= Solution
\b[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.<Molecular structure of a left-handed double helical DNA fragment at atomic resolution by A. H.-J. Wang and others>[pp. 680–686, alternating CG duplex and left-handed structure]{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>.<Sequence-specific recognition of double helical nucleic acids by proteins by Nadrian C. Seeman and others>[pp. 804–808, accessibility of base-edge recognition patterns]{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.
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