Levene, Stephen D.

Permanent URI for this collectionhttps://hdl.handle.net/10735.1/2316

Dr. Steven Levene is a Professor of Bioengineering in the Department of Biological Sciences. He is also an affiliated faculty member in UTD's graduate programs in Bioinformatics and Computational Biology, and in Biotechnology. Professor Levene's research interests "involve protein-DNA interactions in site-specific recombination and the structure and dynamics of nucleic acids in solution."

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    Free-Energy Calculations for Semi-Flexible Macromolecules: Applications to DNA Knotting and Looping
    (American Institute of Physics, 2014-11-07) Giovan, Stefan M.; Scharein, Robert G.; Hanke, Andreas; Levene, Stephen D.; 0000 0001 3818 2397 (Levene, SD); G-3100-2010 (Levene, SD); Giovan, Stefan M.; Levene, Stephen D.
    We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.;
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    Measurements of DNA-Loop Formation via Cre-Mediated Recombination
    (2012-05-15) Shoura, Massa J.; Vetcher, Alexandre; Giovan, Stefan; Levene, Stephen D.; Bardai, Farah; Bharadwaj, Anusha; Kesinger, Matthew R.; Shoura, Massa J.; Vetcher, Alexandre; Giovan, Stefan; Levene, Stephen D.; Bardai, Farah; Bharadwaj, Anusha; Kesinger, Matthew R.
    The Cre recombination system has become an important tool for genetic manipulation of higher organisms and a model for site-specific DNA-recombination mechanisms employed by the λ-Int superfamily of recombinases. We report a novel quantitative approach for characterizing the probability of DNA-loop formation in solution using time-dependent ensemble FRET measurements of intra- and intermolecular Cre-recombination kinetics. Our method uses an innovative technique for incorporating multiple covalent modifications at specific sites in covalently closed DNA. Because the mechanism of Cre recombinase does not conform to a simple kinetic scheme, we employ numerical methods to extract rate constants for fundamental steps that pertain to Cre-mediated loop closure. Cre recombination does not require accessory proteins, DNA supercoiling, or particular metal-ion cofactors and is thus a highly flexible system for quantitatively analyzing DNA-loop formation in vitro and in vivo.
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    Engineering Multiple Site-Specific Modifications in Supercoiled DNAs
    (2012-06-19) Bharadwaj, Anusha; Kesinger, Matthew R.; Shoura, Massa J.; Vetcher, Alexandre; Levene, Stephen D.; Bharadwaj, Anusha; Kesinger, Matthew R.; Shoura, Massa J.; Vetcher, Alexandre; Levene, Stephen D.
    New techniques are needed in order to study the effects of DNA supercoiling on loop-mediated regulation. The thermodynamics of DNA looping depend periodically on the helical phasing between recognition sites. A long-term goal is to provide enabling technologies for ensemble and single-molecule FRET studies of DNA looping mediated by lac repressor in vitro and in vivo. Other applications of the methodology include engineering of DNA substrates for studies of site-specific recombination and other enzyme systems.
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    DNA Looping in Topologically Constrained Domains
    (Oxford University Press., 2012-05-15) Bharadwaj, Anusha; Kesinger, Matthew R.; Shoura, Massa J.; Vetcher, Alexandre; Levene, Stephen D.; Bharadwaj, Anusha; Kesinger, Matthew R.; Shoura, Massa J.; Vetcher, Alexandre; Levene, Stephen D.
    New techniques are needed in order to study the effects of DNA supercoiling on loop-mediated regulation. The thermodynamics of DNA looping depend periodically on the helical phasing between recognition sites. A long-term goal is to provide enabling technologies for ensemble and single-molecule FRET studies of DNA looping mediated by lac repressor in vitro and in vivo. Other applications of the methodology include engineering of DNA substrates for studies of site-specific recombination and other enzyme systems

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