Modeling the secondary structure of eukaryotic mRNA untranslated regions
Current Projects
Mapping the locations of RNA-protein interactions on regulatory regions of mRNAs
Investigating the effect of cellular stress on RNA structure and interactions
RNA Biology
Researchers in our group develop hands-on expertise in extraction, purification, quantitation, and modification of RNA molecules.
Cell Culture
We work with human cell lines utilizing sterile technique and working in biosafety cabinets.
Next-Generation Sequencing (NGS)
We utilize massively paralleled sequencing strategies to read-out RNA chemical probing experiments. We use the Illumina iSeq platform for in-house NGS and Illumina MiSeq via core facilities. To validate molecular clones, we apply the whole-plasmid sequencing workflow using the Oxford Nanopore MinION.
High-Performance Computing
NGS data is processed and analyzed using rigorously validated open-source software for RNA structure modeling and comparisons. We use the System76 THELIO Mega R1 Linux workstation for local computation. Additionally, we have remote access to KSU HPC core facility.
Molecular Cloning
We use recombinant DNA technologies such as NEB HiFi and Gibson Assembly to generate constructs to validate structural investigations.
Reporter Assays and Western Blotting
As orthogonal strategies to validate regulatory functions of RNA regions of interest, we utilize dual-luciferase assays, after in vitro mRNA transcription and mRNA lipofection into human cell lines. We use Western blotting to measure cellular levels of translated proteins.