Monitoring structural dynamics of nascent bacterial riboswitches responding to TPP within transcriptional complexes.

High-resolution mapping of RNA structural maturation during Cas9 assembly with ABEL-FRET

This work explored how the guide RNA of CRISPR genome editing system folds and modulates its structural flexibility to carry out the roles required for each assembly state from its unbound apo form to the functional Cas9 RNP state for target DNA cleavage using ABEL-FRET spectroscopy.

Mapping the RNA Chaperone Activity of the Trypanosoma brucei Editosome Using SHAPE-Chemical Probing.

A synthetic biology approach to bacterial transcription initiation: RNA aptamer based in vitro transcription assay for rapidly testing bacterial RNA polymerases, promoters and inhibitors

We present a robust and versatile in vitro transcription (IVT) assay based on an optimized Broccoli RNA aptamer sequence. When paired with the fluorophore DFHBI-1T, this system enables real-time monitoring of multi-round transcription over several hours. To facilitate streamlined promoter analysis, we developed the pIV...

Characterization of RNA Structure Dynamics with Trans-Factors Using Single-Molecule Optical Tweezers.

16S ribosomal RNA modification drives transcript-specific translation efficiency.

It is proposed that MraW modification of 16S rRNA enhances translation efficiency in general, and that specific transcripts have evolved structural features that fine-tune protein levels that may be prevalent in bacteria which exhibit uncoupled transcription and translation.

Massively Parallel In Vitro Functional Analysis of Evolution-Derived Transcriptional Riboswitch Sequences

A high-throughput protocol to characterize the transcriptional activity of nearly 2,000 natural variants of the fluoride riboswitch in in vitro transcription, offering a scalable method for mapping genotype-to-function relationships across transcriptional riboswitch families, accelerating the identification of function...