Chemical and Genomic Methods in Nucleic Acid Biology

Dr. Eichman is a Professor of Biological Sciences and Biochemistry at Vanderbilt University, where his laboratory investigates the structural mechanisms of protein machines involved in maintenance of genome integrity. Professor Eichman was initially trained as a synthetic organic chemist at the University of Mississippi (B.S., Chemistry, 1993). He received his Ph.D. in Biochemistry and Biophysics in 2000 from Oregon State University, where he used X-ray crystallography to study the effects of crosslinking agents on DNA structure and determined the landmark structure of the Holliday junction, the four-stranded DNA intermediate formed during genetic recombination. As an NIH postdoctoral fellow from 2000-2004 with Tom Ellenberger at Harvard Medical School, Eichman studied the structural enzymology of DNA repair and replication proteins. Current projects in the Eichman lab focus on base excision repair of DNA alkylation damage and restart of stalled replication forks during the DNA damage response. Dr. Eichman holds the 2009 Young Investigator Award from the Sigma Xi Scientific Research Society, the Vanderbilt Chancellor’s Award for Research, two Vanderbilt-Ingram Cancer Center Impact Awards, and in 2013 became a member of the Faculty of 1000. Eichman teaches introductory and advanced undergraduate biochemistry and serves as the co-Director of the Vanderbilt Undergraduate Program in Biochemistry and Chemical 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