Fluorescent Molecular Beacons Mimicking RNA Secondary Structures to Study RNA Chaperone Activity

Thermoregulation of virulence genes in bacterial pathogens is essential for environment-to-host transition. However, the mechanisms governing cold adaptation when outside the host remain poorly understood. Here, we found that the production of cold shock proteins CspB and CspC from Staphylococcus aureus is controlled by two paralogous RNA thermoswitches. Through in silico prediction, enzymatic probing and site-directed mutagenesis, we demonstrated that cspB and cspC 5′UTRs adopt alternative RNA structures that shift from one another upon temperature shifts. The open (O) conformation that facilitates mRNA translation is favoured at ambient temperatures (22°C). Conversely, the alternative locked (L) conformation, where the ribosome binding site (RBS) is sequestered in a double-stranded RNA structure, is folded at host-related temperatures (37°C). These structural rearrangements depend on a long RNA hairpin found in the O conformation that sequesters the anti-RBS sequence. Notably, the remaining S. aureus CSP, CspA, may interact with a UUUGUUU motif located in the loop of this long hairpin and favour the folding of the L conformation. This folding represses CspB and CspC production at 37°C. Simultaneous deletion of the cspB/cspC genes or their RNA thermoswitches significantly decreases S. aureus growth rate at ambient temperatures, highlighting the importance of CspB/CspC thermoregulation when S. aureus transitions from the host to the environment.

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A molecular beacon-like Ag nanocluster fluorescence probe for nucleic acid detection

Zhao

Zhang

Lian

et al. 2022

ANAL. SCI.

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We have developed a type of low-cost, label-free silver nanocluster molecular beacon-like fluorescence sensor with a DNA template. To detect target DNA with this probe, we use a hairpin DNA sequence based on a “turn-on” strategy. The transformation of hairpin DNA would visibly influence the formation of Ag nanoclusters, such that the stronger fluorescence will be measured with the solution containing target nucleic acids than that without targets nucleic acids. There is a good liner relationship between the fluorescence and the target DNA concentrations, ranging from 1 to 750 nmol L −1 . Importantly, the detection sensing platform allows down to 1 nmol L −1 , which is much lower than other studies. Graphical abstract

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Fluorescent Molecular Beacons Mimicking RNA Secondary Structures to Study RNA Chaperone Activity

Cited by 3 publications

References 10 publications

Detection of Long Noncoding RNA Expression by Real-Time PCR

Detection of Long Noncoding RNA Expression by Real-Time PCR

RNA thermoswitches modulateStaphylococcus aureusadaptation to ambient temperatures

A molecular beacon-like Ag nanocluster fluorescence probe for nucleic acid detection

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