Relevant bibliographies by topics / DNA looping

Academic literature on the topic 'DNA looping'

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Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "DNA looping"

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Schleif, Robert. "DNA Looping." Annual Review of Biochemistry 61, no. 1 (June 1992): 199–223. http://dx.doi.org/10.1146/annurev.bi.61.070192.001215.

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Schleif, R. "DNA looping." Science 240, no. 4849 (April 8, 1988): 127–28. http://dx.doi.org/10.1126/science.3353710.

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Matthews, K. S. "DNA looping." Microbiological Reviews 56, no. 1 (1992): 123–36. http://dx.doi.org/10.1128/mmbr.56.1.123-136.1992.

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Matthews, K. S. "DNA looping." Microbiological Reviews 56, no. 1 (1992): 123–36. http://dx.doi.org/10.1128/mr.56.1.123-136.1992.

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Travers, Andrew. "DNA Topology: Dynamic DNA Looping." Current Biology 16, no. 19 (October 2006): R838—R840. http://dx.doi.org/10.1016/j.cub.2006.08.070.

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Perez, Pamela, Nicolas Clauvelin, Michael Grosner, Andrew Colasanti, and Wilma Olson. "What Controls DNA Looping?" International Journal of Molecular Sciences 15, no. 9 (August 27, 2014): 15090–108. http://dx.doi.org/10.3390/ijms150915090.

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Halford, Stephen E., Abigail J. Welsh, and Mark D. Szczelkun. "Enzyme-Mediated DNA Looping." Annual Review of Biophysics and Biomolecular Structure 33, no. 1 (June 9, 2004): 1–24. http://dx.doi.org/10.1146/annurev.biophys.33.110502.132711.

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Crellin, Paul, Sven Sewitz, and Ronald Chalmers. "DNA Looping and Catalysis." Molecular Cell 13, no. 4 (February 2004): 537–47. http://dx.doi.org/10.1016/s1097-2765(04)00052-8.

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Carter, Ashley R., Obinna A. Ukogu, Adam D. Smith, Luka M. Devenica, Ryan McMillan, Yuxing Ma, and Hilary Bediako. "Protamin-Induced DNA Looping." Biophysical Journal 114, no. 3 (February 2018): 443a—444a. http://dx.doi.org/10.1016/j.bpj.2017.11.2452.

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Hao, Nan, Adrienne E. Sullivan, Keith E. Shearwin, and Ian B. Dodd. "The loopometer: a quantitative in vivo assay for DNA-looping proteins." Nucleic Acids Research 49, no. 7 (January 28, 2021): e39-e39. http://dx.doi.org/10.1093/nar/gkaa1284.

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Abstract Proteins that can bring together separate DNA sites, either on the same or on different DNA molecules, are critical for a variety of DNA-based processes. However, there are no general and technically simple assays to detect proteins capable of DNA looping in vivo nor to quantitate their in vivo looping efficiency. Here, we develop a quantitative in vivo assay for DNA-looping proteins in Escherichia coli that requires only basic DNA cloning techniques and a LacZ assay. The assay is based on loop assistance, where two binding sites for the candidate looping protein are inserted internally to a pair of operators for the E. coli LacI repressor. DNA looping between the sites shortens the effective distance between the lac operators, increasing LacI looping and strengthening its repression of a lacZ reporter gene. Analysis based on a general model for loop assistance enables quantitation of the strength of looping conferred by the protein and its binding sites. We use this ‘loopometer’ assay to measure DNA looping for a variety of bacterial and phage proteins.
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Dissertations / Theses on the topic "DNA looping"

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Le, Tung T. "Single-molecule biophysics of DNA bending: looping and unlooping." Diss., Georgia Institute of Technology, 2015. http://hdl.handle.net/1853/53979.

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DNA bending plays a vital role in numerous cellular activities such as transcription, viral packaging, and nucleosome formation. Therefore, understanding the physics of DNA bending at the length scales relevant to these processes is one of the main keys to the quantitative description of life. However, previous studies provide a divided picture on how DNA should be modeled in strong bending condition relevant to biology. My thesis is devoted to answering how far an elastic rod model can be applied to DNA. We consider several subtle features that could potentially lead to the break-down of the worm-like chain model, such as local bendedness of the sequence and large bending angles. We used single-molecule Fluorescence Resonance Energy Transfer to track looping and unlooping of single DNA molecules in real time. We compared the measured looping and unlooping rates with theoretical predictions of the worm-like chain model. We found that the intrinsic curvature of the sequence affects the looping propensity of short DNA and an extended worm-like chain model including the helical parameters of individual base pairs could adequately explain our measurements. For DNA with random sequence and negligible curvature, we discovered that the worm-like chain model could explain the stability of small DNA loops only down to a critical loop size. Below the critical loop size, the bending stress stored in the DNA loop became less sensitive to loop size, indicative of softened dsDNA. The critical loop size is sensitive to salt condition, especially to magnesium at mM concentrations. This finding enabled us to explain several contrasting results in the past and shed new light on the energetics of DNA bending.
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Gemmen, Gregory John. "DNA tethering characterization, enzyme-mediated DNA looping under tension, and nucleosome stability in the force measuring optical tweezers." Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2006. http://wwwlib.umi.com/cr/ucsd/fullcit?p3205050.

