DNA Transcription is a key process that controls gene expression. DNA-dependent RNA polymerases are the primary enzymes that catalyze transcription in all organisms. It is recognized that all stages of transcription, including initiation, elongation, and termination, play essential roles in regulating gene expression. Dissecting initiation, promoter clearance, and elongation processes by determining the rate constants and the energetics of the steps provide the essential framework to understand transcription and its regulation.

Our research is focused on understanding the mechanisms of mitochondrial DNA transcription, which is catalyzed by single subunit class of RNA polymerases analogous to phage T7 RNA polymerase. Using transient state kinetics, CryoEM structures, and fluorescence-based methods, we can measure individual reaction steps and accompanying protein-DNA conformational changes during transcription initiation and elongation. These measurements are combined with computational kinetic modeling that determines the elementary rate constants and identifies rate-limiting steps that regulate transcription as part of the normal cellular process and as therapeutic targets.

Some of the questions that our research addresses are as follows:

• What are the rate-limiting steps of transcription, and how are these regulated by the promoter sequence and transcription factors?
• What is the basis for abortive RNA synthesis during transcription initiation from promoters?
• What are the conformational changes in the RNA polymerase and transcription factors that accompany the growth of RNA/DNA during initial transcription?
• What steps are involved during the transition from initiation to elongation?
• How does the RNA polymerase catalyze DNA strand-displacement RNA synthesis during elongation?