Relevant bibliographies by topics / DNA supercoiling

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'DNA supercoiling'

Author: Grafiati
Published: 4 June 2021
Last updated: 25 May 2024

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Journal articles on the topic "DNA supercoiling"

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LILLEY, DAVID M. J. "DNA supercoiling." Biochemical Society Transactions 14, no. 2 (April 1, 1986): 489–93. http://dx.doi.org/10.1042/bst0140489.

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Eckdahl, Todd T. "Investigating DNA Supercoiling." American Biology Teacher 61, no. 3 (March 1, 1999): 214–16. http://dx.doi.org/10.2307/4450653.

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King, Graeme A., Federica Burla, Erwin J. G. Peterman, and Gijs J. L. Wuite. "Supercoiling DNA optically." Proceedings of the National Academy of Sciences 116, no. 52 (December 5, 2019): 26534–39. http://dx.doi.org/10.1073/pnas.1908826116.

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Cellular DNA is regularly subject to torsional stress during genomic processes, such as transcription and replication, resulting in a range of supercoiled DNA structures. For this reason, methods to prepare and study supercoiled DNA at the single-molecule level are widely used, including magnetic, angular-optical, micropipette, and magneto-optical tweezers. However, it is currently challenging to combine DNA supercoiling control with spatial manipulation and fluorescence microscopy. This limits the ability to study complex and dynamic interactions of supercoiled DNA. Here we present a single-molecule assay that can rapidly and controllably generate negatively supercoiled DNA using a standard dual-trap optical tweezers instrument. This method, termed Optical DNA Supercoiling (ODS), uniquely combines the ability to study supercoiled DNA using force spectroscopy, fluorescence imaging of the whole DNA, and rapid buffer exchange. The technique can be used to generate a wide range of supercoiled states, with between <5 and 70% lower helical twist than nonsupercoiled DNA. Highlighting the versatility of ODS, we reveal previously unobserved effects of ionic strength and sequence on the structural state of underwound DNA. Next, we demonstrate that ODS can be used to directly visualize and quantify protein dynamics on supercoiled DNA. We show that the diffusion of the mitochondrial transcription factor TFAM can be significantly hindered by local regions of underwound DNA. This finding suggests a mechanism by which supercoiling could regulate mitochondrial transcription in vivo. Taken together, we propose that ODS represents a powerful method to study both the biophysical properties and biological interactions of negatively supercoiled DNA.
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LILLEY, DAVID M. J. "DNA supercoiling and DNA structure." Biochemical Society Transactions 14, no. 2 (April 1, 1986): 211–13. http://dx.doi.org/10.1042/bst0140211.

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Burnier, Y., J. Dorier, and A. Stasiak. "DNA supercoiling inhibits DNA knotting." Nucleic Acids Research 36, no. 15 (July 24, 2008): 4956–63. http://dx.doi.org/10.1093/nar/gkn467.

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Westerhoff, Hans V., Mary H. O’Dea, Anthony Maxwell, and Martin Gellert. "DNA supercoiling by DNA gyrase." Cell Biophysics 12, no. 1 (January 1988): 157–81. http://dx.doi.org/10.1007/bf02918357.

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Witz, Guillaume, Giovanni Dietler, and Andrzej Stasiak. "DNA knots and DNA supercoiling." Cell Cycle 10, no. 9 (May 2011): 1339–40. http://dx.doi.org/10.4161/cc.10.9.15293.

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Hobson, Matthew J., Zev Bryant, and James M. Berger. "Modulated control of DNA supercoiling balance by the DNA-wrapping domain of bacterial gyrase." Nucleic Acids Research 48, no. 4 (January 17, 2020): 2035–49. http://dx.doi.org/10.1093/nar/gkz1230.

