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1. DNA - Structure
DR. KALPESH NAKARANI
TUTOR CUM RESIDENT (3RD YEAR)

2. History
• 1869 – Friedrich Miescher
• 1st isolated nucleic acid
• 1928 – Frederick Griffith
• He injected mice with ‘live R’ and ‘heat killed S’ pneumococci, and
observations were
 Death of most of mice
 Blood contain live S type pneumococci
 Their progeny was also S (means, transformation was permanent)
But query remained  What is the nature of this transforming
principle?

3. • 1944 – Oswald Avery, Colin Macleod, Maclyn McCarty answered
that ‘Transforming Principle is DNA’
• Basis of their answer
 Laboriously purified transforming principle had
 All the physical and chemical properties of DNA
 Contained no detectable protein
 Was unaffected by enzymes that hydrolyse protein & RNA
 Was totally inactivated by enzymes that hydrolyse DNA.

4. Late 1940s – Erwin Chargaff
• 1st devised reliable quantitative methods for the separation &
analysis of DNA hydrolysates.
• His conclusions
 The base composition of DNA varies from one species to another.
 Different tissues of the same species have the same base composition.
 The base composition of given species does not change with an organism’s
age, nutrition or change in environment.
 ‘Chargaff rule’: in all cellular DNAs, regardless of the species.
 [A]=[T]
 [G]=[C]
 [Purines]=[Pyrimidines]

6. Early 1950s – Phoebus Levene, later – Alexander Todd
• Nucleic acids are linear polymer of nucleotides whose ‘phosphate
groups’ bridge the 3’ and 5’ positions of successive sugar residues.
• The phosphates of these polynucleotides (Phosphodiester gr) are
acidic
• So, Polyanionic at physiological pH
• Polynucleotides have directionality.

7. DOUBLE HELICAL DNA
• 1953 – James Watson & Francis Crick (Nobel – 1962)
 Determined the structure of DNA

8. How they elucidated the structure of DNA
• Few crude landmarks:
1. Chargaff’s rule
2. Correct tautomeric forms of the DNA.
 Currently its firmly established that nucleic acid bases are overwhelmingly
in the keto tautomeric form.
 But in 1953 – This was not accepted, in fact G&T were widely believed to
be in their enol forms.
 But in 1953  Jerry Donohue (Office mate of Watson & Crick) expert on
the x-ray structure of small organic molecules provided correct tautomeric
forms
 Knowledge of correct tautomeric forms are prerequisite for the prediction
of correct H-bonding patterns of the bases.

9. 3. Rosalin Franklin  taken x-ray diffraction photograph of DNA
fiber.
• Crick concluded
• DNA is helical molecule
• DNA’s Planner aromatic bases form astack of planner rings which is
parallel to the fiber axis

10. The Watson-Crick structure: B DNA
• Fibers of DNA assumes B conformation under following conditions
• The counterion is an alkali metal (Na+)
• Relative humidity >92%
• B-DNA is regarded as the native (Biologically functional) form of
DNA because its x-ray pattern resembles DNA of intact sperm head.

11. Features
• It consists of 2 polynucleotide strands
• Wind about a common axis
• Right handed twist
• Both strands are antiparallel.
• Both strands wrap around each other.
• Core: Base
• Periphery: Sugar-P

12. • The planes of the base are nearly perpendicular
to the helix axis (Not to the backbone).
• Each base is H-bonded to a base on the opposite
strand to form a planar bp.

13. • C1’ to C1’ distance: 10.85 Å
• Angle with glycosidic bond: 51.5⁰
• Series of Pseudo-2 fold symmetry axis
(Dyad Axis), that passes through the
centre of each bp.
• Perpendicular to the helix axis.

14. Dimensions
• Diameter: ~20 Å
• bp/Turn: 10
• Twist/bp: 36⁰
• Rise/bp: 3.4Å
• Pitch (Rise/Turn): 34Å
• Major Groove: Wide & Deep
• Minor Groove: Narrow & Deep
• Sugar pucker: C2’ endo
• Glycosidic bond: Anti

15. Major Groove & Minor Groove
• If glycosidic bonds holding the bases in
each base pairs are directly across the
helix from each other, there will be
common width groove but it is not so in
DNA.
• Minor Groove: exposes that edge of a
base pair from which C1’ extends.
• Major groove: exposes opposite edge of
each base pairs.

