# Control of DNA Topology

> **NIH NIH R01** · FLORIDA INTERNATIONAL UNIVERSITY · 2020 · $323,187

## Abstract

Title: “Control of DNA Topology”
PI: Yuk-Ching Tse-Dinh, PhD
Project Summary/Abstract
The long term goals of this project are to understand how the activity, regulation and interactions of DNA
topoisomerases control DNA topology and affect vital cellular functions. Drugs that target type IB and type IIA
topoisomerases are used in current anti-cancer and anti-bacterial therapy. Bacterial type IA topoisomerases
have been validated as a useful target for discovery and development of novel antibacterial therapy to treat
drug resistant bacterial pathogens that cannot be eliminated with current antibiotics, including the antibiotics
that target bacterial topoisomerase II. The proposed research activities for the next funding period would
elucidate the complete catalytic mechanism and provide new insights into the protein-protein interactions and
regulation of Escherichia coli topoisomerase I activity. This information is needed to fully realize the potential
of discovery of novel antibacterial drugs specific for type IA topoisomerases that is present in every bacterial
pathogen as a potential therapeutic target. Topoisomerase I catalyzes the relaxation of negatively supercoiled
DNA by cleaving a single DNA strand in the underwound duplex DNA and passing the complementary DNA
single strand through the break before religation of the cleaved strand to increase the DNA winding. The
molecular mechanism of the large enzyme conformational changes that are required for the coordinated
movement of the passing DNA is the critical barrier for elucidating how bacterial topoisomerase I can relax
negatively supercoiled DNA with high efficiency to prevent hypernegative DNA supercoiling and R-loop
stabilization that can arise during transcription elongation. Structural and biochemical studies will be
conducted to test hypotheses generated from crystal structures obtained in this project on the mechanism of
enzyme DNA conformational change and DNA passage. Interaction sites of endogenous bacterial toxins that
can act as inhibitors of topoisomerase I catalytic activity will be identified. Our preliminary results showed that
deacetylation of topoisomerase I may be an important function of the E. coli deacetylase CobB. Novel
mechanisms of regulation of DNA topology and bacteria growth via acetylation-deacetylation of topoisomerase
I will be investigated. The project will include direct participations of co-Investigators who are experts in
structural biology and single molecule studies of enzyme-DNA interactions. The results will provide the
molecular basis of bacterial topoisomerase I function, and new insights into growth regulation of bacteria via
modulation of topoisomerase I enzyme activity. Success in these experiments would support the drug
discovery efforts of utilizing bacterial topoisomerase I as a new target for antibiotics.

## Key facts

- **NIH application ID:** 9976333
- **Project number:** 5R01GM054226-20
- **Recipient organization:** FLORIDA INTERNATIONAL UNIVERSITY
- **Principal Investigator:** Yuk-Ching Tse-Dinh
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $323,187
- **Award type:** 5
- **Project period:** 1996-04-01 → 2023-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9976333

## Citation

> US National Institutes of Health, RePORTER application 9976333, Control of DNA Topology (5R01GM054226-20). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9976333. Licensed CC0.

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