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FORMS OF DNA

FORMS OF DNA :A MOLECULAR APPROACH

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FORMS OF DNA

  1. 1. FORMS OF DNA
  2. 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. 3. 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.
  4. 4. 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.
  5. 5. D-DNA: Rare variant with 8 base pairs per helical turn ,form in structure devoid of guanine . E- DNA: Extended or eccentric DNA.
  6. 6. 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.
  7. 7. • 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°.
  8. 8. 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.
  9. 9. • 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°.
  10. 10. 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.
  11. 11. • 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°.
  12. 12. 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°
  13. 13. 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.
  14. 14. Structure devoid of guanine
  15. 15. 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.
  16. 16. • 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.
  17. 17. 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
  18. 18. A-DNA B-DNA Z-DNA
  19. 19. 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
  20. 20. 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
  21. 21. 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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