Frameshifting is an essential process that regulates protein synthesis in many viruses. The ribosome may slip backward when encountering a frameshift motif on the messenger RNA, which usually contains a pseudoknot structure involving tertiary base pair interactions. Due to the lack of detailed molecular explanations, previous studies investigating which features of the pseudoknot are important to stimulate frameshifting have presented diverse conclusions. Here we constructed a bimolecular pseudoknot to dissect the interior tertiary base pairs and used single-molecule approaches to assess the structure targeted by ribosomes. We found that the first ribosome target stem was resistant to unwinding when the neighboring loop was confined along the stem; such constrained conformation was dependent on the presence of consecutive adenosines in this loop. Mutations that disrupted the distal base triples abolished all remaining tertiary base pairs. Changes in frameshifting efficiency correlated with the stem unwinding resistance. Our results demonstrate that various tertiary base pairs are coordinated inside a highly efficient frameshift-stimulating RNA pseudoknot and suggest a mechanism by which mechanical resistance of the pseudoknot may persistently act on translocating ribosomes.

We present a long period grating sensor fabricated in a large mode area photonic crystal fiber. This device is insensitive to temperature change but highly sensitive to refractive index variation (167.5 nm/RI or 2.57×10 -4 limiting resolution).

We report a photonic crystal fiber (PCF) interferometer was realized by fusion splicing a short section of PCF between two standard single mode fibers (Corning SMF-28) using a Fitel-S175 splicer. The fully collapsed air holes of the PCF at the spice regions allow the coupling of PCF core and cladding modes. The transmission spectrum exhibits sinusoidal interference pattern which shifts differently when the cladding/core surface of the PCF is immersed with different RI of the surrounding medium. The results for different concentrations of sucrose solution show that a resolution of 1.21×10 -4 -4.65×10 -4 RIU is achieved for refractive indices in the range of 1.333 to 1.403, suggesting that the PCF interferometer are attractive for chemical, biological, and biochemical sensing with aqueous solutions.