Search Results - "Levene, Stephen D."

DNA-Topology Simplification by Topoisomerases by Hanke, Andreas, Ziraldo, Riccardo, Levene, Stephen D.

“…The topological properties of DNA molecules, supercoiling, knotting, and catenation, are intimately connected with essential biological processes, such as gene…”
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Intricate and Cell Type-Specific Populations of Endogenous Circular DNA (eccDNA) in Caenorhabditis elegans and Homo sapiens by Shoura, Massa J, Gabdank, Idan, Hansen, Loren, Merker, Jason, Gotlib, Jason, Levene, Stephen D, Fire, Andrew Z

“…Investigations aimed at defining the 3D configuration of eukaryotic chromosomes have consistently encountered an endogenous population of chromosome-derived…”
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Functional 20S proteasomes in mature human red blood cells by Neelam, Sudha, Kakhniashvili, David G, Wilkens, Stephan, Levene, Stephen D, Goodman, Steven R

“…The purpose of the present study was to investigate whether functional 20S and/or 26S proteasomes are present within mature human red blood cells (RBCs;…”
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The thermodynamics of DNA loop formation, from J to Z by Levene, Stephen D, Giovan, Stefan M, Hanke, Andreas, Shoura, Massa J

“…The formation of DNA loops is a ubiquitous theme in biological processes, including DNA replication, recombination and repair, and gene regulation. These loops…”
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Contribution of Fluorophore Dynamics and Solvation to Resonant Energy Transfer in Protein-DNA Complexes: A Molecular-Dynamics Study by Shoura, Massa J., Ranatunga, R.J.K. Udayana, Harris, Sarah A., Nielsen, Steven O., Levene, Stephen D.

“…In Förster resonance energy transfer (FRET) experiments, extracting accurate structural information about macromolecules depends on knowing the positions and…”
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Kinetic pathways of topology simplification by Type-II topoisomerases in knotted supercoiled DNA by Ziraldo, Riccardo, Hanke, Andreas, Levene, Stephen D

“…Abstract The topological state of covalently closed, double-stranded DNA is defined by the knot type $K$ and the linking-number difference $\Delta Lk$ relative…”
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Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping by Zhang, Yongli, McEwen, Abbye E, Crothers, Donald M, Levene, Stephen D

“…Interactions of E. coli lac repressor (LacR) with a pair of operator sites on the same DNA molecule can lead to the formation of looped nucleoprotein complexes…”
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Deconvolution of nucleic-acid length distributions: a gel electrophoresis analysis tool and applications by Ziraldo, Riccardo, Shoura, Massa J, Fire, Andrew Z, Levene, Stephen D

“…Next-generation DNA-sequencing (NGS) technologies, which are designed to streamline the acquisition of massive amounts of sequencing data, are nonetheless…”
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DNA Topology and Geometry in Flp and Cre Recombination by Vetcher, Alexandre A., Lushnikov, Alexander Y., Navarra-Madsen, Junalyn, Scharein, Robert G., Lyubchenko, Yuri L., Darcy, Isabel K., Levene, Stephen D.

“…The Flp recombinase of yeast and the Cre recombinase of bacteriophage P1 both belong to the λ-integrase (Int) family of site-specific recombinases. These…”
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Loop-closure kinetics reveal a stable, right-handed DNA intermediate in Cre recombination by Shoura, Massa J, Giovan, Stefan M, Vetcher, Alexandre A, Ziraldo, Riccardo, Hanke, Andreas, Levene, Stephen D

“…In Cre site-specific recombination, the synaptic intermediate is a recombinase homotetramer containing a pair of loxP DNA target sites. The enzyme system's…”
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DNA cyclization and looping in the wormlike limit: Normal modes and the validity of the harmonic approximation by Giovan, Stefan M., Hanke, Andreas, Levene, Stephen D.

“…ABSTRACT For much of the last three decades, Monte Carlo‐simulation methods have been the standard approach for accurately calculating the cyclization…”
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Measurements of DNA-loop formation via Cre-mediated recombination by Shoura, Massa J, Vetcher, Alexandre A, Giovan, Stefan M, Bardai, Farah, Bharadwaj, Anusha, Kesinger, Matthew R, Levene, Stephen D

“…The Cre-recombination system has become an important tool for genetic manipulation of higher organisms and a model for site-specific DNA-recombination…”
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Free-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping by Giovan, Stefan M, Scharein, Robert G, Hanke, Andreas, 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…”
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Statistical-Mechanical Theory of DNA Looping by Zhang, Yongli, McEwen, Abbye E., Crothers, Donald M., Levene, Stephen D.

“…The lack of a rigorous analytical theory for DNA looping has caused many DNA-loop-mediated phenomena to be interpreted using theories describing the related…”
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Normal human chromosomes have long G-rich telomeric overhangs at one end by Wright, W E, Tesmer, V M, Huffman, K E, Levene, S D, Shay, J W

“…Telomeres protect the ends of linear chromosomes from degradation and abnormal recombination events, and in vertebrates may be important in cellular senescence…”
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Analysis of DNA topoisomers, knots, and catenanes by agarose gel electrophoresis by Levene, Stephen D

“…Agarose gel electrophoresis is by far the most widely used method for characterizing the topological state of DNA molecules. Although this technique has been…”
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Telomere Shortening Is Proportional to the Size of the G-rich Telomeric 3′-Overhang by Huffman, Kenneth E., Levene, Stephen D., Tesmer, Valerie M., Shay, Jerry W., Wright, Woodring E.

“…Most normal diploid human cells do not express telomerase activity and are unable to maintain telomere length with ongoing cell divisions. We show that the…”
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Gel mobilities of linking-number topoisomers and their dependence on DNA helical repeat and elasticity by Vetcher, Alexandre A., McEwen, Abbye E., Abujarour, Ramzey, Hanke, Andreas, Levene, Stephen D.

“…Agarose-gel electrophoresis has been used for more than thirty years to characterize the linking-number ( Lk) distribution of closed-circular DNA molecules…”
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Supercoiling-Dependent Flexibility of Adenosine-Tract-Containing DNA Detected by a Topological Method by Tsen, Hua, Levene, Stephen D.

“…Intrinsically bent DNA sequences have been implicated in the activation of transcription by promoting juxtaposition of DNA sequences near the terminal loop of…”
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Bulge Defects Do Not Destabilize Negatively Supercoiled DNA by You, Lijing, Levene, Stephen D.

“…The conformational properties of DNA lesions such as extrahelical bulges are presumed to be essential for recognition of defects in DNA structure by a cell’s…”
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