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FORMS OF DNA
INTRODUCTION
• Nucleic acids are any group of long ,linear
macromolecule that carries genetic information
directing all cellular functions; composed of
linked nucleotides.
• Two types : DNA and RNA
• DNA: Deoxyribonucleic acid: An extremely long,
double-stranded nucleic acid molecule arranged
as double helix that is the main constituent of the
chromosomes and that carries the genes as
segments along its strands.
Variations in DNA
• Most of the DNA is in the classic Watson-Crick
model simply called as B-DNA or B-form DNA.
• In certain condition ,different forms of DNAs
are found to be appeared like A-DNA,Z-DNA,C-
DNA,D-DNA,E-DNA.
• This deviation in forms are based on their
structural diversity.
DIFFERENT FORMS OF DNA
• X-ray analysis of DNA crystals at atomic resolution have
revealed that DNA exhibits much more structural diversity than
formly envisaged. Such variations are:
 B-DNA: Most common ,originally deduced from X-ray diffraction
of sodium salt of DNA fibres at 92% relative humidity.
 A-DNA: Originally identified by X-ray diffraction of analysis of
DNA fibres at 75% relative humidity .
 Z-DNA: Left handed double helical structure winds to the left in
a zig- zag pattern .
 C-DNA: Formed at 66% relative humidity and in presence of Li+
and Mg2+ ions.
D-DNA: Rare variant with 8 base pairs per helical
turn ,form in structure devoid of guanine .
E- DNA: Extended or eccentric DNA.
B-DNA
• Described by James D. Watson & Francis crick.
• Commonly found in DNA.
• DNA molecule consists of 2 helical polynucleotide
chains coiled around common axis.
• 2 helices are wound in such a way so as to
produce 2 interchain spacing or groove –
• Major/wide groove(width 12A°,depth 8.5A°)
• Minor /narrow groove(width 6A°,depth 7.5A°)
• These grooves provide surface with which
proteins,chemicals,drugs can interact.
• 2 helical wind along the molecules.
• 2 chains run in opposite direction ,they are
antiparallel ,the plane of bases are perpendicular
to helix axis.
• Right handed twisting .
• Uniform diameter(20A°)
• Complementary base pairing.
• Base pair per turn is 10.4.
• Rise per base pair is 3.4A°.
A-DNA
• A-DNA is one of the possible double helical
structure which DNA can adopt along with
other two biologically active helix structure(B-
DNA,Z-DNA).
• Right handed double helix .
• Short and fat compared to B-DNA.
• Occur only in dehydrated sample of DNA ,Such
those used in crystallographic experiments.
• A-DNA was originally identified by X-ray
diffraction analysis of DNA fibres at 75% relative
humidity.
• The grooves are not as deep in B-DNA.
• The bases are more tilted (to 20A°).
• The base pairs per turn is 11.
• Rise per base pair is 2.3A°.
Z-DNA
• One of the many possible DNA double helix
structure.
• Left handed double helix structure winds to
left in zig-zag manner.(DNA backbone were in
zig-zag manner)so they are termed as Z-DNA.
• Discovered by Rich, Nordheim &Wang in 1984.
• It has antiparallel strands as B-DNA.
• It is long and thin as compared to B-DNA.
• Remarkable characteristic :adjacent sugar have
alternating orientation (against B-DNA which has
same orientation).
• In Z-DNA ,a)Purines: syn confirmation(bases & sugar
are near & on same side)
b) pyramidines: anti (bases & sugar are
distant ,on opposite sides)
• Only one deep helical grooves.
• There are 12 base pairs per turn with axial rise
3.8A°,& angle of twist 60°.
C-DNA
• C-DNA formed at 66% relative humidity (low)in
presence of Li+ or Mg2+.
• Right handed ,with axial rise of 3.32A° per base
pair .
• 9.33 base pairs per turn.
• Helical pitch 3.32A°×9.33°A=30.97A°.
• Base pair rotation=38.58°.
• Has diameter of19A°,smaller than that of A-&B-
DNA.