16. • A=T 
𝐴𝐷𝐴𝑀
𝐴𝐻𝐴
& T=A 
𝑀𝐴𝐷𝐴
𝐴𝐻𝐴
• G≡C 
𝐴𝐴𝐷𝐻
𝐴𝐷𝐴
& T=A 
𝐻𝐷𝐴𝐴
𝐴𝐷𝐴
• A=T vs T=A & G≡C vs C≡G cant be
distinguished from looking at minor
groove (cf major groove)
Proteins which requires more specificity in binding, binds to major groove
& Sequence recognition by protein binding doesn’t require strand separation

17. Sugar ring pucker
• The sugar ring atoms are eclipsed when
the ring is planar.
• To relieve this crowding, the ring puckers
(Non planar)
• In majority 4/5 ring atoms are coplanar.
(Half chair)
• Endo Conformation
• Exo conformation
• In most cases, out of plane atom is either
C2’ or C3’.

18. Ribose Pucker governs the relative orientation of the
phosphate groups.
DNA structure is regularly repeating  so, DNA must have regularly
repeating sugar puckering.
• B DNA  C2’ endo
• A DNA  C3’ endo
• Z DNA  Purine (C3’ endo) & Pyrimidine (C2’ endo)

19. Glycosidic torsion angle
• It is greatly hindered (Only 1 or 2 stable positions): ‘Anti’ or ‘Syn’
Purine Pyrimidine
Not possible
B & A DNA Anti
Z DNA  Purine (Syn) & Pyrimidine (Anti)

21. Real DNA deviates from the ideal WC structure
• Basis of WC DNA Model:
• DNA was extracted from cells.
• Crude low resolution images
• Later progress:
• Richard Dickerson & Horace Drew  X-ray Crystal structure @ 1.9Å
resolution
• Loren Williams: @ 1.4Å resolution
• This later development demonstrated that B-DNA is irregular in
sequence specific manner.

22. A DNA
B-DNA A-DNA
~75% humidity
~>92% humidity
• Dimensions:
 Wider & Flatter
 Right handed helix
 11 bp/turn
 Pitch ~34Å
 Deep major groove &
v. shallow minor
groove

23. Occurrence of A-DNA
• Only 3 places (Till now)
1. At the cleavage centre of Topoisomerase II
2. At the active site of DNA polymerase.
3. In certain gm +ve bacteria that have undergone sporulation.
Such spores contains a high proportions (~20%) of ‘small acid soluble
spore proteins (SASPs)’
B-DNA A-DNA
SASPs
Observed in vitro
Resistant to UV Damage

24. Z-DNA
• Andrew Wang & Alexander Rich
• Determined x-ray structure of d(CGCGCG)  and got unexpected results.
• The alternating purine & pyrimidine sequence of this oligonucleotide is the
key to its unusual properties.

25. • Purine  flipped at
glycosidic bond (Anti 
Syn)
• Pyrimdine  cant adopt
Syn conformation
• The whole nucleoside flips
180⁰

26. • These flippings are topologically
possible without breaking & reforming
H-bonds
• So BZ transition can take place
without disrupting the bonding
relationships among the atoms
involved.
• Dimensions:
• Left handed
• bp/turn – 12
• Pitch 44 A⁰
• Minor groove – Deep (helix axis pass below
the minor groove)
• Major groove – not discernible

27. • The repeating unit of Z-DNA is a dinucleotide, rather than single
nucleotide as in other DNA helices.
• The backbone follows zig-zag path around helix.

28. Conditions favouring Z-DNA formation.
• Alternating purine & pyrimidine
• High salt concentration

29. Biological functions of Z DNA
• Z-DNA acts as a kind of switch in regulating genetic expressions
• It transiently forms behind the actively transcribing RNA
polymerase
• Z-DNA binding protein domains – Zα, exists in vivo  it suggests Z-
DNA in fact exists in vivo.
• e.g. Adenosine Deaminase Acting on RNA-1 (ADAR1) (RNA editing
enzyme)