Stems and Loops

Abstract

The sequence of a single-stranded nucleic acid is referred to as its primary structure. When it forms a duplex by pairing with a complementary singlc strand it adopts a secondary structure. Chargaff’s first parity rule for duplex DNA was consistent with the Watson-Crick idea of a base in one strand of the duplex pairing with a complementary base in the other strand of the duplex (inlerstrand base pairing), thus stabilizing the secondary structure (Fig. 2-1). By the same token, the existence of a parity rule for single strands of nucleic acid (see Chapter 4), suggested intrastrand base pairing. At least by virtue of the composition of the stems in stem-loop secondary structures, there should be approximately equivalent quantities of the classical pairing bases. Do single-stranded nucleic acids have the potential to form such intrastrand secondary structures? If so, is this a chance event, or are adaptive forces involved? These questions began to be addressed when the sequences of various tRNAs and bacterial viruses became available in the 1970s. It became evident that nucleic acid structure (“flaps”) is a form of information that has the potential to conflict with other forms.

“No system consisting of these elements could possibly have the properties that atoms were known to have. ... In Bohr’s paper of 1913 this paradox was met by introducing the notions of stable orbits and jumps between these orbits. ... These were very irrational assumptions, which shocked ... many physicists ....The crucial point ... is the appearance of a conflict between separate areas of experience, which gradually sharpens into a paradox and must then be resolved by a radically new approach.” Max Delbrück (1949) [1]