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Showing 1 to 20 of 38 for “"supercoiled"”.
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Dynamics and structures of linear and supercoiled DNAs
… global secondary structures.Interactions of supercoiled and linear DNAs with EcoRI endonuclease, and dye molecules have been studied with DLS experiments. Results of these experiments have been useful in understanding the mechanisms of these reactions.
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Deformability and Dynamics in Linear and Looped/Supercoiled DNA with Implications for Damage Sensing
… DNA, but in cells, DNA is often looped and/or supercoiled, introducing bending and torsional strain. These topological changes are expected to impact DNA deformability and damage recognition. We employed advanced fluorescence approaches to study protein-DNA dynamics on biologically relevant …
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Electrophoretic Mobilities of Topoisomers of ΦX174 DNA
… we compared it with relaxed RFI prepared from supercoiled RFI using the DNA relaxing enzyme (DNA topoisomerase) from <em>Agrobacterium tumefaciens</em>. To distinguish the product of the reaction from RF II molecules, it was analyzed by electrophoresis in 1.4% agarose with 0.5 μg/ml ethidium …
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Analysis of the structural changes caused by positive DNA supercoiling
… prevented extensive examination of positively supercoiled DNA. Studies suggest that at sufficiently high levels of overwinding, DNA relieves strain by adopting an elongated structure, where the bases are positioned extrahelically and the backbones occupy the center of the helix. This transition …
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The effect of negative supercoiling on the formation and positioning of nucleosome cores in vitro
… of the linking difference of reconstituted supercoiled plasmid following topoisomerase I relaxation and the yield and fragment size distribution of micrococcal nuclease digests of supercoiled and linearized plasmid, that nucleosome core reconstitution by urea/salt and salt dialysis proceeds …
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Studies on Type I and Type II DNA Topoisomerases From Mammalian Mitochondria
… of relaxing both negatively and positively supercoiled DNA. The relaxation of negatively supercoiled DNA is directly inhibited by camptothecin and indirectly by m- AMSA, a DNA intercalator. The relaxation of positively supercoiled DNA is also inhibited by camptothecin, however, with 10 to 20 …
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Entwicklung und Untersuchung eines Verfahrens zur integrierten Aufreinigung von Plasmid DNA mittels wässriger Zweiphasenextraktion
… acids present and selective renaturation of supercoiled plasmid DNA followed by selective partitioning in an ATPS. During this procedure, chromosomal and open circular DNA are irreversibly denatured. The drastic change of hydrophobicity enabled the separation from native supercoiled plasmid …
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DNA topology and Pol II CTD phosphorylation as stepwise regulators of chromatin architecture in differentiating human stem cells
… Pol II may be recruited to negatively supercoiled or secondary structure-forming sites, while negative supercoiling can also act as a readout of Pol II activity. To test whether DNA topology could play such a regulatory role, we mapped negative supercoiling (bTMP-seq) and non-B DNA …
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A study of DNA-DNA interactions during bacteriophage lambda integrative recombination
… to be proficient in integrative recombination. Supercoiled circular DNA molecules 713 base pairs long containing bacteriophage lambda attachment (attP) sites were constructed by cloning, annealing of the single strands, restriction digestion, and intramolecular ligation. These attP sites, with …
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EFFECT OF MISMATCHED BASE PAIRS ON DNA PLECTONEMES
… approaches are currently limited to positively supercoiled DNA. In the current dissertation, we aim to study plectoneme localization, in physiologically relevant conditions, using state-of-the-art molecular dynamics (MD) simulations and single molecule magnetics tweezers-based experiments.In …
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DNA supercoiling with a twist
… preference for distorted DNA, such as supercoiled DNA and 4-way junctions. HMGB proteins play a role in transiently regulating or conserving DNA torsion. Topoisomerases regulate DNA supercoiling, which has been argued to provide a coherent explanation for the main modes of …
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Studies On The In Vitro Transposition Of Bacteriophage Mu Dna
… Type 1 complex formation requires a supercoiled mini-Mu donor plasmid, Mu A and HU protein. In the Type 1 complex the two ends of Mu are held together, creating two independent topological domains; a supercoiled Mu domain and a relaxed vector domain (due to nicking at the Mu ends). In …
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A New Generation of Idealized Protein Building Blocks Enables Rational Nanomaterial Design
… built from alpha helices that are straight (not supercoiled at all) and have their helical axes all parallel to each other. This strict specification allows us to model protein assemblies with simple blueprint representations. With this new building block set, we have been able to design and …
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Topologically constrained DNA intercalators: Synthesis and DNA binding studies
… of both calf thymus DNA and closed circular supercoiled DNA. Macrocycle 31 dissociates 10 to 40 times slower from poly(d(A-T)) $\sb2$ and poly(d(G-C)) $\sb2$ than its analogous mono-linked analogue, spermine diacridine (7). $\sp1$H NMR studies of 31 complexed to d(CGCG)$\sb2$ indicate that …
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Transposable prophage Mu exists as an independent chromosomal domain in E. coli
… is compacted by segregation into 400-500 supercoiled domains, created by both active and passive mechanisms like transcription and DNA-binding proteins. We find that transposable prophage Mu, transcriptionally silent by definition, is organized into an independent domain as determined by …
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The Future is Now in Twisted Coil Polymer Actuators (TCPA)
… and fabricating a system capable of creating supercoiled muscle fibers consistently, (2) calibrating the Linear Variable Differential Transformer (LVDT) and Core, and (3) analyzing/interpreting the data of the Twisted Coiled Polymer Actuators (TCPA) fibers through the sensors. The proposed …
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DESIGN, SYNTHESIS, AND BIOLOGICAL EVALUATION OF NOVEL INDENOISOQUINOLINES AS POTENTIAL ANTICANCER AGENTS
… intermediate that is formed when Top1 relaxes supercoiled DNA. The effect of this stabilization is that a DNA replication fork can “collide” with the cleavage complex, which produces cytotoxic DNA damage products. Although the present arsenal of Top1 inhibitors is effective in the treatment of …
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Search for new types of deoxyribozymes and development of human topoisomerases inhibitors on the basis of oligonucleotides
… on the basis of oligonucleotides. Certain non-supercoiled DNA sequences with DNA imperfections such as gap or mismatch next to the topoisomerases cleavage site are designed. Our studies demonstrated some of our newly designed oligonucleotides could inhibit human topoisomerases with high …
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