These findings are consistent with the published structural models for these riboswitches and suggest that large modifications at various positions on the ligand can be made to create novel compounds that target c-di-GMP riboswitches. Moreover, we demonstrate the potential of an engineered allosteric most ribozyme for the rapid screening of chemical libraries for compounds that bind c-di-GMP riboswitches.
The proteasome is the degradation machine at the center of the ubiquitin-proteasome system and controls the concentrations Inhibitors,Modulators,Libraries of many proteins in eukaryotes. It is highly processive so that substrates are degraded completely into small peptides, avoiding the formation of potentially toxic fragments. Nonetheless, some proteins are incompletely degraded, indicating the existence of factors that influence proteasomal processivity.
We have quantified proteasomal processivity Inhibitors,Modulators,Libraries and determined the underlying rates of substrate degradation and release. We find that processivity increases with species complexity over a 5-fold range between yeast and mammalian proteasome, and the effect is due to slower but more persistent degradation by proteasomes from more complex organisms. A sequence stretch that has been implicated in causing incomplete degradation, Inhibitors,Modulators,Libraries the glycine-rich region of the NF kappa B subunit p105, reduces the proteasome’s ability to unfold its substrate, Inhibitors,Modulators,Libraries and polyglutamine repeats such as found in Huntington’s disease reduce the processivity of the proteasome in a length-dependent manner.
Understanding the interactions between small interfering RNAs (siRNAs) and the RNA-induced silencing complex (RISC), the key protein complex of RNA interference (RNAi), is of great importance to the development Drug_discovery of siRNAs with improved biological and potentially therapeutic function. Although various chemically modified siRNAs have been reported, relatively few studies with modified nucleobases exist. Here we describe the synthesis and hybridization properties of siRNAs bearing size-expanded RNA (xRNA) nucleobases and their use as a novel and systematic set of steric probes in RNAi. xRNA nucleobases are expanded by 2.4 angstrom using benzo-homologation and retain canonical Watson-Crick base-pairing groups. Our data show that the modified siRNA duplexes display small changes in melting temperature (+1.4 to -5.
0 degrees C); substitutions near the center are somewhat destabilizing to the RNA duplex, selleck Trichostatin A while substitutions near the ends are stabilizing. RNAi studies in a dual-reporter luciferase assay in HeLa cells revealed that xRNA nucleobases in the antisense strand reduce activity at some central positions near the seed region but are generally well tolerated near the ends. Most importantly, we observed that xRNA substitutions near the 3′-end increased activity over that of wild-type siRNAs. The data are analyzed in terms of site-dependent steric effects in RISC.