 Solution

The same base sequence can present different molecular surfaces in different helical conformations. A-DNA, B-DNA and Z-DNA all retain paired antiparallel strands, but differ in handedness, backbone geometry, sugar puckering and groove accessibility. The familiar dimensions are approximate averages: sequence, hydration and bound molecules change the details, so they are structural signatures rather than rigid constants.

B-DNA is a right-handed DNA double helix with about $10.5$ base pairs per turn, a rise near $0.34\mathrm{nm}$ per pair and a diameter near $2\mathrm{nm}$. Its base pairs lie approximately perpendicular to the helical axis; the sugars are predominantly C2′-endo and the glycosidic bonds are anti. A broad accessible major groove and a narrower minor groove expose different edges of the paired nucleobases. Hydrated duplex DNA commonly adopts this family of conformations, although local bends and groove widths depend on sequence.

A-DNA is also right-handed, but is shorter and wider: roughly $11$ base pairs per turn, a rise around $0.26\mathrm{nm}$ per pair, and a diameter near $2.3\mathrm{nm}$. C3′-endo sugar puckering brings successive phosphates closer along each strand. The base pairs are inclined and displaced from the axis, producing a deep narrow major groove and a broad shallow minor groove. Reduced hydration favours A-DNA. Double-stranded RNA and many DNA-RNA hybrids adopt A-like geometry because the ribose 2′-hydroxyl constrains the backbone; this is important when extending a DNA-only comparison to cellular nucleic acids.

Z-DNA is a left-handed duplex with a zigzag backbone and a two-base-pair conformational repeat. It has approximately $12$ base pairs per turn, a rise near $0.37\mathrm{nm}$ per pair and a diameter around $1.8\mathrm{nm}$. Alternating purine–pyrimidine sequences, especially alternating G and C, favour it under suitable conditions. Purines commonly adopt syn glycosidic bonds and C3′-endo sugars, whereas pyrimidines remain anti with C2′-endo sugars. Its minor groove is narrow and deep, while the conventional major groove is flattened and poorly defined. Atomic-resolution analysis of an alternating CG oligomer established that a duplex can adopt this left-handed fold.^[ref] High salt in a crystal experiment is evidence of an accessible conformation, not proof that most cellular DNA is in that state; negative supercoiling and protein binding can instead favour local transitions.

These geometries determine how proteins read sequence. In B-DNA, the pattern of hydrogen bond donors, acceptors and hydrophobic groups in the major groove distinguishes the four oriented base pairs without strand separation. The minor groove carries less direct chemical information: A–T and T–A present similar patterns there, as do G–C and C–G. Specificity can nevertheless arise from DNA shape readout, including groove width, electrostatic potential, deformability and hydration, combined with contacts to the phosphate backbone. The chemical accessibility of base edges underlies the classic analysis of sequence-specific recognition of duplex nucleic acids.^[ref]

An alpha helix from a transcription factor can fit a B-DNA major groove, but the same docking arrangement need not fit the deep narrow groove of A-DNA. Many double-stranded RNA-binding interactions therefore emphasize backbone or shape, although A-form geometry does not make sequence-specific RNA recognition impossible. A Z-DNA-binding domain can recognize the characteristic left-handed backbone, making recognition partly conformation-specific rather than simply recognition of an exposed base code. In cells, nucleosomes, competing proteins, torsional stress and local hydration further determine access. Binding assays should compare sequences and conformations independently, using structural or spectroscopic controls: a sequence mutation can change both the chemical recognition pattern and the probability of adopting the recognized structure.