• The tilt of base is 7.8°
D-DNA
• Extremely rare variant with only 8base pairs per helical
turn .
• This forms of DNA found in some DNA molecules
devoid of guanine.
• Axial rise of 3.03A°per base pairs .Tilt of 16.7° from axis
of helix.
• Actually 2 different forms of D-DNA
1. D(A):Takes part in D-A-B transition.
2. D(B):Associated with D-B change of confirmation.
• 2 DNA structure have same helical parameters.
Structure devoid of guanine
E-DNA
• Cytosine methylation of or bromination of DNA
sequence d(GGCGCC)2 is to induce a novel
extended &eccentric double helix, which we call
E-DNA.
• E-DNA has a long helical axis rise and base
perpendicular to the helical axis.
• Deep major groove and shallow minor groove.
• E-DNA allowed to crystallize for a period time
longer, the methylated sequence forms standard
A-DNA.
• E-DNA is the intermediate in the transition toA-
DNA.
• E-DNA is the intermediate in the
crystallographic pathway from B-DNA to A-DNA.
DNA CONFIRMATION OF A-,B-&Z-DNA
A B Z
HELIX RIGHT HANDED RIGHT HANDED LEFT HANDED
WIDTH WIDEST INTERMEDIATE NARROWEST
PLANE OF
BASE
PERPENDICULAR TO
HELIX AXIS
PERPENDICULAR TO
HELIX AXIS
PERPENDICULAR TO
HELIX AXIS
CENTRAL
AXIS
6A° HOLES ALONG
HELIX AXIS
TINY CENTRAL NO INTERNAL
SPACE
MAJOR AXIS NARROW & DEEP WIDE &DEEP NO MAJOR GROOVE
A-DNA
B-DNA
Z-DNA
B-DNA Z-DNA
COILING RIGHT HANDED LEFT HANDED
NO.OF GROOVE 2 (MAJOR&MINOR) 1(MINOR)
BASE PAIR PER TURN 10.5 12
HELICAL PITCH 34° 44.6°
HELICAL DIAMETER 20° 18°
NUCLEOTIDE
CONFIRMATION
ALL ANTI
CONFIRMATION
PURINES:SYN
PYRAMIDINES:ANTI
CONFIGURATIONAL DIFFERENCE BETWEEN B-&Z-DNA
C-G
G-C
G-C
C-G
T-A
A-T
C-G
G-C
G-C
C-G
T-A
A-T
5’
5’
5’
5’
3’
3’ 3’
3’
B-DNA Z-DNA
ANTI ANTI
ANTI ANTI
ANTI ANTI
ANTI ANTI
ANTI ANTI
ANTI ANTI
ANTI SYN
SYN ANTI
ANTI SYN
SYN ANTI
ANTI SYN
SYN ANTI
CHARACTRISTICS A-DNA B-DNA C-DNA Z-DNA
CONDITIONS 75% RELATIVE
HUMIDITY;NA+,K+,C
s IONS
92% R.H:;LOW ION
STRENGTH
60%R.H;Li/Mg IONS VERY HIGH SALT CONC.
SHAPE BROADEST INTERMEDIATE NARROW NARROWEST
HELIX SENSE RIGHT RIGHT RIGHT LEFT
HELIX DIAMETER 25.5A° 20.7A° 19.0A° 18.4A°
RISE PER BASE
PAIR(H)
2.3A° 3.4A° 3.32A° 3.8A°
BASE PAIR PER
TURN(N)
11 10.4 9.33 12
HELIX PITCH(H×N) 25.5A° 35.36A° 30.97A° 45.60A°
ROTATION PER BASE
PAIR
+32.72° +34.61° +38.58° -60°
BASE PAIR TILT 19° 1° 7.8° 9°
GLYCOSIDIC BOND ANTI ANTI _ ANTI FOR C,T. SYN FOR A,G.
