DNA Nucleotides and the Double Helix

The chemical building blocks of genetic information

A cell passes information across generations using the order of chemical subunits in nucleic acids. DNA is a polymer of deoxyribonucleotides; its sequence can encode functional RNA molecules and, through RNA, protein sequences. A nucleotide has a five-carbon sugar, a nitrogen-containing base and one or more phosphate groups. DNA contains deoxyribose, which lacks the 2′-hydroxyl group of ribose in RNA. Adenine (A) and guanine (G) are two-ring purines; cytosine (C) and thymine (T) are one-ring pyrimidines. RNA normally uses uracil (U) in place of thymine.

A base joined to the sugar by an N-glycosidic bond is a nucleoside. Adding phosphate makes a nucleotide. Thus adenine is a base, adenosine is a ribose-containing nucleoside, and adenosine monophosphate is a nucleotide. The sugar's carbons are numbered 1′ to 5′ so they cannot be confused with positions on the nitrogenous base. The base attaches at 1′, phosphate typically occupies 5′, and an available 3′-hydroxyl enables chain extension.

Phosphodiester bonds and strand direction

When nucleotides join, a phosphodiester linkage connects the 3′ oxygen of one sugar to a phosphate associated with the next nucleotide's 5′ carbon. Repeating sugar and phosphate groups form a relatively uniform backbone, while different bases extend from it and carry sequence information. The chain has chemical polarity: a 5′ end and a 3′ end. Scientists therefore write sequences in the 5′→3′ direction unless stated otherwise. Reversing the written order without reversing strand orientation changes the represented sequence.

A DNA sequence does not physically consist of isolated letters. Letters are a convenient symbolic code for ordered molecular structures. Likewise, the hydrogen bonds between paired bases do not join adjacent nucleotides along one chain; those covalent phosphodiester bonds are stronger backbone connections. Distinguishing bonds within a strand from interactions between strands prevents a frequent misunderstanding of DNA structure.

How two strands form a double helix

Watson and Crick's model, informed by structural evidence and Chargaff's observations, describes two antiparallel polynucleotide chains coiled into a predominantly right-handed double helix. One strand runs 5′→3′ while its partner runs 3′→5′ when read in the same spatial direction. A pairs with T through two hydrogen bonds and G pairs with C through three. Pairing one purine with one pyrimidine helps maintain a nearly uniform helix width. Complementarity means that knowing the sequence and orientation of one strand determines the paired sequence and orientation of the other.

Base pairs are stacked along the helix; stacking interactions make a major contribution to helix stability in addition to hydrogen bonding. Typical B-form DNA has about 10–10.5 base pairs per helical turn and adjacent pairs about 0.34 nm apart. For simple calculations the chapter uses 10 pairs per turn and 3.4 nm per turn. These are useful model values, not constants for every DNA conformation.

From complementary structure to reliable copying

Complementarity explains two seemingly different properties: information can be stored as an arbitrary order of bases, yet that information can also be copied. If a template reads 3′-TACG-5′, its complementary product reads 5′-AUGC-3′ during RNA transcription or 5′-ATGC-3′ in DNA synthesis. The difference is U in RNA versus T in DNA. The base-pairing rules do not make every DNA molecule identical: differences in the sequence of paired bases carry the distinct instructions of different genes.

In a double-stranded molecule, the numbers of A and T are equal and the numbers of G and C are equal, assuming canonical Watson–Crick pairs. If cytosine contributes 20% of all bases, guanine also contributes 20%; the remaining 60% is equally divided between adenine and thymine, so A = 30%. These percentages describe both strands combined, not necessarily one isolated strand.

Why molecular structure matters for copying

The 5′ end of a polynucleotide is chemically different from its 3′ end, so a nucleotide sequence has direction as well as content. During replication, a polymerase must position the incoming deoxyribonucleoside triphosphate next to the growing chain's 3′-OH. The energy associated with breaking the incoming nucleotide's triphosphate bonds drives a new phosphodiester linkage. This is why writing only the letters A, T, G and C is not sufficient for reasoning about a replication fork: one must also show which end is available for extension. The same polarity convention underlies transcription and codon recognition later in the chapter.

The bases in the double helix face inward, with relatively hydrophilic sugar–phosphate backbones exposed to the surrounding water. Complementary pairing and stacking stabilise the paired structure. A purine–purine pair would be too wide, whereas a pyrimidine–pyrimidine pair would be too narrow for the usual geometry. Pairing a purine and a pyrimidine explains why base pairs are similar in width even though their sequences differ. Local DNA structure is not an absolutely rigid ladder: grooves, sequence-dependent flexibility and supercoiling contribute to how proteins recognise particular regions of DNA.

How the double-helix model emerged

Friedrich Miescher isolated a phosphorus-rich material from cell nuclei in 1869 and called it nuclein. Decades later, the chemical constituents of nucleic acids were clarified, but a reliable three-dimensional model remained elusive. X-ray diffraction evidence produced by Rosalind Franklin and Maurice Wilkins, together with Chargaff's quantitative base relationships, constrained the structural possibilities. In 1953, Watson and Crick proposed a complementary, antiparallel double-helix model capable of explaining copying. Distinguishing observation from model is important: X-ray patterns and base ratios were evidence, whereas antiparallel complementary helical structure was the proposed explanation that subsequently gained extensive support.

DNA lengths vary enormously among biological systems. The small bacteriophage φX174 has a single-stranded DNA genome of 5,386 nucleotides, whereas bacteriophage λ contains about 48,502 base pairs of double-stranded DNA. A typical E. coli chromosome contains roughly 4.6 million base pairs, and the haploid human nuclear genome contains approximately 3.1–3.3 billion base pairs, depending on the reference and the measurement. A 'nucleotide count' and a 'base-pair count' are not identical units: base pairs count paired positions in double-stranded DNA, while nucleotide count can describe a single strand. This difference matters when comparing genome sizes.

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