Reckoning / Code of life / Bases and pairing
Code of life · the letters
Bases and pairing
Each letter of DNA is a base, a flat ring of carbon and nitrogen. Two are double rings, the purines adenine and guanine; two are single rings, the pyrimidines cytosine and thymine. RNA uses uracil in place of thymine. The edges of the bases carry hydrogen atoms and lone pairs placed so that A fits only T and G fits only C.
Skeletal formulas: each corner without a letter is a carbon atom, and hydrogens on carbon are not drawn. Small numbers are the standard ring numbering. Blue: nitrogen; red: oxygen. Checked when the site is built: counting the drawn atoms and filling each one’s valence with hydrogen gives the molecular formula in the table.
| Base | Ring | Formula | Groups | In | |
|---|---|---|---|---|---|
| A | Adenine | purine | C₅H₅N₅ | amino group on C6 | DNA and RNA |
| G | Guanine | purine | C₅H₅N₅O | C6=O (keto), amino group on C2 | DNA and RNA |
| C | Cytosine | pyrimidine | C₄H₅N₃O | amino group on C4, C2=O | DNA and RNA |
| T | Thymine | pyrimidine | C₅H₆N₂O₂ | C2=O, C4=O, methyl group on C5 | DNA |
| U | Uracil | pyrimidine | C₄H₄N₂O₂ | C2=O, C4=O | RNA |
The pairs
Red dashes are hydrogen bonds: a hydrogen on one base held by a nitrogen or oxygen on the other. A·T makes two, G·C makes three, so DNA rich in G and C holds its strands together more firmly and needs more heat to separate. The bonds to the sugars (bottom left and bottom right) lie the same distance apart in both pairs. Because of this, either pair fits the same helix, and the sequence can be anything at all. This was the key observation of Watson & Crick 1953.
The nucleotide
A nucleotide is a base on a sugar (deoxyribose in DNA, ribose in RNA) with a phosphate. The sugar’s carbons are numbered with primes: the phosphate hangs on 5′ and links to the 3′ carbon of the next sugar, so every strand has a direction, written 5′ → 3′. The two strands of a double helix run in opposite directions, which is why the partner of a sequence is read backwards: its reverse complement.
Chargaff found in 1950 that DNA contains as much A as T and as much G as C, without knowing why. The answer was the pairing above (1953). The bases were drawn for years in other tautomeric forms, with hydrogens in different places; Watson and Crick’s model worked only once the keto and amino forms shown here were used.