The
loop length, loop composition, salt concentration, and number of G-quartets
are major determinants of G-quadruplex stability. We examined the
effect of each of these factors on the thermal stability and folding
topology of a library of RNA quadruplexes. The thermal stability of
G2 and G3 RNA quadruplexes was investigated upon varying the loop
length (from 1-1-1 to 15-15-15) and salt concentration (from 1 to
100 mM KCl), while the effect of loop composition was explored using
18 naturally occurring potential RNA quadruplexes predicted in untranslated
regions (UTRs). We found loop length and quadruplex stability to be
inversely related for G2 RNA quadruplexes and G3 RNA quadruplexes
with shorter loops. However, melting temperature saturates for G3
RNA quadruplexes with longer loops. RNA G-quadruplexes with longer
loops (G3 15-15-15) displayed <i>T</i><sub>m</sub> values
significantly higher than the physiological temperature. This study
thus highlights the need to modify the consensus motif presently used
by quadruplex prediction tools. An increase in the loop size from
7 bases to 15 bases in the consensus motif will add to its predictive
value for the discovery of potential RNA quadruplexes across transcriptomes