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Abstract Negative supercoiling by DNA gyrase is essential for maintaining chromosomal compaction, transcriptional programming, and genetic integrity in bacteria. Questions remain as to how gyrases from different species have evolved profound differences in their kinetics, efficiency, and extent of negative supercoiling. To explore this issue, we analyzed homology-directed mutations in the C-terminal, DNA-wrapping domain of the GyrA subunit of Escherichia coli gyrase (the ‘CTD’). The addition or removal of select, conserved basic residues markedly impacts both nucleotide-dependent DNA wrapping and supercoiling by the enzyme. Weakening CTD–DNA interactions slows supercoiling, impairs DNA-dependent ATP hydrolysis, and limits the extent of DNA supercoiling, while simultaneously enhancing decatenation and supercoil relaxation. Conversely, strengthening DNA wrapping does not result in a more extensively supercoiled DNA product, but partially uncouples ATP turnover from strand passage, manifesting in futile cycling. Our findings indicate that the catalytic cycle of E. coli gyrase operates at high thermodynamic efficiency, and that the stability of DNA wrapping by the CTD provides one limit to DNA supercoil introduction, beyond which strand passage competes with ATP-dependent supercoil relaxation. These results highlight a means by which gyrase can evolve distinct homeostatic supercoiling setpoints in a species-specific manner.
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Schvartzman, Jorge B., Pablo Hernández, Dora B. Krimer, Julien Dorier, and Andrzej Stasiak. "Closing the DNA replication cycle: from simple circular molecules to supercoiled and knotted DNA catenanes." Nucleic Acids Research 47, no. 14 (July 5, 2019): 7182–98. http://dx.doi.org/10.1093/nar/gkz586.

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AbstractDue to helical structure of DNA, massive amounts of positive supercoils are constantly introduced ahead of each replication fork. Positive supercoiling inhibits progression of replication forks but various mechanisms evolved that permit very efficient relaxation of that positive supercoiling. Some of these mechanisms lead to interesting topological situations where DNA supercoiling, catenation and knotting coexist and influence each other in DNA molecules being replicated. Here, we first review fundamental aspects of DNA supercoiling, catenation and knotting when these qualitatively different topological states do not coexist in the same circular DNA but also when they are present at the same time in replicating DNA molecules. We also review differences between eukaryotic and prokaryotic cellular strategies that permit relaxation of positive supercoiling arising ahead of the replication forks. We end our review by discussing very recent studies giving a long-sought answer to the question of how slow DNA topoisomerases capable of relaxing just a few positive supercoils per second can counteract the introduction of hundreds of positive supercoils per second ahead of advancing replication forks.
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Frank-Kamenetskii, Maxim. "Waves of DNA supercoiling." Nature 337, no. 6204 (January 1989): 206. http://dx.doi.org/10.1038/337206a0.

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Dissertations / Theses on the topic "DNA supercoiling"

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Cortini, Ruggero. "Chiral theory of DNA supercoiling." Thesis, Imperial College London, 2013. http://hdl.handle.net/10044/1/10935.

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DNA supercoiling is a fundamental biological process occurring in all cells. We developed a theory of braiding (supercoiling) of a pair of DNA molecules that takes into account the contribution of the bending and the electrostatic energy. The electrostatic interaction was calculated within the framework of the Kornyshev-Leikin theory of DNA interactions, which takes into account realistic helical patterns of charge. Because of the chirality of the charge patterns, we predict that left-handed braiding of a pair of DNA molecules is more favourable than right-handed braiding. Applying our model to the case of closed loop DNA supercoiling and to single molecule DNA micromanipulations, we predict novel effects that have not yet been experimentally observed. We show that supercoiling may occur in topologically relaxed plasmids, as a consequence of attractive chiral forces. We speculate about the potential biological role of the predicted effects in the case of topoisomerase action, and the occurrence of positively supercoiled DNA in hyperthermophilic bacteria and archea. Our findings also suggest alternative an explanation of well-known experiments that proved that divalent ions overwind DNA. We also give an explanation for pairing of homologous DNA molecules in monovalent salt, and explain the occurrence of tight supercoiling observed in cryo-electron and atomic force microscopy. The analysis of existing experimental data shows that in most cases the chiral effects that we predict remain elusive. The theory therefore awaits final experimental verification.
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Mitelheiser, Sylvain. "DNA gyrase, quinolone drugs and supercoiling mechanism." Thesis, University of East Anglia, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.423811.

