The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch

<div><p>Riboswitches sense cellular concentrations of small molecules and use this information to adjust synthesis rates of related metabolites. Riboswitches include an aptamer domain to detect the ligand and an expression platform to control gene expression. Previous structural studies of riboswitches largely focused on aptamers, truncating the expression domain to suppress conformational switching. To link ligand/aptamer binding to conformational switching, we constructed models of an S-adenosyl methionine (SAM)-I riboswitch RNA segment incorporating elements of the expression platform, allowing formation of an antiterminator (AT) helix. Using Anton, a computer specially developed for long timescale Molecular Dynamics (MD), we simulated an extended (three microseconds) MD trajectory with SAM bound to a modeled riboswitch RNA segment. Remarkably, we observed a strand migration, converting three base pairs from an antiterminator (AT) helix, characteristic of the transcription ON state, to a P1 helix, characteristic of the OFF state. This conformational switching towards the OFF state is observed only in the presence of SAM. Among seven extended trajectories with three starting structures, the presence of SAM enhances the trend towards the OFF state for two out of three starting structures tested. Our simulation provides a visual demonstration of how a small molecule (<500 MW) binding to a limited surface can trigger a large scale conformational rearrangement in a 40 kDa RNA by perturbing the Free Energy Landscape. Such a mechanism can explain minimal requirements for SAM binding and transcription termination for SAM-I riboswitches previously reported experimentally.</p></div

Hollow Microtube Resonators via Silicon Self-Assembly toward Subattogram Mass Sensing Applications

Fluidic resonators with integrated microchannels (hollow resonators) are attractive for mass, density, and volume measurements of single micro/nanoparticles and cells, yet their widespread use is limited by the complexity of their fabrication. Here we report a simple and cost-effective approach for fabricating hollow microtube resonators. A prestructured silicon wafer is annealed at high temperature under a controlled atmosphere to form self-assembled buried cavities. The interiors of these cavities are oxidized to produce thin oxide tubes, following which the surrounding silicon material is selectively etched away to suspend the oxide tubes. This simple three-step process easily produces hollow microtube resonators. We report another innovation in the capping glass wafer where we integrate fluidic access channels and getter materials along with residual gas suction channels. Combined together, only five photolithographic steps and one bonding step are required to fabricate vacuum-packaged hollow microtube resonators that exhibit quality factors as high as ∼13 000. We take one step further to explore additionally attractive features including the ability to tune the device responsivity, changing the resonator material, and scaling down the resonator size. The resonator wall thickness of ∼120 nm and the channel hydraulic diameter of ∼60 nm are demonstrated solely by conventional microfabrication approaches. The unique characteristics of this new fabrication process facilitate the widespread use of hollow microtube resonators, their translation between diverse research fields, and the production of commercially viable devices