DNA can exist in 3 forms A, B & Z. Although only B- DNA and Z-DNA have been directly observed in functional organism. The conformation that DNA adopts depends on the hydration level, DNA sequence, the amount and direction of supercoiling, chemical modification of bases, type and concentration of metal ions as well as the presence of polyamines in the solution.

B form of DNA is most stable structures under physiological conditions.

A form is generally observed in partially dehydrated samples of DNA while in the cell it may be produced in hybrid pairings of DNA and RNA strands as well as in enzyme − DNA duplex complexes. DNA is still arranged in right handed double helix but the helix is wider and the number of base pairs per helical turn is 11 rather than 10 in B- DNA. The plane of Base pairs in A- DNA is tilted about 20° with respect to helix axis. These structural changes deepen the major groove while making minor groove shallower. The reagents used to promote crystallization of DNA tend to dehydrate it and thus most short DNA molecules tend to crystallize in the A form.

Z form on the other hand shows left handed helical rotation. There are 12 base pairs per helical turn and the structure appears more slender and elongated. DNA backbone takes a zig-zag appearance and that is the reason, why Z-DNA also known as zig-zag DNA. Sequences in which pyrimidine alternate with purines tend to form Z helices much more readily. In the left helices the purine residues flip to the syn conformation alternating with pyrimidines in the anti conformation.

Some Unusual structures

Bends occur in DNA helix wherever four or more adenosine residues appear sequentially in one strand. This bending may be important in binding of some proteins to DNA.

Some unusual structures involve three or even four DNA strands. As nucleotides participating in a Watson- Crick base pair can form a number of additional hydrogen bonds. The N- 7, O⁶ and N⁶ of purines, the atoms that participate in hydrogen bonding of triplex DNA are often referred to as Hoogsteen position and the non Watson−Crick pairing is called Hoogsteen pairing.