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Kampranis, Sotirios C. "DNA gyrase : mechanism of supercoiling and interaction with quinolones." Thesis, University of Leicester, 1998. http://hdl.handle.net/2381/29626.

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DNA gyrase is unique among topoisomerases in its ability to introduce negative supercoils into closed-circular DNA. Deletion of the C-terminal DNA-binding domain of the A subunit of gyrase gives rise to an enzyme that behaves like a conventional type II topoisomerase, suggesting that the unique properties of DNA gyrase are attributable to the wrapping of DNA around the C-terminal DNA-binding domains of the A subunits. However, these results do not unveil the detailed mechanism by which the transported DNA segment is captured and directed through the DNA gate. This mechanism was addressed by probing the topology of the bound DNA segment at distinct steps of the catalytic cycle. A model is proposed in which gyrase captures a contiguous DNA segment with high probability, irrespective of the superhelical density of the DNA, while the efficiency of strand passage depends on the superhelical free-energy. This mechanism is concerted, in that capture of the transported segment induces opening of the DNA gate, which in turn, stimulates ATP hydrolysis. Mutation of Glu42 to Ala in the B subunit of DNA gyrase abolishes ATP hydrolysis but not nucleotide binding. Gyrase complexes that contain one wild-type and one Ala42 mutant B protein were formed and the ability of such complexes to hydrolyse ATP was investigated. It was found that ATP hydrolysis was able to proceed only in the wild-type subunit, albeit at a lower rate. With only one ATP molecule hydrolysed at a time, gyrase could still perform supercoiling but the limit of this reaction was lower than that observed when both subunits can hydrolyse the nucleotide. Limited proteolysis was used to identify conformational changes in DNA gyrase and the proteolytic signatures observed were interpreted in terms of four complexes of gyrase, each representing a particular conformational state. Quinolone binding to the gyrase-DNA complex induces a conformational change that results in the blocking of supercoiling. Under these conditions gyrase is still capable of ATP hydrolysis. The kinetics of this reaction have been studied and found to differ from those of the reaction of the drug-free enzyme. By observing the conversion of the ATPase rate to the quinolone-characteristic rate, the formation and dissociation of the gyrase-DNA-quinolone complex can be monitored. Comparison of the time dependence of the conversion of the gyrase ATPase with that of DNA cleavage reveals that formation of the gyrase-DNA-quinolone complex does not correspond to the formation of cleaved DNA. Quinolone binding and drug-induced DNA cleavage are separate processes constituting two sequential steps in the mechanism of action of quinolones on DNA gyrase.
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LaMarr, William Albino 1969. "The effect of supercoiling on small molecule-DNA interactions." Thesis, Massachusetts Institute of Technology, 1998. http://hdl.handle.net/1721.1/50414.

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Corless, Samuel. "Role of DNA supercoiling in genome structure and regulation." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/9623.

