By David Charles, Updated Aug 30, 2022
DNA’s informational content is encoded by four nucleotides: adenine (A), cytosine (C), guanine (G), and thymine (T). Complementary base pairing—A with T and C with G—creates stable hydrogen bonds that lock the genetic code into place. Because each strand carries a full copy of the sequence, only one template is needed for replication or repair, underscoring the robustness of the pairing system.
Most genomic DNA adopts a right‑handed double helix. The backbone, a repeating sugar‑phosphate chain, twists around a central axis, while the nitrogenous bases sit inside, protected from solvent. Three conformations exist: B‑DNA, the most common form in human cells; A‑DNA, which is shorter and more tightly packed and often appears in dehydrated or highly compressed regions; and Z‑DNA, a left‑handed variant that arises transiently during transcription. These structural variations influence how DNA interacts with proteins and other molecules.
Beyond hydrogen bonds, DNA’s stability is largely due to hydrophobic base‑stacking interactions. The aromatic bases align perpendicular to the backbone, minimizing exposure to water and reducing electrostatic repulsion. This arrangement not only maintains the helix but also facilitates the binding of transcription factors and other regulatory proteins.
DNA is intrinsically directional, with a 5’ end—bearing a phosphate group on the fifth carbon of deoxyribose—and a 3’ end—terminating in a hydroxyl group on the third carbon. All enzymatic processes, from transcription to replication, proceed from 5’ to 3’, ensuring fidelity and coordination across the genome.
Near the 5’ end of many promoters lies a TATA box—a stretch of thymine–adenine repeats. Because A‑T pairs form weaker hydrogen bonds than G‑C pairs, TATA boxes facilitate the unwinding of DNA strands during transcription initiation, acting as a critical signal for RNA polymerase binding.