MAJOR GROOVE NARROW &VERY
DEEP
WIDE & QUITE DEEP _ NO
MINOR GROOVE VERY BROAD &
SHALLOW
NARROW & QUITE
DEEP
_ VERY NARROW & DEEP

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FORMS OF DNA

  • 2. INTRODUCTION • Nucleic acids are any group of long ,linear macromolecule that carries genetic information directing all cellular functions; composed of linked nucleotides. • Two types : DNA and RNA • DNA: Deoxyribonucleic acid: An extremely long, double-stranded nucleic acid molecule arranged as double helix that is the main constituent of the chromosomes and that carries the genes as segments along its strands.
  • 3.
  • 4.
  • 5. Variations in DNA • Most of the DNA is in the classic Watson-Crick model simply called as B-DNA or B-form DNA. • In certain condition ,different forms of DNAs are found to be appeared like A-DNA,Z-DNA,C- DNA,D-DNA,E-DNA. • This deviation in forms are based on their structural diversity.
  • 6. DIFFERENT FORMS OF DNA • X-ray analysis of DNA crystals at atomic resolution have revealed that DNA exhibits much more structural diversity than formly envisaged. Such variations are:  B-DNA: Most common ,originally deduced from X-ray diffraction of sodium salt of DNA fibres at 92% relative humidity.  A-DNA: Originally identified by X-ray diffraction of analysis of DNA fibres at 75% relative humidity .  Z-DNA: Left handed double helical structure winds to the left in a zig- zag pattern .  C-DNA: Formed at 66% relative humidity and in presence of Li+ and Mg2+ ions.
  • 7. D-DNA: Rare variant with 8 base pairs per helical turn ,form in structure devoid of guanine . E- DNA: Extended or eccentric DNA.
  • 8.
  • 9. B-DNA • Described by James D. Watson & Francis crick. • Commonly found in DNA. • DNA molecule consists of 2 helical polynucleotide chains coiled around common axis. • 2 helices are wound in such a way so as to produce 2 interchain spacing or groove – • Major/wide groove(width 12A°,depth 8.5A°) • Minor /narrow groove(width 6A°,depth 7.5A°) • These grooves provide surface with which proteins,chemicals,drugs can interact.
  • 10.
  • 11. • 2 helical wind along the molecules. • 2 chains run in opposite direction ,they are antiparallel ,the plane of bases are perpendicular to helix axis. • Right handed twisting . • Uniform diameter(20A°) • Complementary base pairing. • Base pair per turn is 10.4. • Rise per base pair is 3.4A°.
  • 12. A-DNA • A-DNA is one of the possible double helical structure which DNA can adopt along with other two biologically active helix structure(B- DNA,Z-DNA). • Right handed double helix . • Short and fat compared to B-DNA. • Occur only in dehydrated sample of DNA ,Such those used in crystallographic experiments.
  • 13. • A-DNA was originally identified by X-ray diffraction analysis of DNA fibres at 75% relative humidity. • The grooves are not as deep in B-DNA. • The bases are more tilted (to 20A°). • The base pairs per turn is 11. • Rise per base pair is 2.3A°.
  • 14.
  • 15. Z-DNA • One of the many possible DNA double helix structure. • Left handed double helix structure winds to left in zig-zag manner.(DNA backbone were in zig-zag manner)so they are termed as Z-DNA. • Discovered by Rich, Nordheim &Wang in 1984. • It has antiparallel strands as B-DNA. • It is long and thin as compared to B-DNA.
  • 16. • Remarkable characteristic :adjacent sugar have alternating orientation (against B-DNA which has same orientation). • In Z-DNA ,a)Purines: syn confirmation(bases & sugar are near & on same side) b) pyramidines: anti (bases & sugar are distant ,on opposite sides) • Only one deep helical grooves. • There are 12 base pairs per turn with axial rise 3.8A°,& angle of twist 60°.
  • 17.
  • 18. C-DNA • C-DNA formed at 66% relative humidity (low)in presence of Li+ or Mg2+. • Right handed ,with axial rise of 3.32A° per base pair . • 9.33 base pairs per turn. • Helical pitch 3.32A°×9.33°A=30.97A°. • Base pair rotation=38.58°. • Has diameter of19A°,smaller than that of A-&B- DNA. • The tilt of base is 7.8°
  • 19.