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A principle challenge of modern biology is to understand how the human genome is organised and regulated within a nucleus. The field of chromatin biology has made significant progress in characterising how protein and DNA modifications reflect transcription and replication state. Recently our lab has shown that the human genome is organised into large domains of altered DNA helical twist, called DNA supercoiling domains, similar to the regulatory domains observed in prokaryotes. In my PhD I have analysed how the maintenance and distribution of DNA supercoiling relates to biological function in human cells. DNA supercoiling domains are set up and maintained by the balanced activity of RNA transcription and topoisomerase enzymes. RNA polymerase twists the DNA, over-winding in front of the polymerase and under-winding behind. In contrast topoisomerases relieve supercoiling from the genome by introducing transient nicks (topoisomerase I) or double strand breaks (topoisomerase II) into the double helix. Topoisomerase activity is critical for cell viability, but the distribution of topoisomerase I, IIα and IIβ in the human genome is not known. Using a chromatin immunoprecipitation (ChIP) approach I have shown that topoisomerases are enriched in large chromosomal domains, with distinct topoisomerase I and topoisomerase II domains. Topoisomerase I is correlated with RNA polymerase II, genes and underwound DNA, whereas topoisomerase IIα and IIβ are associated with each other and over-wound DNA. This indicates that different topoisomerase proteins operate in distinct regions of the genome and can be independently regulated depending on the genomic environment. Transcriptional regulation by DNA supercoiling is believed to occur through changes in gene promoter structure. To investigate DNA supercoiling my lab has developed biotinylated trimethylpsoralen (bTMP) as a DNA structure probe, which preferentially intercalates into under-wound DNA. Using bTMP in conjunction with microarrays my lab identified a transcription and topoisomerase dependent peak of under-wound DNA in a meta-analysis of several hundred genes (Naughton et al. (2013)). In a similar analysis, Kouzine et al. (2013) identified an under-wound promoter structure and proposed a model of topoisomerase distribution for the regulation of promoter DNA supercoiling. To better understand the role of supercoiling and topoisomerases at gene promoters, a much larger-scale analysis of these factors was required. I have analysed the distribution of bTMP at promoters genome wide, confirming a transcription and expression dependent distribution of DNA supercoils. DNA supercoiling is distinct at CpG island and non-CpG island promoters, and I present a model in which over-wound DNA limits transcription from both CpG island promoters and repressed genes. In addition, I have mapped by ChIP topoisomerase I and IIβ at gene promoters on chromosome 11 and identified a different distribution to that proposed by Kouzine et al. (2013), with topoisomerase I maintaining DNA supercoiling at highly expressed genes. This study provides the first comprehensive analysis of DNA supercoiling at promoters and identifies the relationship between supercoiling, topoisomerase distribution and gene expression. In addition to regulating transcription, DNA supercoiling and topoisomerases are important for genome stability. Several studies have suggested a link between DNA supercoiling and instability at common fragile sites (CFSs), which are normal structures in the genome that frequently break under replication stress and cancer. bTMP was used to measure DNA supercoiling across FRA3B and FRA16D CFSs, identifying a transition to a more over-wound DNA structure under conditions that induce chromosome fragility at these regions. Furthermore, topoisomerase I, IIα and IIβ showed a pronounced depletion in the vicinity of the FRA3B and FRA16D CFSs. This provides the first experimental evidence of a role for DNA supercoiling in fragile site formation.
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Sekibo, Doreen. "The effects of DNA supercoiling and G-quadruplex formation." Thesis, University of Southampton, 2013. https://eprints.soton.ac.uk/367077/.

