Department of Biological Sciences

School of Natural Sciences and Mathematics

Faculty and Research

Stephen Levene, Ph.D.

[email protected]  Professor Bioengineering
Office - ECS 3.208
Mailstop - EC39

Education and Professional Affiliations

A.B., Chemistry, Columbia University
Ph.D, Chemistry, Yale University
Postdoctoral work, University of California at Berkeley
Postdoctoral work, University of California at San Diego
Member, National Institutes of Health Interdisciplinary Special Emphasis Study Section
Member, Graduate Education Committee
Member, Biophysical Society
Member, New York Academy of Sciences
Member, American Association of University Professors


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).

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).

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).

Zhang, Y., McEwen, A.E., Crothers, D.M., and Levene, S.D.  Statistical-mechanical theory of DNA looping. Biophys. J. 90, 1903-1912 (2006).

You, L. and Levene, S.D.  Bulge defects do not destabilize negatively supercoiled DNA.  Biophys. J. 89, L43-L45 (2005).

Zein, S.S. and Levene, S.D. Structural aspects of RecA-dependent homologous strand exchange involving human telomeric DNA.  Biochemistry 44, 4817-4828 (2005).


  • Updated: February 6, 2006