  • 20. D-DNA • Extremely rare variant with only 8base pairs per helical turn . • This forms of DNA found in some DNA molecules devoid of guanine. • Axial rise of 3.03A°per base pairs .Tilt of 16.7° from axis of helix. • Actually 2 different forms of D-DNA 1. D(A):Takes part in D-A-B transition. 2. D(B):Associated with D-B change of confirmation. • 2 DNA structure have same helical parameters.
  • 22. E-DNA • Cytosine methylation of or bromination of DNA sequence d(GGCGCC)2 is to induce a novel extended &eccentric double helix, which we call E-DNA. • E-DNA has a long helical axis rise and base perpendicular to the helical axis. • Deep major groove and shallow minor groove. • E-DNA allowed to crystallize for a period time longer, the methylated sequence forms standard A-DNA.
  • 23. • E-DNA is the intermediate in the transition toA- DNA. • E-DNA is the intermediate in the crystallographic pathway from B-DNA to A-DNA.
  • 24.
  • 25. DNA CONFIRMATION OF A-,B-&Z-DNA A B Z HELIX RIGHT HANDED RIGHT HANDED LEFT HANDED WIDTH WIDEST INTERMEDIATE NARROWEST PLANE OF BASE PERPENDICULAR TO HELIX AXIS PERPENDICULAR TO HELIX AXIS PERPENDICULAR TO HELIX AXIS CENTRAL AXIS 6A° HOLES ALONG HELIX AXIS TINY CENTRAL NO INTERNAL SPACE MAJOR AXIS NARROW & DEEP WIDE &DEEP NO MAJOR GROOVE
  • 26.
  • 28.
  • 29. B-DNA Z-DNA COILING RIGHT HANDED LEFT HANDED NO.OF GROOVE 2 (MAJOR&MINOR) 1(MINOR) BASE PAIR PER TURN 10.5 12 HELICAL PITCH 34° 44.6° HELICAL DIAMETER 20° 18° NUCLEOTIDE CONFIRMATION ALL ANTI CONFIRMATION PURINES:SYN PYRAMIDINES:ANTI CONFIGURATIONAL DIFFERENCE BETWEEN B-&Z-DNA
  • 30.
  • 31. C-G G-C G-C C-G T-A A-T C-G G-C G-C C-G T-A A-T 5’ 5’ 5’ 5’ 3’ 3’ 3’ 3’ B-DNA Z-DNA ANTI ANTI ANTI ANTI ANTI ANTI ANTI ANTI ANTI ANTI ANTI ANTI ANTI SYN SYN ANTI ANTI SYN SYN ANTI ANTI SYN SYN ANTI
  • 32. CHARACTRISTICS A-DNA B-DNA C-DNA Z-DNA CONDITIONS 75% RELATIVE HUMIDITY;NA+,K+,C s IONS 92% R.H:;LOW ION STRENGTH 60%R.H;Li/Mg IONS VERY HIGH SALT CONC. SHAPE BROADEST INTERMEDIATE NARROW NARROWEST HELIX SENSE RIGHT RIGHT RIGHT LEFT HELIX DIAMETER 25.5A° 20.7A° 19.0A° 18.4A° RISE PER BASE PAIR(H) 2.3A° 3.4A° 3.32A° 3.8A° BASE PAIR PER TURN(N) 11 10.4 9.33 12 HELIX PITCH(H×N) 25.5A° 35.36A° 30.97A° 45.60A° ROTATION PER BASE PAIR +32.72° +34.61° +38.58° -60° BASE PAIR TILT 19° 1° 7.8° 9° GLYCOSIDIC BOND ANTI ANTI _ ANTI FOR C,T. SYN FOR A,G. MAJOR GROOVE NARROW &VERY DEEP WIDE & QUITE DEEP _ NO MINOR GROOVE VERY BROAD & SHALLOW NARROW & QUITE DEEP _ VERY NARROW & DEEP