Study Notes On Deoxyribonucleic Acid (DNA)
There are 3 forms of DNA in which A and B forms are right-handed helix while Z form is left-handed. Watson - Crick Model is of B-form. The strands run anti-parallel in nature. There are about 10 base pairs per turn of the helix. One turn of the helix is 34 Å, and the base pairs are 3.4 Å apart. Sugar phosphates are on the outside, while base pairs are on the inside. There is a minor groove and a major groove.
B-form of DNA is stable at high humidity conditions (95%), but at 75% humidity, it is converted into A form. B-DNA is the most hydrated and stable form of DNA under high humidity conditions. Since salt dehydrates DNA, thus, A-DNA converts to Z-DNA in solutions with high salt concentration. Phosphates are individually hydrated in B-form, but one water molecule forms a bridge between two phosphates in A and Z-forms, stabilizing these forms in low humidity.
In A-form, the helix axis is inclined by about 13 degrees, and there is ~10.9 bp per turn. The major groove is also very deep (~1.35 nm) and narrower (~0.27 nm) than the B form and is extensively hydrated. The minor groove is relatively wide (~1.1 nm) and shallow (~0.28nm) than B-form. It is a right-handed double helix and is short and stout compared to B-DNA. The A-form occurs only in dehydrated samples of DNA like those used in X-ray crystallographic experiments. Crystal structures of an intermediate form between A and B forms have been reported, often called the E-DNA eccentric DNA.
Z-DNA has an interesting feature; it is left-handed with the backbone following a zig-zag pattern and contains 12 bp per turn. In contrast to B-DNA, where a repeating unit is 1 bp, the repeating unit is 2 bp in Z-form. The major groove of Z-DNA is shallow, allowing it to accommodate bulky substituents at C8 of purines or C5 of pyrimidines.
Z-from is favoured in the regions rich in G-C pairs. E. coli and Halobacterium are known to contain left-handed forms of DNA. Segments of Z-DNA may occur in the enhancer region or may be formed behind RNA polymerase molecules that are moving along a gene while synthesizing mRNA. The associated negative supercoiling of the DNA could cause it to assume the Z-form. This region of Z-form can, in turn, be a site for interaction with specific proteins.
Other Rare Variants -
C-DNA - Formed at 66% relative humidity in the presence of Li+ and Mg2+ ions.
D-DNA - Scarce variant with 8 bp per helical turn found in some DNA molecules devoid of the guanine base.
Table 1. Comparison of different DNA types
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