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The self-association of guanine bases in a tetrameric square planar arrangement was first determined in the early 1960s. The tetramer, commonly termed the G-quartet, can stack upon other G-quartets to form four-stranded helices termed G-quadruplexes. Bioinformatics studies have revealed that guanine-rich sequences with the propensity to adopt these structures are found in telomeric DNA and throughout the human genome, particularly in gene promoter regions. It is thought that the location of these sequences is not a coincidence and that the folding potential of guanine-rich DNA in vivo may play an important role in biological events such as gene regulation. Repetitive guanine tracts of G-quadruplex-forming DNAs form highly polymorphic structures with parallel or antiparallel strand orientations, depending the on ionic condition and the length of the connecting loops, and can be assembled as inter- or intra-molecular complexes. While extensive research has demonstrated their formation in vitro, there is little direct evidence to support their formation in vivo. With the exception of the single-stranded telomeric DNA, all genomic guanine-rich sequences are always present in the duplex configuration. Therefore, these structures will need to compete with the duplex that is normally generated with the complementary cytosine-rich strand. In order for this to happen would first require the local dissociation of the strands. Negative supercoiling results from the unwinding of the DNA helix and is known to provide energy to facilitate the formation of a number of alternative DNA structures. The work described in this thesis therefore aims to investigate the formation of G-quadruplexes under negatively supercoiled conditions. This was examined by preparing plasmids that contained multiple copies of G-rich oligonucleotides, based on the sequences (G3T)n and (G3T4)n, cloned into the pUC19 vector. The formation of G-quadruplexes within these repeats has been assessed using the chemical probes dimethyl sulphate (DMS) and potassium permanganate, and the single-strand specific endonuclease S1. DMS probing revealed some evidence for G-quadruplex formation in (G3T)n sequences, though this was not affected by DNA supercoiling. However, probing with KMnO4 failed to detect exposed thymines in the loop regions, though there was some supercoil-dependent reactivity in the surrounding sequences, suggesting that this had been affected by the G-rich region. In contrast, the (G3T4)n sequences did not demonstrate protection from DMS, suggesting that G-quadruplex formation had not taken place. Surprisingly, the KMnO4 reactions identified structural alterations around, but not within, the inserted G-rich fragments. S1 nuclease digestions did not detect any structural perturbations in any of the sequences apart from a mutant plasmid containing an inverted quadruplex repeat at the 3’-end. Two-dimensional gel electrophoresis of DNA topoisomers was also conducted to detect any supercoil-dependent B-DNA to quadruplex transitions. Neither the (G3T)n nor (G3T4)n plasmids showed any such structural changes. However, the mutant plasmid did demonstrate some supercoil-dependent changes, though these may correspond to cruciform rather than G-quadruplex formation. These results do not support the suggestion that negative supercoiling can induce the formation of G-quadruplex structures.
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Barth, Marita Christine. "Analysis of the structural changes caused by positive DNA supercoiling." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/39907.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2007.
Includes bibliographical references.
The procession of helix-tracking enzymes along a DNA molecule results in the formation of supercoils in the DNA, with positive supercoiling (overwinding) generated ahead of the enzyme, and negative supercoiling (underwinding) in its wake. While the structural and physiological consequences of negative supercoiling have been well studied, technical challenges have 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 has only been identified, however, at a degree of supercoiling substantially higher than is generated physiologically. To examine the structural changes resulting from physiological levels of positive DNA supercoiling, I have developed a method for preparing highly purified positively supercoiled plasmid substrates. Based on a method previously developed in this laboratory, this allows for preparation of large quantities of very pure, highly positively supercoiled plasmid. It also expands on earlier methods by exploiting ionic strength to modulate the direction of supercoiling introduced, allowing preparation of either positively or negatively supercoiled substrates.
(cont.) A combination of approaches has been used to elucidate changes to DNA structure that result from physiological levels of positive supercoiling. Enzymatic probes for regions of single-stranded character are not reactive with positively supercoiled plasmid, indicating that stably unpaired regions are not present. Additionally, the effect of supercoiling on the activity of restriction enzymes has been examined. With the enzymes tested, no substantial differences in cleavage rates were observed with either positively or negatively supercoiled substrates. To examine structural changes at a wider range of superhelical densities, design and preparation was undertaken on 2-aminopurine-containing DNA substrates for use in fluorescence studies with a magnetic micromanipulator. Technical limitations rendered these experiments infeasible with current instrumentation, but important insights were gained for future fluorescence-based A destabilizing effect on the base pairs, however, can be seen using Raman difference spectroscopy, suggesting a subtle shift toward the more extreme extrahelical state.
(cont.) The Raman data suggest that structural adjustments due to positive supercoiling are small but significant, and in addition to the base-pairing effects, alterations are observed in phosphodiester torsion and the minor groove environment, as well as a slight shift in sugar pucker conformation to accommodate lengthening of the DNA backbone. These results point to subtle changes in DNA structure caused by biologically relevant levels of positive superhelical tension and positive supercoiling. All of the changes are consistent with the mechanical effects of helical overwinding and suggest a model in which base pair destabilization in overwound DNA could affect the search mechanisms used by DNA repair enzymes and the binding of other proteins to DNA.
by Marita Christine Barth.
Ph.D.
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Bond, Christine M. "Study of the DNA topoisomerases of human placental mitochondria." Thesis, University of York, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.235725.

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Zhi, Xiaoduo. "Transcription-Coupled DNA Supercoiling in Escherichia Coli: Mechanisms and Biological Functions." FIU Digital Commons, 2012. http://digitalcommons.fiu.edu/etd/865.

