DNA, Nucleotides, Structure of DNA, Features of DNA, watson-crick Model of DNA,base pairing rule, Denaturation of DNA,Higher organization of DNA, Histones, chromosomes, nucleosomes, introns, extrons, repeat sequences of DNA

1. By: Neha Sheth
structure, Function and
its organization.

2. Structure of DNA
Deoxyribonucleotide
Deoxyadenylate (A)
Deoxyguanylate (G)
Deoxycytidylate (C)
Thymidylate (T)
Phosphodiester Bonds
3’ –5’

3. Phosphodiester linkage

4. The genetic information is encoded in the specific
sequence of bases; if the base is altered, the
information is also altered…

6. • Deoxyribose and
Phosphodiester
linkages are the
same in all the
repeating
nucleotides.

7. Polarity of DNA Structure
• In the case of DNA, the
base sequence is always
written from the 5' end to
the 3' end.
• This is called the polarity
of the DNA chain.

8. Watson-Crick Model of double
helical structure of DNA
8

9. Watson-Crick Model of DNA Structure
• Right handed double helix
• Complementary Base
pairing Rule (Chargaff's
Rule)
( A+ G= C+T )
• Hydrogen Bonding
• Antiparallel

10. The salient features of Watson-Crick model of DNA
1. The DNA is a right handed double
helix. lt consists of two
polydeoxyribonucleotide chains
(strands) twisted around each other
on a common axis.
2. The two strands are antiparallel, i.e.,
one strand runs in the 5' to 3'
direction while the other in 3'to
5'direction. This is comparable to two
parallel adjacent roads carrying traffic
in opposite direction

11. 3. The width (or diameter) of a
double helix is 20 A° (2 nm).
3. Each turn (pitch) of the helix is
34 A° (3.4 nm) with 10 pairs of
nucleotides, each pair placed at
a distance of about 3.4 A°.

12. 5. The double helix has (wide)
major grooves and (narrow)
minor grooves along the
phosphodiester backbone.
Proteins interact with DNA at
these grooves, without
disrupting the base pairs and
double helix.

13. 6. Each strand of DNA has a
hydrophilic deoxyribose
phosphate backbone (3'-5'
phosphodiester bonds) on
the outside (periphery) of
the molecule while the
hydrophobic bases are
stacked inside (core).
The bases are located
perpendicular to the helix axis,
whereas the sugars are nearly
at right angles to the axis.

14. 7. The two polynucleotide chains are not identical but
complementary to each other due to base pairing.
8. The base pairing (A with T; G with C) is called Chargaff's rule,
which states that the number of purines is equal to the number of
pyrimidines.

15. 9. The two strands are held together by hydrogen bonds
formed by complementary base pairs.
A-T pair has 2 hydrogen bonds
G-C pair has 3 hydrogen bonds
The G = C is stronger by about 50% than A=T.

16. 10. Each strand
acts as a template
for the synthesis of
the opposite strand
during replication
process.

17. DNA is the more suitable storehouse of
genetic information
RNA is more prone to
spontaneous hydrolysis of the
P-O-P bonds.
On other hands the DNA chain
is much more stable and the
half-life for spontaneous
hydrolysis is about 200 million
years.

18. Denaturation of DNA strands
• The double stranded DNA may be denatured and separated by heat. This is called as
melting of DNA.
• Tm or melting temperature is the temperature when half of the helical structure is
denatured.
• At lower temperature, the melted strands are re-associated; this is called annealing.

19. Higher Organization of DNA

20. Chromatin is a loose term
employed for a long
stretch of DNA in
association with histones.
Chromatin is then
further is folded and
compressed to 10,000
fold condensed to
form chromosomes.
Double stranded
DNA is first wound
over histones; this is
called nucleosomes

21. Histones

22. • Higher concentration of
basic amino acids.
• Synthesized in the
cytoplasm migrate to the
nucleus.
• Histone synthesis stops
when DNA synthesis
ceases.
Amino terminal one-third region of
H2A and H2B are lysine rich.
H3 and H4 are arginine rich
histones.

23. • Acetylation of histones leads to activation of transcription, whereas
de-acetylation causes depression of transcription.
• Phosphorylation is associated with condensation of chromosomes.
ADP-ribosylation is associated with DNA repair.

24. • Methylation generally occurs when the gene is repressed. Sometimes
histones are fixed to small ubiquitin related modifier (abbreviated as
Sumo), and the process is called sumoylation.
• Sumoylation of histones is seen during repression of transcription

25. Apart from histones, there are many other special proteins
which will interact at specific regions of DNA.
Helix-turn-helix
motif
Zinc finger motif
Leucine slipper
motif
Helix-loop-helix
motif
Only small regions of the protein make direct contact with the DNA; the rest of the
proteins are involved in other activities, like ligand-binding, interaction with co-
activators and corepressors etc

26. Nucleosomes
• The double stranded DNA wraps
twice around a histone octamer
formed by H2A, H2B, H3 and H4.
This super-twisted helix forms a
spherical particle of 10 nm
diameter; called nucleosome.
• Function: to condense DNA; this
arrangement also stabilises DNA.

27. Further condensation of DNA
• A group of such nucleosomes form
the "DNA fibrils".
• About 6 such fibrils are further
supercoiled to form 30 nm diameter
chromatin fibers or chromatin
threads.
• By this time, the DNA is folded to
about 100 times. Histones stabilise
these fibers.
• In interphase chromosomes,
chromatin fibers condense to
100,000 bp loops, anchored in some
supporting matrix (nuclear matrix).

