The double helix structure of DNA can exist in three distinct forms: A, B, and Z. The B form, which is the most prevalent and was famously described by Watson and Crick, is characterized by its right-handed helical structure. In contrast, the A form, also a right-handed helix, is more condensed than the B form, occupying less space despite having the same number of base pairs. Notably, double-stranded RNA adopts the A form, while most double-stranded DNA is found in the B form.
The Z form of DNA is unique as it is a left-handed helix, typically located near regulatory sequences. This form is significant because it features B-Z junctions, where the helix transitions between the B and Z forms. During this transition, nucleotides flip out from the strands, causing a shift in the helical direction. This abrupt change in shape is crucial for cellular mechanisms, as it allows cells to identify regulatory sequences based on the physical structure of DNA.
When examining the structures from a top-down perspective, the A form reveals a central hollow space, while both the B and Z forms lack this opening. The stability of these structures is maintained not only by hydrogen bonds but also by hydrophobic stacking forces. These forces arise from the hydrophobic nature of the bases, which stack closely together in the center of the helix, contributing to the overall stability of the B form. Additionally, the phosphate groups on the outside of the DNA molecule interact with the aqueous environment, further stabilizing its structure through hydration.