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Thesis (Ph. D.)--University of California, San Diego, 2006.
Title from first page of PDF file (viewed April 4, 2006). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.
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Cui, Lun. "DNA looping mediated transcriptional regulation." Thesis, 2014. http://hdl.handle.net/2440/92805.

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Protein binding to DNA sequences is the foundation of transcriptional regulation. By binding at specific DNA sequences, such as promoters, proteins can recruit other proteins to regulate gene transcription. Some proteins, which bind at separated DNA binding sites, can interact via the formation of a DNA loop. DNA looping is essential in many processes, such as replication, recombination and gene regulation. In prokaryotic systems, DNA looping is involved in some genetic switches, which can control bacteriophage lysogenic/lytic pathways or bacterial catabolic pathways. Small DNA loops are essential for effective repression of several operons in bacteria. In eukaryotic systems, enhancers are distal gene regulatory elements, which can be located far away from the promoter. The formation of DNA looping is thought to be necessary for the function of enhancers. Bacteriophage λ CI repressor activates the transcription of its own gene, while the CI mediated looping represses its own transcription. This DNA looping mediated long-range repression improves the efficiency of the lambda lysogenic/lytic switch. However, evidence in the literature suggests an additional activation effect of λ CI DNA looping. In Chapters 2 and 3, I investigated this long-range λ CI DNA looping mediated transcriptional activation. By using a synthetic λ CI DNA looping reporter system, I confirmed that λ CI DNA looping can mediate enhancer-like long-range transcriptional activation. In vivo experiments showed that the λ PRM promoter was activated by the α C-terminal domain (CTD) of RNA polymerase contacting an UP element located 2.3 kilobases away from the PRM promoter. A physicochemical model of the in vivo data showed that an RNA polymerase α subunit recruitment mechanism could fully explain this activation effect. DNA-protein structural modelling found that the bending of linker sequence between OL2 and the UP element is required for the contact. The efficiency of long range DNA looping has been studied in Chapter 4. In vivo Lac looping and lambda CI DNA looping constructs were used to generate data for calculating DNA looping efficiency. DNA loop sizes ranging from 250 bp to 10000 bp were tested. Tethered particle motion (TPM) experiments, performed by our collaborators, generated in vitro DNA looping data by using Lac mediated DNA loops ranging from 600 bp to 3200 bp. Based on these in vitro and in vitro data, mathematical modelling calculated DNA looping parameters for understanding DNA looping efficiency. The insertion of DNA looping constructs into the E.coli chromosome (by using a bacteriophage integrase based approach) also led us to make a one-step integration system (OSIP), described in Chapter 5. The OSIP system is a set of OSIP plasmids, which can mediate one-step bacterial chromosomal integration of DNA sequences. The cloning module of each OSIP plasmid has both the integrase gene and corresponding att sequences, which are required for integrating the OSIP plasmid into the bacterial chromosome. An integration protocol, called clonetegration, was developed by coupling the OSIP system with in vitro isothermal DNA assembly. Clonetegration bypasses plasmid propagation and purification procedures by transferring assembly products directly into target competent cells.
Thesis (Ph.D.) -- University of Adelaide, School of Molecular and Biomedical Science, 2014
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Law, Scott Michael. "Effects of interoperator length and DNA sequence on lac repressor-mediated DNA looping and the local concentration of lac repressor in Vivo." 1993. http://catalog.hathitrust.org/api/volumes/oclc/31276254.html.

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Priest, David Geoffrey. "Testing the DNA loop domain model in Escherichia coli." Thesis, 2014. http://hdl.handle.net/2440/99568.

