Transcription

Elongation through transcription factors

Understanding how RNA polymerases transcribe through transcription factors that decorate DNA without interfering with their physiological role is paramount to our understanding of maintenance of transcription regulation. We are particularly interested in roadblocks that alter topology by inducing DNA to wrap, kink or loop. Are these protein-induced DNA topological barriers strong roadblocks? Why, or why not? Using single molecule approaches, we observe E. coli RNAP traverse a protein roadblock, or entering and exiting a loop, and suggest mechanical pathways by which RNAP may do so.

Non canonical transcription termination

We are investigating alternative pathways to canonical termination where RNA polymerase releases the template, lets the DNA substrate go and diffuses in solution.

RNA polymerase I

RNA polymerase I (Pol I) is the eukaryotic polymerase that transcribes the genes that encode ribosomal RNA and is responsible for more than 60% of the cellular transcriptional activity. In collaboration with David Schneider (Univ. of Alabama, Birmingham), we characterized its elongation kinetics.

Topoisomerases

Topoisomerases are crucial in managing the level of DNA supercoiling largely arising from transcriptional activity of RNA polymerases. We study Type II topoisomerases using magnetic tweezers.