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Transcription by RNA polymerase can induce the formation of hypernegatively supercoiled DNA both in vivo and in vitro. This phenomenon has been explained by a “twin-supercoiled-domain” model of transcription where a positively supercoiled domain is generated ahead of the RNA polymerase and a negatively supercoiled domain behind it. In E. coli cells, transcription-induced topological change of chromosomal DNA is expected to actively remodel chromosomal structure and greatly influence DNA transactions such as transcription, DNA replication, and recombination. In this study, an IPTG-inducible, two-plasmid system was established to study transcription-coupled DNA supercoiling (TCDS) in E. coli topA strains. By performing topology assays, biological studies, and RT-PCR experiments, TCDS in E. coli topA strains was found to be dependent on promoter strength. Expression of a membrane-insertion protein was not needed for strong promoters, although co-transcriptional synthesis of a polypeptide may be required. More importantly, it was demonstrated that the expression of a membrane-insertion tet gene was not sufficient for the production of hypernegatively supercoiled DNA. These phenomenon can be explained by the “twin-supercoiled-domain” model of transcription where the friction force applied to E. coli RNA polymerase plays a critical role in the generation of hypernegatively supercoiled DNA. Additionally, in order to explore whether TCDS is able to greatly influence a coupled DNA transaction, such as activating a divergently-coupled promoter, an in vivo system was set up to study TCDS and its effects on the supercoiling-sensitive leu-500 promoter. The leu-500 mutation is a single A-to-G point mutation in the -10 region of the promoter controlling the leu operon, and the AT to GC mutation is expected to increase the energy barrier for the formation of a functional transcription open complex. Using luciferase assays and RT-PCR experiments, it was demonstrated that transient TCDS, “confined” within promoter regions, is responsible for activation of the coupled transcription initiation of the leu-500 promoter. Taken together, these results demonstrate that transcription is a major chromosomal remodeling force in E. coli cells.
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Hobbs, Jeanette Roseanna. "Structural studies on the DNA binding modes of topoisomerase poisons." Thesis, University of Reading, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.342117.

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Books on the topic "DNA supercoiling"

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McBride, A. J. A. Studies on DNA supercoiling and potential Z-DNA forming sequences in streptomyces. Manchester: UMIST, 1995.

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Book chapters on the topic "DNA supercoiling"

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Gabibov, A., E. Yakubouskaya, M. Lukin, P. Favorov, A. Reshetnyak, and M. Monastyrsky. "Dynamics of DNA Supercoiling." In Topology in Molecular Biology, 43–67. Berlin, Heidelberg: Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/978-3-540-49858-2_4.

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Thompson, J. M. T. "Supercoiling of DNA Molecules." In Solid Mechanics and Its Applications, 513–24. Dordrecht: Springer Netherlands, 2002. http://dx.doi.org/10.1007/978-94-015-9930-6_39.

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Drlica, K., M. Malik, and J. Rouviere-Yaniv. "Intracellular DNA Supercoiling in Bacteria." In Nucleic Acids and Molecular Biology, 55–66. Berlin, Heidelberg: Springer Berlin Heidelberg, 1992. http://dx.doi.org/10.1007/978-3-642-77356-3_3.

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Wang, James C. "DNA Supercoiling and Gene Expression." In The Jerusalem Symposia on Quantum Chemistry and Biochemistry, 173–81. Dordrecht: Springer Netherlands, 1986. http://dx.doi.org/10.1007/978-94-009-5466-3_18.

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Tang, G.-Q., and S. Kunugi. "DNA Supercoiling Under High Pressure." In Advances in High Pressure Bioscience and Biotechnology, 315–18. Berlin, Heidelberg: Springer Berlin Heidelberg, 1999. http://dx.doi.org/10.1007/978-3-642-60196-5_70.

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Liu, Yingting, Zhi-Chun Hua, and Fenfei Leng. "DNA Supercoiling Measurement in Bacteria." In Methods in Molecular Biology, 63–73. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7459-7_4.

