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DNA - Structure
DR. KALPESH NAKARANI
TUTOR CUM RESIDENT (3RD YEAR)
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?
• 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.
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]
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.
DOUBLE HELICAL DNA
• 1953 – James Watson & Francis Crick (Nobel – 1962)
 Determined the structure of DNA
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.
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
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.
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
• 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.
• 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.
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
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.
• 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
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’.
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)
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)
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.
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
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
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.
• Purine  flipped at
glycosidic bond (Anti 
Syn)
• Pyrimdine  cant adopt
Syn conformation
• The whole nucleoside flips
180⁰
• 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
• 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.
Conditions favouring Z-DNA formation.
• Alternating purine & pyrimidine
• High salt concentration
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)

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Dna structure

  • 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]
  • 5.
  • 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)
  • 20.
  • 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)