Jonathan Marcus Fogg, Ph.D.
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Positions
- Senior Staff Scientist
-
Virol & Micro: Zechiedrich
Baylor College of Medicine
Houston, TX US
Education
- Postdoctoral Training at Baylor College of Medicine
- 11/2011 - Houston, Texas United States
- Postdoctoral Training at University of California at Santa Barbara
- 06/2005 - Santa Barbara, California United States
- BS from University of Leeds
- 07/1996 - Leeds, United Kingdom
- PhD from University of Dundee
- 07/2001 - Dundee, United Kingdom
Professional Statement
Throughout my research I have focused on how DNA is able to be an active participant in its transactions. DNA structure, particularly the structure of supercoiled DNA, is much more variable and dynamic than many people realize. This insight has allowed me to contribute to a better understanding of protein-DNA interactions and DNA itself. In the process, I have also developed unique DNA tools that are proving to be extremely useful, not only for basic research, but also clinical applications. I have developed a patented protocol to generate milligram quantities of supercoiled minicircle DNA, as small as 250 bp. Using these DNA minicircles, I precisely determine the supercoiling dependence of topoisomerase binding and additionally elucidate the mechanism through which DNA topoisomerases recognize their supercoiled DNA substrate and determine where to act. These minicircles also provide a unique insight into the structure of supercoiled DNA, including previously unappreciated differences between overwound and underwound DNA. Throughout my career I have collaborated with researchers from many disciplines including biochemistry, biophysics, physics, mathematics, structural biology, and medicine.Selected Publications
- Wang, Q.; Irobalieva R.N.; Chiu W., Schmid M.F.; Fogg J.M.; Zechiedrich L.; Pettitt B.M. "Influence of DNA sequence on the structure of minicircles under torsional stress." Nucleic Acids Res.. 2017 Jul 27;45(13):7633-7642. Pubmed PMID: 28609782
- Fogg J.M.; Catanese D.J. Jr.; Randall G.L.; Swick M.C.; Zechiedrich L. "Differences between positively and negatively supercoiled DNA that topoisomerases may distinguish." Mathematics of DNA Structure, Function and Interactions. 2009;150:73-121.
- Fogg, J.M.; Randall, G.L.;Pettitt, B.M.;Sumners, D.W.; Harris, S.A.; and Zechiedrich, L.. "Bullied no more: when and how DNA shoves proteins around.." Quarterly Review of Biophysics. 2012;45:257-299.
- Fogg J.M.; Kvaratskhelia, M.; White M.F.; Lilley D.M.J. "Distortion of DNA junctions imposed by the binding of resolving enzymes: a fluorescence study.." J. Mol. Biol.. 2001 Nov 3;313(4):751-764. Pubmed PMID: 11697901
- Fogg D.M.J.; Lilley D.M.J. "Ensuring productive resolution by the junction-resolving enzyme RuvC: large enhancement of the second-strand cleavage rate.." Biochemistry. 2000 Dec 26;39(51):16125-16134. Pubmed PMID: 11123941
- Fogg J.M.; Kolmakova N.; Rees I.; Magonov S.; Hansma H.; Perona J.J.; Zechiedrich E.L. "Exploring writhe in supercoiled minicircle DNA.." J Phys Condens Matter. 2006 Mar 24;18(14):S145-S159. Pubmed PMID: 19337583
