DNA Structure – A, B and Z Form

Will it be possible to carry or pack an elongated copper wire inside a tiny box? Apparently no, so we do intend to make a loop of the wire in such a manner that it occupies a minimum volume and area. Nature does the same with our DNA inside the cell. The hereditary information of every organism is generally stored in long double-stranded molecules called DNA. We all are familiar with the shape and structure of the deoxyribonucleic acid (DNA). However, in nature, this structure is unlikely to exist commonly within the cells of every living organism. Various factors affect the conformation of the DNA in a cell leading to structural transitions into other DNA forms. A-form, B-form and Z-form of DNA are the three generally found structural conformations of DNA.

There are three major families of DNA helices which it forms: A-DNA, B-DNA and Z-DNA.

A-DNA

A form of DNA is a structural conformation that any DNA molecule favours under dehydrating condition and also certain purine stretches favours the A-DNA forms. Discovered by Rosalind Franklin, the A-DNA helix conformation is wider when compared with the B-DNA conformations because of the base pairs stacking. The bases in the A-DNA are stacked little off-centre due to which a hollow region at the centre is visible when looked at the cross-section. Like B-DNA, A-DNA is the right-handed double helix structure with antiparallel strands held together by Watson-Crick base-pairing. Compared to B-DNA, it is more compact and shorter structure.

The helical parameters of A-DNA are given below:

Parameter
A-form of DNA
Helix sense
Right-handed
Diameter
23 Å (2.3 nm)
Helix rotation on per base pair
32.7°
Base pair tilt to axis
+20°
Helix pitch (rise per turn)
28.6 Å (2.86 nm)
Helix rise per base pair
2.6 Å (0.26 nm)
Base pairs per turn
11
Glycosyl bond angle
Anti
Sugar pucker
C3′-endo
Major groove
Narrow and Deep
Minor groove
Wide and Shallow

B-DNA

The deoxyribonucleic acid conformation in the cells is the Watson–Crick form of the double helix. The right-handed helix B-DNA exists in relatively much higher hydrating conditions, unlike A-DNA. As under physiological conditions, the B form of DNA is predominant in the cells. Among the three different families of DNA helices, the B-DNA conformation is the most common and variable in structure.

The helical parameters of B-DNA are given below:

Parameter
B-form of DNA
Helix sense
Right-handed
Diameter
20 Å (2.0 nm)
Helix rotation on per base pair
34.3°
Base pair tilt to axis
-6°
Helix pitch (rise per turn)
34 Å (3.4 nm)
Helix rise per base pair
3.4 Å (0.34 nm)
Base pairs per turn
10.5
Glycosyl bond angle
Anti
Sugar pucker
C2′-endo
Major groove
Wide and Deep
Minor groove
Narrow and Deep

Z-DNA

The Z-DNA is a left-handed double helical structure obtaining its name “Z-DNA” because of the irregular and zigzag shape of it backbone. The occurrence of Z-DNA is generally unfavourable, however, DNA sequences with alternating of purines and pyrimidines adopt left-handed Z-DNA conformation. A fascinating feature about Z-DNA, which makes it easily distinguishable from B-DNA that there is no major groove exists in Z-DNA and a single narrow groove corresponding to the minor groove of the B-DNA. The Z-DNA is thinner and more extended when compared to B-DNA.

The helical parameters of Z-DNA are given below:

Parameter
Z-form of DNA
Helix sense
Left-handed
Diameter
18 Å (2.0 nm)
Helix rotation on per base pair
9° or 51°
Base pair tilt to axis
-7°
Helix pitch (rise per turn)
44 Å (4.4 nm)
Helix rise per base pair
3.8 Å (0.38 nm)
Base pairs per turn
12
Glycosyl bond angle
Pyrimidine: anti, Purine: syn
Sugar pucker
C2′-endo for pyrimidines
C3′-endo for purines
Major groove
Flat
Minor groove
Narrow and Deep

References:

Potaman VN, Sinden RR. DNA: Alternative Conformations and Biology. In: Madame Curie Bioscience Database [Internet]. Austin (TX): Landes Bioscience; 2000-2013. Available from: https://www.ncbi.nlm.nih.gov/books/NBK6545/

A-form, DNA-RNA Structure Tutorials, Tulane University

Herbert, A. & Rich, A. Genetica (1999) 106: 37. https://doi.org/10.1023/A:1003768526018

Ghosh, Anirban & Bansal, Manju. (2003). A glossary of DNA structures from A to Z. Acta crystallographica. Section D, Biological crystallography. 59. 620-6. 10.1107/S0907444903003251


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Questions:

DNA Structure – A, B and Z Form

  1. What are the three major DNA helices families?
  2. Name the left-handed double helical structure.
    a) B-DNA
    b) A-DNA
    c) Z-DNA
    d) Both A and B form of DNA
  3. What is the conformation of the Glycosyl bond angle for purines in Z-form of DNA?
  4. The most common form of DNA at neutral pH and physiological salt concentrations is –
    a) Z-DNA
    b) A-DNA
    c) B-DNA
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