doi: bioRxiv preprint their components rapidly with the surrounding medium (Hyman et al., 2014;. Most of the liquid condensates possess common characteristics, which include their formation mechanism as well as their physical properties. For instance, multivalent proteins or nucleic acids associate through weak intermolecular interactions and reach a solubility limit to form liquid condensates (Banani et al., 2017;. These condensates are highly mobile, spherical, but get deformed on physical contact, fuse and eventually relax back to their spherical shape (Brangwynne et al., 2009;Brangwynne et al., 2011;Molliex et al., 2015;Nott et al., 2015). Several proteins undergoing LLPS, however, contain intrinsically disordered regions (IDRs) that are closely associated with prion-like domains (PLDs) and low complexity domains (LCDs) (

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 Tm 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.

G-quadruplexes are non-canonical secondary structures found in guanine rich regions of DNA and RNA. Reports have indicated the wide occurrence of RNA G-quadruplexes across the transcriptome in various regions of mRNAs and non-coding RNAs. RNA G-quadruplexes have been implicated in playing an important role in translational regulation, mRNA processing events and maintenance of chromosomal end integrity. In this review, we summarize the structural and functional aspects of RNA G-quadruplexes with emphasis on recent progress to understand the protein/trans factors binding these motifs. With the revelation of the importance of these secondary structures as regulatory modules in biology, we have also evaluated the various advancements towards targeting these structures and the challenges associated with them. Apart from this, numerous potential applications of this secondary motif have also been discussed.

Biological role for existence of overlapping structures in RNA is possible yet remains very less explored. G-rich tracts of RNA form G-quadruplexes while GC-rich sequences prefer stem-loop structures. Equilibrium between alternate structures within RNA may occur and influence its functionality. We tested equilibrium between G-quadruplex and stem-loop structure in RNA and its effect on biological processes using pre-miRNA as a model system. Dicer enzyme recognizes canonical stem-loop structures in pre-miRNA to produce mature miRNAs. Deviation from stemloop leads to deregulated mature miRNA levels, providing readout of existence of alternate structure per se G-quadruplex mediated structural interference in miRNA maturation. In vitro analysis using beacon and Dicer cleavage assays indicated that mature miRNA levels depend on relative amounts of K + and Mg 2+ ions suggesting an ion-dependent structural shift. Further in cellulo studies with and without TmPyP 4 (RNA G-quadruplex destabilizer) demonstrated that miRNA biogenesis is modulated by G-quadruplex-stem-loop equilibrium in a subset of premiRNAs. Our combined analysis thus provides evidence for formation of non-canonical Gquadruplexes in competition with canonical stem-loop structure inside the cell and its effect on miRNA maturation in a comprehensive manner.