suggests that there is probably a high level of order in such loops, notably of base-stacking and base-triples.
One general opinion is that the major differences between loop and stem regions are dynamic rather than
structural.
Junctionsare regions that connect three or more stems (the connecting region for two stems is an internal
loop) and are a common feature of computer-generated secondary structures for large RNAs. A prime
example is the four-stem junction in the cloverleaf structure of tRNAs in which stacking continuity
between the acceptor and the T stems and between the anti-codon and D stems is maintained (Section
7.1.4).^62 A junction of three stems forms the hammerhead structure of self-cleaving RNA (Section 7.6.2)
and junctions of up to five stems have been observed for 16S RNA.
62 Chapter 2
Figure 2.41 A possible secondary structure for a 55-nucleotide fragment from R17 virus which illustrates hairpin
loop, interior loop and bulge structures. The free energy of this structure has been calculated to have a
net GĀ° of ā90 kJ mol^1 using appropriate values for base pairs (Table 2.6) and for loops and bulges