Chemical and Genomic Methods in Nucleic Acid Biology

MIE 704: Chemical and genomic methods in nucleic acid biology1. A real-time FRET-based biochemical assay for DNA deaminase enzymology and inhibitionHideki Aihara2. DEER spectroscopy to probe DNA wrapping by protein complexesEdwin Antony3. PAR-dCLIP: Enhancing PhotoActivatable Ribonucleoside analog-enhanced CrossLinking and Immunoprecipitation through capture of bound 5' terminal RNA fragmentsManuel Ascano4. Site-specific targeting of transgene cDNA insertionKathleen collins5. Simultaneous Profiling of the RNA Targets of Two RNA-Binding Proteins Using TRIBE-STAMPMathieu Flamand6. Ensemble FRET Approach to Directly and Continuously Monitor Protein?DNA InteractionsMark Hedglin7. Utilizing nuclear extracts to characterize protein-DNA interactions at the single-molecule levelBennett Van Houten8. RNA-Guided Protease Activation in CRISPR-CasAilong Ke9. Activity-based profiling of RNA modifying enzymesRalph Kleiner10. Purification of Cas9 and Cas12a for Peptide-Assisted Genome EditingRahul M. Kohli11. Studying the intersection of nucleoside modifications and SARS-CoV-2 RNA-dependent RNA transcription using an in vitro reconstituted systemKristin Koutmou12. Measuring protein stoichiometry with single-molecule imaging in cell-free extractsJoseph Loparo13. Simultaneous probing of transcription, G-quadruplex, and R-loopSua Myong14. A user guide to RT-based mapping of RNA modificationsSigrid Nachtergaele15. AP Endonuclease 1: Biological updates and advances in activity analysisRobert W. Sobol16. Strand-specific PCR-competitive replication and adduct bypass assay for assessing how DNA adducts perturb DNA replication in mammalian cellsYinsheng Wang17. Expression, purification, and biochemical analysis of the RNA-DNA Hybrid Helicase Sen1/SETX from Chaetomium thermophilumR. Scott Williams