Small molecule chaperones facilitate the folding of long-non coding RNA

RNA G-quadruplexes (rG4) have recently emerged as major regulatory elements in both mRNA and non-coding RNA. To investigate the biological roles of the rG4 structures, chemists have developed a variety of highly specific and potent ligands. All these ligands bind to the rG4 by staking on their top, and the specificity of binding is demonstrated in comparison to other structures such as duplex or three-way junctions. It remains unclear whether rG4-ligands merely stabilize fully formed rG4 structures, or if they actively participate in the folding of the rG4 structure through their association with an unfolded RNA sequence. In order to access the innate steps of ligand-rG4 association and mechanisms, robust in vitro techniques, including FRET, electrophoretic mobility shift assay and reverse transcriptase stalling assays, were used to examine the capacity of five well-known G4 ligands to induce rG4 structures derived from either long non-coding RNAs of from synthetic RNAs. It was found that both PhenDC3 and PDS induce rG4 formation in unfolded single RNA strands. This discovery has important implications for the interpretation of RNA-seq experiments. Overall, in vitro data that can assist biochemists in selecting the optimal G4-ligands for their RNA cellular experiments are presented, while also considering the effects induced by these ligands of the rG4. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC="FIGDIR/small/535601v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@ec5191org.highwire.dtl.DTLVardef@df26ddorg.highwire.dtl.DTLVardef@707dc5org.highwire.dtl.DTLVardef@15117ea_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstractA schematic representation of the potential structures that may arise from unfolded RNA that is rich in G nucleotides. rG4 can be stabilized by K+ either with or without G4 ligand and can be induced by a molecular chaperone in the presence of Li+.