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Harvey, Stephen C., and Robert K. Z. Tan. "Development of a Model for DNA Supercoiling." In Unusual DNA Structures, 91–101. New York, NY: Springer New York, 1988. http://dx.doi.org/10.1007/978-1-4612-3800-3_6.

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Clark, David J., and Benoît Leblanc. "Analysis of DNA Supercoiling Induced by DNA-Protein Interactions." In Methods in Molecular Biology™, 523–35. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-015-1_30.

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Clark, David J., and Benoît P. Leblanc. "Analysis of DNA Supercoiling Induced by DNA–Protein Interactions." In Methods in Molecular Biology, 161–72. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2877-4_10.

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Wang, James C., and A. Simon Lynch. "Effects of DNA Supercoiling on Gene Expression." In Regulation of Gene Expression in Escherichia coli, 127–47. Boston, MA: Springer US, 1996. http://dx.doi.org/10.1007/978-1-4684-8601-8_7.

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Conference papers on the topic "DNA supercoiling"

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Ikenna, Ivenso, and Todd D. Lillian. "The Dynamics of DNA Supercoiling: A Brownian Dynamics Study." In ASME 2015 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/detc2015-47444.

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Induced torsional stresses lead to an increase in the magnitude of torque sustained by double stranded DNA. There exists a critical magnitude of torque at which the DNA buckles signaling the beginning of the formation of a plectonemically supercoiled domain in the DNA. Further torsional deformation leads to an increase in the size of the supercoiled domain while the torque sustained by the DNA remains constant. The formation of the supercoiled domain also leads to a reduction in the end-to-end extension of the DNA starting with an abrupt reduction at the onset of buckling. Experiments have shown that this reduction in extension follows a linear trend. We investigate, by means of Brownian dynamics simulations, the extensional and torsional response of dsDNA to induced torsional stresses.
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Rainford, Penn Faulkner, Aalap Mogre, Victor Velasco-Berrelleza, Charles J. Dorman, Sarah Harris, Carsten Kröger, and Susan Stepney. "A π-calculus Model of Supercoiling DNA Circuits." In The 2023 Conference on Artificial Life. MIT Press, 2023. http://dx.doi.org/10.1162/isal_a_00582.

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Lillian, Todd D., and N. C. Perkins. "Electrostatics and Self Contact in an Elastic Rod Approximation for DNA." In ASME 2009 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2009. http://dx.doi.org/10.1115/detc2009-86632.

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DNA is a life-sustaining molecule that enables the storage and retrieval of genetic information. In its role during essential cellular processes, this long flexible molecule is significantly bent and twisted. Previously, we developed an elasto-dynamic rod approximation to study DNA deformed into a loop by a gene regulatory protein (lac repressor) and predicted the energetics and topology of the loops. Although adequate for DNA looping, our model neglected electrostatic interactions which are essential when considering processes that result in highly super-coiled DNA including plectonemes. Herein we extend the rod approximation to account for electrostatic interactions and present strategies that improve computational efficiency. Our calculations for the stability for a circularly bent rod and for an initially straight rod compare favorably to existing equilibrium models. With this new capability, we are now well-positioned to study the dynamics of transcription and other dynamic processes that result in DNA supercoiling.
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Samori, Bruno, Giuliano Siligardi, Carla Quagliarello, Albrecht L. Weisenhorn, James Vesenka, and Carlos J. Bustamante. "Chirality of the local supercoiling of individual DNA molecules assigned by atomic force microscopy." In OE/LASE'93: Optics, Electro-Optics, & Laser Applications in Science& Engineering, edited by Clayton C. Williams. SPIE, 1993. http://dx.doi.org/10.1117/12.146374.

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Reports on the topic "DNA supercoiling"

1

Cook, David Nelson. Studies of DNA supercoiling in vivo and in vitro. Office of Scientific and Technical Information (OSTI), October 1990. http://dx.doi.org/10.2172/10191743.

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2

Cook, D. N. Studies of DNA supercoiling in vivo and in vitro. Office of Scientific and Technical Information (OSTI), October 1990. http://dx.doi.org/10.2172/6993672.

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