is now possible to predict double-helical sections by computer analysis of primary sequence data, and this
technique has been used extensively to identify secondary structural components of ribosomal RNA and
viral RNA species. In this section, we shall focus attention mainly on regular RNA secondary structure.
2.4.1 Primary Structure of RNA
The first degradation studies of RNA using mild alkaline hydrolysis gave a mixture of mono-nucleotides,
originally thought to have only four components – one for each base, A, C, G and U. However, Waldo
Cohn used ion-exchange chromatography to separate each of these four into pairs of isomers, which were
identified as the ribonucleoside 2- and 3-phosphates. This duplicity was overcome by Dan Brown’s use
of a phosphate diesterase isolated from spleen tissue which digests RNA from its 5-end to give the four
3 -phosphates Ap, Cp, Gp and Up, while an internal diesterase (snake venom phosphate diesterase was
used later) cleaved RNA to the four 5-phosphates, pA, pC, pG and pU. It follows that RNA chains are
made up of nucleotides that have 3→ 5 -phosphate diester linkages just like DNA (Figure 2.38).
The 3→ 5 linkage in RNA is, in fact, thermodynamically less stable than the ‘unnatural’ 2→ 5 linkage,
which might therefore have had an evolutionary role. A rare example of such a polymer is produced in ver-
tebrate cells in response to viral infection. Such cells make a glycoprotein called interferon, which stimu-
lates the production of an oligonucleotide synthetase. This polymerises ATP to give oligoadenylates with
2 → 5 phosphate diester linkages and from 3 to 8 nucleotides long. Such (2→ 5 ) (A)n(Figure 2.39) then
activates an interferon-induced ribonuclease, RNase L, whose function seems to be to break down the viral
messenger RNA (Note also the 2→ 5 ester linkage is a key feature of self-splicing RNA (Section 7.2.2)).
56 Chapter 2
Figure 2.37 Structure of the anti-parallel duplex observed in the crystal structure of d(ATATAT) which displays
Hoogsteen pairing between adenine and thymine bases (PDB: 1GQU). The view is across the major
(right) and minor (left) grooves. Atoms are coloured green, red, blue and magenta for carbon, oxygen,
nitrogen and phosphorus, respectively, and base planes of A and T are filled yellow and blue, respectively