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 biology
1. A real-time FRET-based biochemical assay for DNA deaminase enzymology and inhibition
Hideki Aihara
2. DEER spectroscopy to probe DNA wrapping by protein complexes
Edwin Antony
3. PAR-dCLIP: Enhancing PhotoActivatable Ribonucleoside analog-enhanced CrossLinking and Immunoprecipitation through capture of bound 5’ terminal RNA fragments
Manuel Ascano
4. Site-specific targeting of transgene cDNA insertion
Kathleen collins
5. Simultaneous Profiling of the RNA Targets of Two RNA-Binding Proteins Using TRIBE-STAMP
Mathieu Flamand
6. Ensemble FRET Approach to Directly and Continuously Monitor Protein?DNA Interactions
Mark Hedglin
7. Utilizing nuclear extracts to characterize protein-DNA interactions at the single-molecule level
Bennett Van Houten
8. RNA-Guided Protease Activation in CRISPR-Cas
Ailong Ke
9. Activity-based profiling of RNA modifying enzymes
Ralph Kleiner
10. Purification of Cas9 and Cas12a for Peptide-Assisted Genome Editing
Rahul M. Kohli
11. Studying the intersection of nucleoside modifications and SARS-CoV-2 RNA-dependent RNA transcription using an in vitro reconstituted system
Kristin Koutmou
12. Measuring protein stoichiometry with single-molecule imaging in cell-free extracts
Joseph Loparo
13. Simultaneous probing of transcription, G-quadruplex, and R-loop
Sua Myong
14. A user guide to RT-based mapping of RNA modifications
Sigrid Nachtergaele
15. AP Endonuclease 1: Biological updates and advances in activity analysis
Robert W. Sobol
16. Strand-specific PCR-competitive replication and adduct bypass assay for assessing how DNA adducts perturb DNA replication in mammalian cells
Yinsheng Wang
17. Expression, purification, and biochemical analysis of the RNA-DNA Hybrid Helicase Sen1/SETX from Chaetomium thermophilum
R. Scott Williams