A nucleotide is made of three parts: a nitrogenous base — a purine (adenine A, guanine G: two fused rings) or a pyrimidine (cytosine C, thymine T, uracil U: one ring); a five-carbon sugar, ribose in RNA or 2′-deoxyribose in DNA (lacking the hydroxyl on carbon 2′); and one to three phosphate groups on the sugar’s carbon 5′. The base is attached to carbon 1′; the sugar carbons are numbered with primes to distinguish them from the base’s. Base plus sugar is a nucleoside (adenosine, guanosine, cytidine, thymidine, uridine); with phosphates it is a nucleotide (AMP, ADP, ATP and their kin).
Examples
Example 11.4 (RNA is fragile, DNA is durable)
The 2′ hydroxyl of ribose can attack the neighbouring phosphodiester bond: in mild alkali RNA is hydrolysed to nucleotides within hours, while DNA, lacking that hydroxyl, survives boiling in alkali and has been recovered intact from bones tens of thousands of years old. Uracil in RNA is thymine without a methyl group; DNA uses thymine so that cytosine, which slowly loses its amino group to become uracil, can be recognised as damaged and repaired — a uracil in DNA is always a mistake.
Example 11.7 (Reading a strand)
If one strand reads 5′-ATGGCATTC-3′, its partner, written 5′→3′, is 5′-GAATGCCAT-3′: complement each base, then reverse the order. Nine pairs, 3.1nm of helix, twenty-two hydrogen bonds (five G–C, four A–T). A human chromosome of 2.5×108 pairs is 8.5cm long in this form and must be folded a hundred thousand times to fit a nucleus (Chapter 17).
Example 11.11 (A probe finds a gene)
A twenty-nucleotide probe complementary to one gene, at 5∘C below its own Tm, binds its exact complement and nothing else in three billion base pairs: a single mismatch in twenty lowers Tm by several degrees and the mismatched hybrid melts. The specificity of base pairing, multiplied over twenty positions, is what every DNA test, from paternity to pathogen detection, relies on.
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