- Kvaratskhelia M.; Wardleworth B.N.; Bond C.S.; Fogg J.M.; Lilley D.M.J.; White M.F. "Holliday junction resolution is modulated by archaeal chromatin components in vitro.." 2002 Jan 25;277(4):2992-2996. Pubmed PMID: 11709558
- Fogg J.M.; Schofield M.J.; White M.F.; Lilley D.M.J. "Sequence and functional-group specificity for cleavage of DNA junctions by RuvC of Escherichia coli.." Biochemistry. 1999 Aug 31;38(35):11349-11358. Pubmed PMID: 10471285
- Hiller D.A.; Fogg J.M.; Martin A.M.; Beechem J.M.; Reich N.O.; Perona J.J. "Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence.." Biochemistry. 2003 Dec 16;42(49):14375-14385. Pubmed PMID: 14661948
- Irobalieva, R.N.; Fogg J.M.; Catanese D.J. Jr.; Sutthibutpong, T.; Chen M.; Barker A.K.; Ludtke S.J.; Harris S.A.; Schmid M.F.; Chiu W.; Zechiedrich L. "Structural diversity of supercoiled DNA." Nat Commun.. 2015 Oct 12;6:8440. Pubmed PMID: 26455586
- Catanese D.J. Jr.; Fogg J.M.; Schrock D.E. 2nd.; Gilbert B.E.; Zechiedrich L. "Supercoiled Minivector DNA resists shear forces associated with gene therapy delivery.." Gene Ther.. 2012 Jan;19(1):94-100. Pubmed PMID: 21633394
- Déclais A.C.; Fogg J.M.; Freeman A.D.; Coste F.; Hadden J.M.; Phillips S.E.; Lilley D.M.J. "The complex between a four-way DNA junction and T7 endonuclease I.." EMBO J.. 2003 Mar 17;22(6):1398-1409. Pubmed PMID: 12628932
- Bizard, A.H.; Yang, X.; Débat, H.; Fogg, J.M.; Strick, T.R.; Garnier, F.; Nadal, M. "TopA, the Sulfolobus solfataricus topoisomerase III, is a decatenase.." Nucleic Acids Res.. 2018 Jan 25;46(2):861-872. Pubmed PMID: 29253195
- Zhao, N.; Fogg, J.M.; Zechiedrich L.; Yu Z. "Transfection of shRNA-encoding Minivector DNA of a few hundred base pairs to regulate gene expression in lyphoma cells." Gene Ther.. 2011;18(3):220-224. Pubmed PMID: 20962872
- Fogg J.M.; Schofield M.J.; Déclais A.C.; Lilley D.M.J. "Yeast resolving enzyme CCE1 makes sequential cleavages in DNA junctions within the lifetime of the complex.." Biochemistry. 2000 Apr 11;39(14):4082-4089. Pubmed PMID: 10747798
- Fogg, J.M., Judge, A.K., Stricker, E., Chan, H.L., Zechiedrich, L. "Supercoiling and looping promote DNA base accessibility and coordination among distant sites." Nat. Commun.. 2021 Sep;12(1):5683. Pubmed PMID: 34584096
- Waszkiewicz, R., Ranasinghe, M., Fogg, J.M., Catanese, D.J., Ekiel-Jeżewska, M.L., Lisicki, M., Demeler, B., Zechiedrich, L. Szymczak, P. "DNA supercoiling-induced shapes alter minicircle hydrodynamic properties." Nucleic Acids Res.. 2023 May;51(8):4027-4042. Pubmed PMID: 36971110
- Ranasinghe, M., Fogg, J.M., Catanese Jr., D.J., Zechiedirch, L., Demeler, B. "Suitability of double-stranded DNA as a molecular standard for the validation of analytical ultracentrifugation instruments." Eur Biophys J.. 2023 Jul;52:267-280. Pubmed PMID: 37501021
- Arévalo-Soliz, L.M., Hardee, C.L., Fogg, J.M., Corman, N.R., Noorbakhsh, C., Zechiedrich, L. "Improving therapeutic potential of non-viral minimized DNA vectors." Cell Gene Ther Insights. 2020 Nov;6(10):1489-1505. Pubmed PMID: 33953961
- Zechiedrich, L., Fogg, J.M. "Biophysics meets gene therapy: How exploring supercoiling-dependent structural changes in DNA led to the development of minivector DNA." Technol Innov .. 2019 Aug;20(4):427-439. Pubmed PMID: 33815681
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