Fenfei Leng

Dr. Leng's laboratory focuses on studying how transcription affects DNA structural changes and activates or inhibits nearby promoters. Using defined protein systems and in vivo E. coli cells, they have found that transcription is a major chromosome remodeling force in bacteria at exponential phase and certain DNA binding proteins, such as FIS and HU, function as topological barriers to modulate localized DNA supercoiling stemming from transcription. We are also utilizing our in vitro and in vivo systems derived from these basic studies to identify or discover antibiotics targeting bacterial DNA gyrase.

A second project in Dr. Leng's laboratory focuses on studies of the mammalian high mobility group protein AT-hook 2 (HMGA2), a nuclear transcription factor associated with many physiological functions including oncogenesis, obesity, stem cell youth, human height, and human intelligence. This protein contains three "AT hook" DNA binding motifs and specifically recognizes the minor groove of AT-rich DNA sequences. They are particularly interested in understanding the structures and functions of this intriguing protein, and hope to use their knowledge from this basic research to discover or identify small molecular compounds to combat cancers by targeting HMGA2-DNA interactions.

Research Areas

Our laboratory focuses on studying how transcription affects DNA structural changes and activates or inhibits nearby promoters. Using defined protein systems and in vivo E. coli cells, we found that transcription is a major chromosome remodeling force in bacteria and certain DNA binding proteins, such as FIS and HU, function as topological barriers to modulate localized DNA supercoiling stemming from transcription. We are also utilizing our in vitro and in vivo systems derived from these basic studies to identify or discover antibiotics targeting bacterial DNA gyrase. Specifically, we have developed three unique fluorescence-based high throughput screening (HTS) assays methods to identify/discover gyrase inhibitors and poisons for antibiotics development. These fluorescence-based assays can also be used to discover/identify inhibitors targeting other DNA topoisomerases. They are the only fluorescence-based assays for DNA topoisomerases.

Recently, we have developed an in vitro enzymatic system to synthesize relaxed and supercoiled circular DNA molecules through a combination of DNA synthesis via PCR or rolling circle amplification by phi29 DNA polymerase, DNA circularization by Cre recombinase, and digestion of unwanted linear DNA by T5 exonuclease. These circular DNA molecules do not carry any bacterial DNA elements or modifications and can be used in DNA vaccines and gene therapy. For more details, please refer to our recent publication: Rezaei S, Moncada-Restrepo M, Leng S, Chambers JW, Leng F. Synthesizing supercoiled circular DNA molecules in vitro. Nucleic Acids Res. 2025 Sep 5;53(17):gkaf889. doi: 10.1093/nar/gkaf889. PMID: 40930535; PMCID: PMC12421384.

Education

• Nanjing University, Nanjing, China, BS, Biochemistry
• The University of Mississippi Medical Center, PhD, Biochemistry
• Postdoctoral research fellow, Johns Hopkins University

Representative Publications

1. Rezaei S, Moncada-Restrepo M, Leng S, Chambers JW, Leng F.* Synthesizing supercoiled circular DNA molecules in vitro. Nucleic Acids Res. 2025; 53:gkaf889.

2. Deng Z, Chapagain P, Leng F.* Macromolecular crowding potently stimulates DNA supercoiling activity of Mycobacterium tuberculosis DNA gyrase. Journal of Biological Chemistry, 2023;299:105439.

3. Zhi, X., Dages, S., Dages, K., Makemson, J., and Leng, F.* Transient and dynamic DNA supercoiling potently stimulates the leu-500 promoter in Escherichia coli. Journal of Biological Chemistry, 2017, 292: 14566-14575.

4. Gu, M., Berrido, A., Gonzalez, W.G., Miksovska, J., Chambers, J., and Leng, F.* Fluorescently labeled circular DNA molecules for DNA topology and topoisomerases. Sci Rep. 2016, 6:36006.

5. Leng, F.*, Chen, B. and Dunlap, D. Dividing a supercoiled DNA molecule into two independent topological domains, Proceedings of the National Academy of Sciences U S A, 2011, 108, 19973-19978.