Expression of the information in DNA is mediated by RNA

Genetic expression always involves the synthesis of another nucleic acid polymer called ribonucleic acid (RNA) that is composed of four nucleotide monomers – the monophosphates of adenosine (AMP), guanosine (GMP), cytidine (CMP), and uridine (UMP) (Fig. 2.1). These all contain the sugar ribose instead of deoxyribose found in DNA, and the individual nucleotides are linked together through 3′-, 5′-phosphodiester bridges, just as in DNA. Uracil, which is present rather than thymine, lacks the methyl group of the latter base. RNA is generally single-stranded, though its bases can pair by hydrogen bonding to give hairpin-like or stem structures (Fig. 2.2). Guanine occasionally pairs with uracil, though this pairing is less stable than the more usual A–U and G–C pairs. RNA molecules are much smaller than DNA molecules, and only comparatively short stretches of DNA are used to direct the synthesis of individual RNAs.

The stability of stem structures can be calculated in terms of the energy required to open them up. To a first approximation, this is the sum of the energies needed to break the individual hydrogen bonds in the base-pairs in the stem, but they have to be considered in adjacent pairs because there is considerable dependence on neighbouring bases. An allowance also has to be made for loops at the end of a stem and for bulges in the stem if there are bases that are not paired with bases on the opposite side.