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-DNA1. 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-DNAA 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

MINOR AXIS WIDE AND SHALLOW

NARROW & DEEP NARROW & DEEP

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:SYNPYRAMIDINES: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+,Cs 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