Atul Rangadurai, PhD

- Production and quality control of 250mg of mRNA for internal needs - Optimized IVT protocols to increase capping efficiency of mRNAs - Established protocols for Next-Gen sequencing experiments to quantify transfection efficiency of lipid nanoparticles

- Established protocols for synthesizing RNA oligonucleotides in milligram quantities using in-vitro transcription, and purification using gel electrophoresis and chromatography. Developed protocols to keep equipment used RNAse free owing to concurrent use for protein purification - Coordinated monthly zoom meetings with collaborators in University of Innsbruck, Austria - Expressed and purified proteins (enzymes, kinases, disordered) from over 200 liters of bacterial culture for NMR studies - Optimized sample preparation for studying structure of RNA fragments in protein complexes involved in RNA processing and transport by NMR spectroscopy in 2 months - Peer reviewer for CIHR Doctoral Awards competition for 2 years - Mentored 2 graduate students with lab experiments

- Synthesized DNA and RNA oligonucleotides, including with chemical modifications, using chemical synthesizers and biochemical enzyme based methods - Curated information from over 200 scientific publications for writing a review on NMR experiments for studying structural changes in biomolecules - Wrote Python scripts for numerical simulation, analysis and visualization of NMR data to characterize structural changes in nucleic acids - Developed protocols for performing NMR CEST experiments to study thermodynamics and kinetics of conformational changes in biomolecules, used by other lab members in over five additional projects till date - Lead a team of 3 graduate students to develop method to measure energetics of structural changes in RNA/DNA by UV melting, using 10 fold lesser sample relative to usual methods. Made entire raw data/analyses open source for reproducibility (https://github.com/atulkr93/delta-melt-data/tree/main). - Mined ~6,000 structures deposited in the Protein Data Bank database to analyze structure of mismatched base pairs in RNA and DNA - Performed molecular dynamics simulations of over 50 DNA-protein complexes to understand the impact of mutations on binding - Regularly updated software and hardware for 4 Linux GPU workstations, implemented systems for remote access and automatic data backup - Performed a survey of the genders of speakers invited for talks across departments in the school of medicine, showing systemic disparities in the genders of invitees - Made zoom tutorials for knowledge transfer of NMR experiments to fellow graduate students and postdocs during the pandemic - Maintenance of lab equipment such as UV spectrophotometers and nucleic acid synthesizers

Wrote C++ scripts to analyze MD simulations of DNA nanotubes in order to characterize their mechanical stability and structure.

Wrote scripts in the Nucleic Acid Builder language of the AMBER simulation suite in order to generate starting structures of DNA nanotubes for Molecular Dynamics simulations.