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Stephen Levene

Stephen Levene

Professor - Bioengineering
Associate Dept. Head - Bioengineering Department
Physical Genomics Laboratory

Professional Preparation

Ph.D. - Chemistry
Yale University - 1985
A.B. - Chemistry
Columbia University (College) - 1979

Research Areas

Dr. Levene's research interests involve protein-DNA interactions in site-specific recombination and the structure and dynamics of nucleic acids in solution.

Research Interests
Chemical and enzymatic probing methods are powerful techniques for examining details of sequence-dependent structure in DNA and RNA. Reagents that cleave nucleic acid molecules in a structure-specific, but relatively sequence-non-specific manner, such as hydroxyl radical or DNase I, have been used widely to probe helical geometry in nucleic acid structures, nucleic acid-drug complexes, and in nucleoprotein assemblies. Application of cleavage-based techniques to structures present in superhelical DNA has been hindered by the fact that the cleavage pattern attributable to supercoiling-dependent structures is heavily mixed with non-specific cleavage signals that are inevitable products of multiple cleavage events. We present a rigorous mathematical procedure for extracting the cleavage pattern specific to supercoiled DNA and use this method to investigate the hydroxyl radical cleavage pattern in a cruciform DNA structure formed by a 60 bp inverted repeat sequence embedded in a negatively supercoiled plasmid. Our results support the presence of a stem-loop structure in the expected location and suggest that the helical geometry of the cruciform stem differs from that of the normal duplex form.


Metzler, R. , Hanke, A., Zhang, Y., and Levene, S.D. Single DNA conformations and biological function. Computational and Theoretical Nanoscience (in press). in press - Publication
Vetcher, A.A., Srinivasan, S., Vetcher, I.A., Abramov, S.M., Kozlov, M., Baughmann, R.H., and Levene, S.D. Fractionation of SWNT/nucleic acid complexes by agarose gel electrophoresis Nanotechnology 17, 4263-4269 (2006). 2006 - Publication
Vetcher, A.A., Lushnikov, A.Y., Navarra-Madsen, J., Scharein, R.G., Darcy, I.K., Lyubchenko, Y.L., and Levene, S.D. DNA topology and geometry in Flp and Cre recombination. J. Mol. Biol. 357, 1089-1104 (2006). 2006 - Publication
Zhang, Y., McEwen, A.E., Crothers, D.M., and Levene, S.D. Statistical-mechanical theory of DNA looping. Biophys. J. 90, 1903-1912 (2006). 2006 - Publication
You, L. and Levene, S.D. Bulge defects do not destabilize negatively supercoiled DNA. Biophys. J. 89, L43-L45 (2005). 2005 - Publication
Zein, S.S. and Levene, S.D. Structural aspects of RecA-dependent homologous strand exchange involving human telomeric DNA. Biochemistry 44, 4817-4828 (2005). 2005 - Publication

Additional Information

27 publications in related fields
Graduate and Postdoctoral Advisors
  • Donald M. Crothers (Yale University, graduate advisor)
  • Bruno H. Zimm (UC San Diego, postdoctoral, deceased)
  • Nicholas R. Cozzarelli (UC Berkeley, postdoctoral, deceased)
Collaborators and Other Affiliations (last 48 mos.)
  • Crothers, Donald Yale University
  • Malko, Anton UT-Dallas
  • Darcy, Isabel Univ. of Iowa
  • Martinez, Jennifer LANL
  • Hanke, Andreas UT-Brownsville
  • Metzler, Ralf TU, München
  • Lushnikov, Univ. of Nebraska
  • Pace, Betty UT-Dallas
  • Alexander School of Medicine
  • Peterson, Kenneth KU School of Med.
  • Lyubchenko, Yuri Univ. of Nebraska, School of Medicine
  • Scharein, Robert Hypnagogic Software

News Articles

Biology Prof to Defend Darwins Theory at Debate
Biology Prof to Defend Darwins Theory at Debate UT Dallas biology professor Stephen D. Levene has been asked to serve on a panel debating the film Expelled: No Intelligence Allowed. Dr. Levene will speak against the movie’s premise, which accuses academia of unfair bias against educators who espouse the theory of intelligent design. The Dallas Philosopher’s Forum is hosting the discussion at 7:15 p.m. Tuesday, April 29, at the Angelika Mockingbird Theater. It will include an open question-and-answer session. The event is free for forum members and $5 for non-members.
Scientists Use Light To ‘Tag and Track’ Genetic Processes
Scientists Use Light To ‘Tag and Track’ Genetic Processes In a new study, UT Dallas researchers outline how they used fluorescent molecules to “tag” DNA and monitor a process called DNA looping, a natural biological mechanism involved in rearranging genetic material in some types of cells.

The UT Dallas “tag and track” method not only sheds light on how DNA loops form, but also might be adapted to screen drugs for effectiveness against certain viruses that shuffle genetic material, such as  HIV.


Synergistic Activities
  1. Ad hoc member, NIH Macromolecular Structure and Function study section (MSFB).
  2. Editorial Board Member, Journal of Experimental Biology and Medicine.
  3. Instructor, Summer Institute Program to Increase Diversity (SIPID), an NHLBI-funded training program for underrepresented minority and disabled junior scientists.
  4. Mentor, Summer Institute of Biomedical Scholars at UT-Dallas (a summer research program for undergraduates and gifted high-school students sponsored by the UT-Dallas Sickle Cell Disease Research Center).
  5. Affiliated faculty member, UT-Dallas graduate program in Bioinformatics and Computational Biology and graduate program in Biotechnology.
  6. Research Fellow, Obermann Center for Advanced Studies, University of Iowa, 2005. Mathematical Sciences Research Institute/Program


Tangle Analysis of DNA Recombinases and Related Proteins
code[2] - [2018–2018]