Intrinsic flexibility of snRNA hairpin loops facilitates protein binding

Abstract

Stem-loop II of U1 snRNA and Stem-loop IV of U2 snRNA typically have 10 or 11 nucleotides in their loops. The fluorescent nucleobase 2-aminopurine was used as a substitute for the adenines in each loop to probe the local and global structures and dynamics of these unusually long loops. Using steady-state and time-resolved fluorescence, we find that, while the bases in the loops are stacked, they are able to undergo significant local motion on the picosecond/nanosecond timescale. In addition, the loops have a global conformational change at low temperatures that occurs on the microsecond timescale, as determined using laser T-jump experiments. Nucleobase and loop motions are present at temperatures far below the melting temperature of the hairpin stem, which may facilitate the conformational change required for specific protein binding to these RNA loops.

Host miRNA degradation by Herpesvirus saimiri small nuclear RNA requires an unstructured interacting region

“…Interestingly, it has been reported that intrinsic dynamism of snRNA hairpin loops facilitates protein binding (Rau et al 2012). Thus, it seems likely that structural flexibility occurring within the central hairpin region of HSUR1 may also facilitate interaction with Argonaute-loaded miR-27.…”

Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps

“…Further, the stem loops of the U12 snRNA might help in binding of SF3b proteins such as SF3b145. 101 The three RNA-binding proteins p14, SF3b49 and SF3b145 face the inner layer of SF3b155 HEAT repeats in the SF3b complex. Hence, it is likely that the binding of the U12 snRNA, coupled with the phosphorylation of the partly disordered protein SF3b155, 28 acts as a trigger for the SF3b to undergo such a huge conformational change during its integration into the U11/U12 complex.…”

Determination of the secondary structure of group II bulge loops using the fluorescent probe 2-aminopurine

“…The fluorescence of 2-AP is sensitive to its local environment (Menger et al 2000;Ballin et al 2007;Sarkar et al 2010;Rau et al 2012). The change in fluorescence with temperature has been used to examine the change in local structure as a molecule denatures.…”

“…The change in fluorescence with temperature has been used to examine the change in local structure as a molecule denatures. Typically, when a basepaired 2-AP base denatures, the fluorescence intensity of the base increases due to the decrease in stacking of the base with its neighbors; conversely, an unpaired 2-AP base decreases its fluorescence as it denatures due to increased interactions with its neighbors in the single-stranded form (Menger et al 2000;Jiao et al 2002;Hardman and Thompson 2006;Ballin et al 2007;Sarkar et al 2009Sarkar et al , 2010Rau et al 2012;). The major goal of this study was to use the change in 2-AP fluorescence to investigate the structural ambiguity of the group II single nucleotide bulge loops.…”

“…In addition to local environment, the fluorescence of 2-AP is strongly influenced by temperature (Menger et al 2000;Ballin et al 2007;Sarkar et al 2010;Rau et al 2012). Therefore, to accurately use 2-AP fluorescence to monitor the structural changes, fluorescent measurements for the 2-AP labeled RNA hairpins were corrected for the fluorescence of a five nucleotide short strand of RNA that was analogous to the region of the RNA hairpin where the 2-AP was inserted (Ballin et al 2007).…”