Genetics Molecular Biology

Forms of DNA

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There are three major forms of DNA. These are known as A-form, B-form,and Z-form DNA.

B-form

Dimensions of B-form 

  • 0.34 nm between bp, 3.4 nm per turn, about 10 bp per turn
  • 1.9 nm (about 2.0 nm or 20 Angstroms) in diameter
  • 34o helix pitch; -6o base-pair tilt; 36o twist angle

The major groove is wider than the minor groove in DNA and many sequence specific proteins interact in the major groove. The N7 and C6 groups of purines and the C4 and C5 groups of pyrimidine face into the major groove, thus they can make specific contacts with amino acids in DNA-binding proteins. Thus specific amino acids serve as H-bond donors and acceptors to form H-bonds with specific nucleotides in the DNA. H-bond donors and acceptors are also in the minor groove, and indeed some proteins bind specifically in the minor groove. Base pairs stack, with some rotation between them.

B-DNA is the Watson–Crick form of the double helix that is the most common type of DNA.

A-form DNA

A-DNA is fairly similar to B-DNA given that it is a right-handed double helix with major and minor grooves. However there is a slight increase in the number of base pairs (bp) per turn (resulting in a smaller twist angle), and smaller rise per base pair (making A-DNA 20-25% shorter than B-DNA). The major groove of A-DNA is deep and narrow, while the minor groove is wide and shallow. A-DNA is broader and apparently more compressed along its axis than B-DNA.

One turn of the helix consists of 11 base pairs with a length of 2.86nm. The backbone of A-DNA is formed by sugar phosphates that are linked continuously using phosphodiester bonds. All the nitrogenous bases are at the core centre of the helix. Hydrogen bonds between nitrogenous bases allow the molecule to exhibit the double helix structure. The helix width of A-DNA is 2.3nm. Overall, A-DNA is wider than the more commonly found B-DNA. 

Z-form DNA

Z-DNA is a radically different duplex structure, with the two strands coiling in left-handed helices and a pronounced zig-zag (hence the name) pattern in the phosphodiester backbone. Z-DNA can form when the DNA is in an alternating purine-pyrimidine sequence such as GCGCGC, and indeed the G and C nucleotides are in different conformations, leading to the zig-zag pattern. The big difference is at the G nucleotide. It has the sugar in the C3′ endoconformation (like A-form nucleic acid, and in contrast to B-form DNA) and the guanine base is in the synconformation. 

The duplex in Z-DNA has to accommodate the distortion of this G nucleotide in the synconformation. The cytosine in the adjacent nucleotide of Z-DNA is in the “normal” C2′ endo, anticonformation.

It was discovered by Rich, Nordheim &Wang in 1984.

  • It has antiparallel strands as B-DNA.
  • It is long and thin as compared to B-DNA.
  • 12 bp per turn; 0.45 nm axial rise; 45o helix pitch; 7o base-pair tilt.
  • -30o twist angle; 1.8 nm helix diameter,

C-DNA

  • Formed at 66% relative humidity and in presence of Li+ and Mg2+ ions.
  • Right-handed with the axial rise of 3.32A° per base pair
  • 33 base pairs per turn
  • Helical pitch is 30.97A°.
  • Base pair rotation is 38.58°.
  • Has a diameter of 19 A°, smaller than that of A-& B- DNA.
  • The tilt of base is 7.8°

D-DNA

  • Rare variant with 8 base pairs per helical turn
  • These forms of DNA found in some DNA molecules devoid of guanine.
  • The axial rise of 3.03A°per base pairs
  • The tilt of 16.7° from the axis of the helix.

E- DNA

  • Extended or eccentric DNA.
  • E-DNA has a long helical axis rise and base perpendicular to the helical axis.
  • Deep major groove and the shallow minor groove.
  • E-DNA allows crystallizing for a period of time longer, the methylated sequence forms standard A-DNA.
  • E-DNA is the intermediate in the crystallographic pathway from B-DNA to A-DNA.

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