow
groove called minor groove (-
1.2nm) and a deep groove called
major groove (- 2.2nm) across.

10.
The conformation of a nucleotide unit is determined by the seven indicated torsion angles.

11.
Forms of DNA
DNA is remarkably flexible molecule. Considerable
rotation is possible a number of bonds in the
sugar-phosphate backbone, and thermal
fluctuation can produce bending, stretching, and
unpairing of strands. Many significant deviations
from the Watson-Crick. DNA structure are found in
cellular DNA, some of which may play important
• A- DNA
• B- DNA
• Z-DNA
• Cruciform DNA and Hairpin DNA
• H- DNA or triplex
• G4- DNA
A- DNA B-DNA Z-DNA

12.
Comparison Between different form of DNA

13.
Cruciform and Hairpin DNA

14.
H-DNA or Triplex DNA

15.
G4- DNA

16.
G4- DNA
• FIG. 8.Hypothetical mechanism of
formation and/or stabilization of G4 DNA
by Hop1 protein. In the model, bold and
light DNA molecules represent homologs
and closed circles denote guanine
residues. Once a DSB is produced at a hot
spot by Spo11 endonuclease, the free
ends are resected by exonuclease and/or
helicase activities to generate a 3′
overhang. Subsequently, Hop1 protein, by
binding to the guanine repeats in the 3′
overhang and to the G-rich strand in the
partially unwound homologous duplex
DNA, promotes the formation of
intermolecular G4 DNA. Alternatively
(right side), interstitial interactions
between chromatids could be mediated
by the formation of intermolecular G-G
pairing, regardless of whether the flanking
nucleotide sequences are homologous.
We suggest that such interactions might
either join homologs (as diagrammed
here) to facilitate interhomolog
recombination or join sister chromatids in
a manner that delimits sister chromatid
exchange.

17.
Quaternary structure of the DNA molecule
• DNA is associated with proteins: histones and non histone
proteins, to form the chromatin.
•DNA as a whole is acidic (negatively charged) and binds to basic
(positively charged) proteins called histones
•There is 3 x 10 9 nucleotide pairs in the human haploid genome
representing about 30 000 genes dispersed over 23
chromosomes for a haploid set.

18.
DNA Packaging

19.
DNA Stability…..?
DNA double stranded helical structure is stabilize by
• Hydrogen bonding
• Base stacking interaction
• Hydrophobic force
• Ionic interaction

20.
DNA Stability…..?
Hydrogen bonding-
 hydrogen bond b/w base pairs- G with C, and A
with T.
 It is important to note that three hydrogen bonds
can form between G and C, but only two bonds
can be found in A and T pairs.
 This is why it is more difficult to
separate DNA strands that contain more G-C pairs
than A-T pairs. On the other hand, A-T pairs seem
to destabilize the double helical structures. This
conclusion was made possible by a known fact that
in each species the G content is equal to that of C
content and the T content is equal to that of A
content.
 Although weak energy-wise, is able to stabilize the
helix because of the large number present
in DNA molecule

21.
DNA Stability…..?
Base stacking interaction-
• also known as Van der Waals interactions between bases are weak, but the
large amounts of these interactions help to stabilize the overall structure of
the helix.
– Double helix is stabilized by hydrophobic effects by burying the bases in
the interior of the helix increases its stability; having the hydrophobic
bases clustered in the interior of the helix keeps it away from the
surrounding water, whereas the more polar surfaces, hence hydrophilic
heads are exposed and interaction with the exterior water
– Stacked base pairs also attract to one another through Van der Waals
forces the energy associated with a single van der Waals interaction has
small significant to the overall DNA structure however, the net effect
summed over the numerous atom pairs, results in substantial stability.
– Stacking also favors the conformations of rigid five-membered rings of the
sugars of backbone.
– Evidence of Stacking interactions: Compounds that interfere with
Hydrogen bonds (urea, formamide) don’t separate strands by themselves,
still requires heat.

22.
DNA Stability…..?
Ionic interaction-
• Ion-ion repulsion of the negatively charged phosphate make DNA duplex
unstable.
• However the presence of Mg2+ and cationic proteins with abundant
Arginine and Lysine residues that stabilizes the double helix.
• Double-stranded helix structure thus, promoted by having phosphates on
outside, interact with H2O and counter ions (K+, Mg2+, etc.).

23.
DNA Stability…..?
Hydrophobic force-
• The hydrophobic interactions
between the planar base pairs
stabilize the bases on the inside
of the helix, so these provide
stability to the structure but do
not contribute to the specificity.
• Hydrophobic Interactions are
important for the folding, stability
and biological activity.

24.
References
• http://faculty.washington.edu/trawets/vc/theory/dna/DNA_big.jpg
• nptel.ac.in/courses/104103018/module4/lec3/2.html
• http://www.googleimage.com
• http://chem.libretexts.org/Core/Physical_and_Theoretical_Chemistry/Phy
sical_Properties_of_Matter/Atomic_and_Molecular_Properties/Intermole
cular_Forces/Hydrophobic_Interactions
• Text book of biology by True man
• bioinfosu.okstate.edu/um/napsweb/Lec.htmlfolder/836NAPS.ppt
• www.bio.brandeis.edu/classes/biochem104/DNA_lecture.pdf
• http://atlasgeneticsoncology.org/Educ/DNAEngID30001ES.html
• Principle of Biochemistry by Lehninger-forth edition

25.
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