Search Results - "Brenowitz, M"

Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins by Shcherbakova, Inna, Mitra, Somdeb, Beer, Robert H., Brenowitz, Michael

“…‘Footprinting’ describes assays in which ligand binding or structure formation protects polymers such as nucleic acids and proteins from either cleavage or…”
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Principles of RNA Compaction: Insights from the Equilibrium Folding Pathway of the P4-P6 RNA Domain in Monovalent Cations by Takamoto, Keiji, Das, Rhiju, He, Qin, Doniach, Sebastian, Brenowitz, Michael, Herschlag, Daniel, Chance, Mark R.

“…Counterions are required for RNA folding, and divalent metal ions such as Mg 2+ are often critical. To dissect the role of counterions, we have compared global…”
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Perturbation of the Hierarchical Folding of a Large RNA by the Destabilization of its Scaffold's Tertiary Structure by Shcherbakova, Inna, Brenowitz, Michael

“…The P4–P6 domain serves as a scaffold against which the periphery and catalytic core organize and fold during Mg 2+-mediated folding of the Tetrahymena…”
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Local Kinetic Measures of Macromolecular Structure Reveal Partitioning among Multiple Parallel Pathways from the Earliest Steps in the Folding of a Large RNA Molecule by Laederach, Alain, Shcherbakova, Inna, Liang, Mike P., Brenowitz, Michael, Altman, Russ B.

“…At the heart of the RNA folding problem is the number, structures, and relationships among the intermediates that populate the folding pathways of most large…”
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Concordant Exploration of the Kinetics of RNA Folding from Global and Local Perspectives by Kwok, Lisa W., Shcherbakova, Inna, Lamb, Jessica S., Park, Hye Yoon, Andresen, Kurt, Smith, Heather, Brenowitz, Michael, Pollack, Lois

“…Time-resolved small-angle X-ray scattering (SAXS) with millisecond time-resolution reveals two discrete phases of global compaction upon Mg 2+-mediated folding…”
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Determination of Macromolecular Folding and Structure by Synchrotron X-Ray Radiolysis Techniques by Maleknia, Simin D., Ralston, Corie Y., Brenowitz, Michael D., Downard, Kevin M., Chance, Mark R.

“…Radiolysis of water by synchrotron X-rays generates oxygen-containing radicals that undergo reactions with solvent accessible sites of macromolecules inducing…”
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Monovalent Ion-mediated Folding of the Tetrahymena thermophila Ribozyme by Shcherbakova, Inna, Gupta, Sayan, Chance, Mark R., Brenowitz, Michael

“…The time-course of monovalent cation-induced folding of the L-21 Sca1 Tetrahymena thermophila ribozyme and a selected mutant was quantitatively followed using…”
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An Alternative Route for the Folding of Large RNAs: Apparent Two-state Folding by a Group II Intron Ribozyme by Su, Linhui Julie, Brenowitz, Michael, Pyle, Anna Marie

“…Despite a growing literature on the folding of RNA, our understanding of tertiary folding in large RNAs derives from studies on a small set of molecular…”
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Concerted binding and bending of DNA by Eschericia coli integration host factor by Dhavan, Gauri M, Crothers, Donald M, Chance, Mark R, Brenowitz, Michael

“…Integration host factor (IHF) is a heterodimeric Eschericia coli protein that plays essential roles in a variety of cellular processes including site-specific…”
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Solution Structure and Interdomain Interactions of the Saccharomyces cerevisiae “TATA Binding Protein” (TBP) Probed by Radiolytic Protein Footprinting by Rashidzadeh, Hassan, Khrapunov, Sergei, Chance, Mark R, Brenowitz, Michael

“…Although atomic-resolution crystal structures of the conserved C-terminal domain of several species of TBP and their complexes with DNA have been determined,…”
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Folding Mechanism of the Tetrahymena Ribozyme P4−P6 Domain by Deras, Michael L, Brenowitz, Michael, Ralston, Corie Y, Chance, Mark R, Woodson, Sarah A

“…Synchrotron X-ray-dependent hydroxyl radical footprinting was used to probe the folding kinetics of the P4−P6 domain of the Tetrahymena group I ribozyme, which…”
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Catching RNA Polymerase in the Act of Binding: Intermediates in Transcription Illuminated by Synchrotron Footprinting by Brenowitz, Michael, Erie, Dorothy A., Chance, Mark R.

“…The article by Sclavi et al. in this issue of PNAS addresses 'initiation, ' the first step in transcription. Gene transcription is catalyzed in cells by large…”
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Determination of binding constants for cooperative site-specific protein-DNA interactions using the gel mobility-shift assay by Senear, D F, Brenowitz, M

“…We have investigated the question of whether the gel mobility-shift assay can provide data that are useful to the demonstration of cooperativity in the…”
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The Oct-2 protein binds cooperatively to adjacent octamer sites by LEBOWITZ, J. H, CLERC, R. G, BRENOWITZ, M, SHARP, P. A

“…Recombinant proteins derived from the cloned human oct-2 gene were used to investigate cooperative binding by Oct-2 to adjacent DNA-binding sites. Oct-2, a…”
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The manganese superoxide dismutase of Escherichia coli K-12 associates with DNA by Steinman, H M, Weinstein, L, Brenowitz, M

“…Superoxide dismutases (SODs) are vital components in the resistance of aerobic organisms to the toxicity of oxygen. Escherichia coli contains two highly…”
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Footprint'' Titrations Yield Valid Thermodynamic Isotherms by Brenowitz, Michael, Senear, Donald F., Shea, Madeline A., Ackers, Gary K.

“…A central issue in gene regulation is the mechanism, and biological function, of the cooperative binding of regulatory protein ligands to specific sites on…”
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The allosteric interaction between D-galactose and the Escherichia coli galactose repressor protein by BROWN, M. P, SHAIKH, N, BRENOWITZ, M, BRAND, L

“…The Escherichia coli galactose repressor protein (GalR) inhibits transcription of the gal operon upon binding to two operator sites (1-7). This DNA binding…”
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DNA-binding properties of a lac repressor mutant incapable of forming tetramers by Brenowitz, M, Mandal, N, Pickar, A, Jamison, E, Adhya, S

“…The interaction of proteins bound to sites widely separated on the genome is a recurrent motif in both prokaryotic and eukaryotic regulatory systems. Lac…”
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Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs by Shcherbakova, Inna, Mitra, Somdeb, Laederach, Alain, Brenowitz, Michael

“…Large, multidomain RNA molecules are generally thought to fold following multiple pathways down rugged landscapes populated with intermediates and traps. A…”
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A molecular model of the inducer binding domain of the galactose repressor of Escherichia coli by HSIEH, M, HENSLEY, P, BRENOWITZ, M, FETROW, J. S

“…The C-terminal inducer binding domain of the Escherichia coli galactose repressor (GalR) is homologous to several periplasmic chemoreceptor proteins whose…”
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