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Two nucleic acid strands with opposite directional alignment: a $5^{\prime }$-to-$3^{\prime }$ direction on one is aligned with the $3^{\prime }$-to-$5^{\prime }$ direction on the other.

In the usual DNA context, deoxyribose means 2-deoxy-D-ribose, a five-carbon monosaccharide with molecular formula ${\mathrm{C}}_5{\mathrm{H}}_{10}{\mathrm{O}}_4$. Relative to D-ribose, the hydroxy group at C2 is replaced by hydrogen. The locant 2 matters: it identifies which position loses its oxygen. See Favre and Powell, IUPAC Blue Book, P-102.5.3: deoxy sugars and IUPAC: nucleic acids and their component sugars.

The paired Fischer projections in ribose make the change concrete. C2 has hydrogen on both sides, while C3 and C4 retain their hydroxy groups on the right. C2 is therefore not a stereocenter: exchanging its two identical hydrogen substituents cannot produce a distinct configuration. The unchanged C3 and C4 still carry stereochemical information.

Replacing $\mathrm{OH}$ by $\mathrm{H}$ removes one oxygen but leaves the total hydrogen count unchanged: the hydrogen belonging to the removed hydroxy group is replaced by a hydrogen bonded directly to carbon. Thus ${\mathrm{C}}_5{\mathrm{H}}_{10}{\mathrm{O}}_5$ becomes ${\mathrm{C}}_5{\mathrm{H}}_{10}{\mathrm{O}}_4$. This comparison describes structures, rather than a complete chemical reaction or its mechanism.

In DNA, deoxyribose is incorporated as a ring in each nucleotide, with phosphate connections building the backbone. Its C2′ bears hydrogen where RNA's ribose bears a hydroxy group. This small local difference lets the sugar structure identify the two kinds of nucleic acid; the nucleobases supply their sequence information. See Alberts et al.: nucleotides as the subunits of DNA and RNA.

A nucleic acid is a polymer built from linked nucleotides. The two principal kinds are DNA and RNA. Each nucleotide contributes a sugar, a nucleobase, and phosphate to the chain; the nucleobase is only the letter-bearing component, not the entire nucleotide. DNA uses deoxyribose, whereas RNA uses ribose. A chain of six nucleotides is therefore not six free nucleobases placed beside one another. See NHGRI: nucleic acids.

The chemical scaffold and the variable lettering do different jobs. Covalent bonds maintain the sugar–phosphate backbone, while the order of attached nucleobases specifies the nucleic acid sequence. A phosphodiester bond links the $3^{\prime }$ position of one sugar to the $5^{\prime }$ position of the next through phosphate. These position numbers refer to carbon chemical atoms in the sugar; they define a strand's direction even when it bends or forms a circle. See Brown, Genomes, 2nd edition: the human genome.

This division is useful: the backbone supplies a connected physical record, and base pairing allows its letters to recognize partners. DNA replication copies that record, and transcription uses a DNA template to make RNA. RNA can also fold into functional shapes through base pairing within one chain; a nucleic acid sequence specifies chemical order, not a requirement for a straight shape. The beauty is that the same kind of polymer can carry a message and form a structure that acts on messages.

A nucleic acid double helix consists of two nucleic acid strands winding around a common axis. In the familiar DNA arrangement, sugar–phosphate backbones lie outside and paired nucleobases lie inside, stacked along the axis. The strands are antiparallel nucleic acid strands. The flattened base pairing ladder above displays partners and direction; winding that ladder into a helix adds spatial organization. RNA can also form double-helical paired regions, so the geometry is not exclusive to DNA. See Alberts et al., Molecular Biology of the Cell: DNA structure.

The useful surprise is that a structure explains a copying principle. Complementary base pairs allow each DNA strand to specify the other's nucleic acid sequence; separate strands can each act as templates in DNA replication. This is a structural constraint, while the enzymes and stages of DNA replication supply the actual process. A nucleic acid sequence specifies letter order without, by itself, giving every detail of the three-dimensional helix.

On 25 April 1953, James Watson and Francis Crick published a model with two oppositely directed chains, outside phosphate groups, and specific base pairs. Their short paper explicitly connected this pairing to a possible copying mechanism, while describing the model as requiring further experimental tests. See the original ^[ref], with an accessible ^[ref].

Rosalind Franklin and Raymond Gosling's paper in the same issue had a different role: it presented X-ray diffraction evidence from DNA fibres and its structural interpretation, including the helical character of the wetter B form and evidence for phosphate groups on the outside. They distinguished forms produced at different water contents and assessed compatibility with the Watson–Crick model. Read their original ^[ref]. The model and the experimental analysis are distinct contributions; a diffraction pattern is evidence constraining a molecular geometry, rather than a direct picture of letter-by-letter base pairing.

A nucleic acid sequence records the ordered nucleobases of a nucleic acid strand, conventionally read from $5^{\prime }$ to $3^{\prime }$. The standard DNA alphabet is adenine A, cytosine C, guanine G, and thymine T; the standard RNA alphabet uses uracil U in place of thymine T. Each letter denotes the nucleobase attached to one nucleotide, so the six-letter DNA nucleic acid sequence $5^{\prime }\text{-}\mathrm{ACGTAC}\text{-}{3}^{\prime }$ describes six linked nucleotides. See NHGRI: representing DNA by a sequence of letters.

Order carries information that composition loses. Both ACGTAC and AACCGT contain two adenine, two cytosine, one guanine, and one thymine nucleobase, but their nucleic acid sequences differ at positions 2, 3, 4, 5, and 6. At position 2, for example, the first has cytosine and the second adenine. Reporting only the four counts cannot reconstruct either ordered record.

To obtain the partner of $5^{\prime }\text{-}\mathrm{ACGTAC}\text{-}{3}^{\prime }$, apply the DNA base pairing rules position by position: A selects T, C selects G, G selects C, T selects A, A selects T, and C selects G. Alignment gives $3^{\prime }\text{-}\mathrm{TGCATG}\text{-}{5}^{\prime }$. Its opposite end labels matter because the two are antiparallel nucleic acid strands. Reading the partner from its own $5^{\prime }$ end reverses the aligned lettering and yields the reverse complement, $5^{\prime }\text{-}\mathrm{GTACGT}\text{-}{3}^{\prime }$.

Reversal alone gives CATGCA; complementation alone gives aligned TGCATG. Neither operation alone gives the partner written in the usual $5^{\prime }$-to-$3^{\prime }$ convention. Applying the reverse complement operation twice returns ACGTAC: GTACGT complements to CATGCA, which reverses to ACGTAC. This convention makes a single reported strand sufficient to specify an ideally complementary DNA duplex, provided its direction is known.

A phosphodiester bond connects two groups through a phosphate diester. In a nucleic acid backbone, the bridging phosphate is connected through oxygen to the $3^{\prime }$ carbon position of one sugar and the $5^{\prime }$ carbon position of another. These covalent bonds connect successive nucleotides along a strand; they are distinct from the hydrogen bonds between paired nucleobases.