28. Chromosomes • These fibers are further supercoiled
and condensed to form
chromosomes during the M phase
of cell cycle.
• The packaging of nucleoproteins
within chromosome is specific,
(banding) observed by Giemsa's
staining .
• During metaphase, the DNA can be
seen under a microscope, a
superpacked chromosomes, where
identical sister chromatids are
connected at the centromere.

29. •Depending on the length of the chromosome and the
position of the centromere, the chromosomes are
numbered.
•In humans, there are 23 pairs of chromosomes.
•The centromere is AT rich region, and has repeated
DNA sequences of about one million base pairs in
mammals.
•This region is called kinetochore, which provides the
anchor for the mitotic spindle.

30. Transcriptionally, inactive
chromatin is densely packed and is
called heterochromatin.
Active regions stain less densely
and are called euchromatin.
Euchromatin fills up the majority
of the nucleus.

31. DNA is a very long molecule
• The length (2 meter ) of a DNA molecule is compressed to 8,000 to 10,000 fold to generate the
chromosomes
• Human diploid genome consists of about 7 x 109 base pairs

33. • A Cistron is the unit of genetic expression. It is the biochemical
counterpart of a "gene" of classical genetics. One cistron will code for
one polypeptide chain.
• If a protein contains 4 subunits, these are produced under the direction
of 4 cistrons ("one cistron–one polypeptide" concept).

34. Repeat Sequences of DNA
• Only about 1-2% of the human DNA contain genes; the rest
are silent areas.
• About 1% of DNA is present inside mitochondria.
• There are only about 25,000 to 30,000 protein coding
regions in the human DNA. Thus, most of the DNA is made
of noncoding sequences.
• About 90% of DNA is introns.
• About 50% of DNA is unique or nonrepetitive.

35. • About 30% of the genome consists of repetitive
sequences; they contain 5- 500 base pairs repeated many
times.
[regions are clustered mainly in centromeres and
telomeres; but are seen randomly in other regions also.]
▪ Highly repetitive sequences
▪ Moderately repetitive sequences
▪ Long interspersed repeat sequences (LINEs)
▪ Short interspersed repeat sequences (SINEs).

36. • LINE are 6-7 kbp length and are repeated about 50,000 times.
• SINE are 100-300 bp in length, but are repeated 100,000 times.
[ One such sequence, the Alu family, is repeated about 500,000 times,
and accounts for about 5% of total human DNA.]
Characteristics:
✓ These interspersed repeat sequences are mobile elements, and they
can jump from one region to another region of the genome.
✓They appear to be retroposons, i.e. they can move from one location
to another (transposition) through an RNA intermediate by the action
of reverse transcriptase.

37. • Microsatellite repeat sequences are AC repeats on one strand and TG
on the other strand; such repeats are 100,000 in the genome.
• Trinucleotide sequence repeats are associated with diseases.
CGG repeat sequence -- fragile X syndrome
CAG repeat sequence -- Huntingon's chorea
CTG repeat sequence -- myotonic dystrophy,
CAG repeat sequence -- spinobulbar muscular atrophy.

42. Conformations of DNA double
helix
• The double helical structure of DNA exists in 6 forms A,B,C,D,E and
Z form.
• Among these, B, A & Z forms are important.
• B-form is most predominant form under physiological conditions.
• A-from is also right-handed helix.
• Contains 11 base pairs.
• There is a tilting of the base pairs by 200 away from the central axis.
• Z-form is a left –handed helix and contains 12 base pairs per turn.

43. DNA Conformation

44. Bent DNA
• Adenine base containing DNA tracts are rigid & straight.
• Bent conformation of DNA occurs when A-tracts are replaced by
other bases or a collapse of the helix into minor groove of A-tract.
• Bending in DNA structure is due to photochemical damage or
mispairing bases.
• Certain antitumor drugs (e.g.,cisplastin) produce bent structure in
DNA.
• Such changed structure can take up proteins that damage the DNA.

45. Bent DNA
45

46. Triple-stranded DNA
• Triple stranded DNA formation may occur due to additional hydrogen bonds
between the bases.
• Thymine can selectively form two Hoogsteen hydrogen bonds to the adenine
of A-T pair to form T-A-T.
• Cytosine can also form two hydrogen bonds with guanine of G-C pairs that
results in C-G-C.
• Triple helical structure is less stable than double helix.
• Due to three negatively charged backbone strands in triple helix results in an
increased electrostatic repulsion.

47. Triple-stranded DNA
47

48. Four-stranded DNA
• Polynucleotides with very high content of guanine can form a tetrameric
structure called G-quartets.
• These structures are planar & are connected by Hoogsteen hydrogen
bonds.
• Antiparallel four stranded DNA structures referred to as G-tetraplexes.
• The ends of eukaryotic chromosomes namely telomeres are rich in
guanine,& forms G-tetraplexes.

49. Four-stranded DNA

50. Primary Structure Secondary Structure

51. Tertiary structure :
• Supercoils: double-stranded circular DNA
form supercoils if the strands are
underwound (negatively supercoiled) or
overwound (positively supercoiled).
Relaxed supercoiled
Increasing degree of supercoiling

52. • If the strands
are overwound,
form positively
supercoiled;
• If the strands
are underwound,
form negatively
supercoiled.