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The ability of DNA to form loops has been employed by evolution in almost every aspect of biology involving DNA, not least the regulation of gene transcription. The biophysical constraints on looping of the DNA polymer at short range (< 300 bp) have been extensively studied, however it is uncertain how the probability of DNA looping decays at longer range. The first part of this thesis presents a quantitative investigation of long range DNA looping both in vivo in E. coli and in vitro. DNA looping is more efficient in vivo than measured in vitro (by our collaborators) with the technique of Tethered Particle Motion (TPM), and we suggest that DNA supercoiling aids DNA looping in vivo. By measuring long-range looping in vivo using the two well-characterised looping proteins (the LacI and λCI repressors) and thermodynamic models of DNA looping, the decay in looping probability is quantified over the range 242–10000 bp. Furthermore this decay is shown to be a property of the DNA tether linking the loop, independent of the nature of the DNA looping protein(s). Enhancers activate genes at long distance irrespective of position and orientation, so why don’t enhancers activate the wrong genes? In other words, what mechanisms drive efficiency and specificity in enhancer-promoter looping? The loop domain model proposes that DNA loops formed by insulators pose a topological barrier that restricts the reach of enhancers to the vicinity of desired target promoter(s). Specifically, the model predicts that two DNA loops in an alternating arrangement should form somewhat mutually exclusively (i.e. they should interfere with one another’s formation), whereas nested DNA loops are predicted to assist one another’s formation, and side-by-side loops should form independently. In the second part of this thesis, the loop domain model is tested in E. coli by combining LacI and λCI-mediated DNA loops in these different orientations. Accordingly, we quantify DNA looping assistance and interference by fitting experimental data to a statistical-mechanical model, confirming the predictions of the loop domain model. Furthermore, TPM measurements of the same looping constructs support predictions that non-supercoiled DNA in vitro should facilitate DNA looping assistance, but not interference. In addition to confirming the loop domain model in E. coli, this thesis provides a strong experimental and theoretical foundation for further investigations of enhancer-promoter looping in prokaryotes and eukaryotes, and the relationship between chromatin architecture and gene expression in metazoans.
Thesis (Ph.D.) (Research by Publication) -- University of Adelaide, School of Molecular and Biomedical Science, 2014.
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Vogel, Sabine Katja [Verfasser]. "Mechanistic studies on transcription activation via DNA looping in a prokaryotic promoter-enhancer system / presented by Sabine Katja Vogel." 2004. http://d-nb.info/972519467/34.

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MacPherson, Melissa. "Biochemical Studies of the CTCF Insulator Protein: Determination of Protein Interactions with CTCF using Tandem Affinity Purification, Characterization of its Post-translational Modification by the Small Ubiquitin-like Modifier Proteins and Studies of CTCF DNA Looping Ability." Thesis, 2010. http://hdl.handle.net/1807/26205.

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The CTCF protein is involved in several important aspects of gene regulation including transcriptional activation, transcriptional repression and insulator ability. It is also involved in the regulation of epigenetic processes including X-chromosome inactivation and the maintenance of genomic imprinting. CTCF has been shown to bind to approximately 15 000 sites in the mammalian genome and has been implicated in nuclear organization. The CTCF protein mediates long-range chromatin interactions and is believed to form DNA loops. It also acts to block the communication of an enhancer with a promoter by acting as an insulator. Despite its importance in gene regulation, the molecular mechanisms that govern CTCF’s ability to perform its myriad functions remain enigmatic. In this thesis, I add insight into our understanding of the mechanisms behind CTCF’s function. I show that CTCF is post-translationally modified by the Small Ubiquitin-like Modifier proteins and that this post-translational modification contributes to its repressive ability at the c-myc P2 promoter. I also show that CTCF is localized to the sub-nuclear compartment called the Polycomb bodies. The Polycomb protein Pc2 acts as an E3 ligase to enhance the SUMOylation of CTCF by SUMOs 2 and 3. These findings help to explain CTCF’s ability to act as a transcriptional repressor. I also report biochemical evidence to support the role for CTCF in forming an unusual DNA structure, possibly a loop. I hypothesize that a single CTCF binding site is able to form DNA loops. These findings suggest mechanisms by which CTCF is able to organize the mammalian genome and to function as an insulator protein. In addition to these findings I have also purified CTCF interacting proteins through the use of the tandem affinity purification technique. The interacting proteins contain many chromatin and DNA binding proteins further suggesting a role for CTCF in chromatin organization. The results in this thesis enhance our knowledge of the molecular mechanisms of CTCF function and provide a basis for the improved understanding of CTCF mediated gene expression.
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Books on the topic "DNA looping"

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Chess, Andrew, and Schahram Akbarian. The Human Brain and its Epigenomes. Edited by Dennis S. Charney, Eric J. Nestler, Pamela Sklar, and Joseph D. Buxbaum. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190681425.003.0003.

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Conventional psychopharmacology elicits an insufficient therapeutic response in more than one half of patients diagnosed with schizophrenia, bipolar disorder, depression, anxiety, or related disorders. This underscores the need to further explore the neurobiology and molecular pathology of mental disorders in order to develop novel treatment strategies of higher efficacy. One promising avenue of research is epigenetics.Deeper understanding of genome organization and function in normal and diseased human brain will require comprehensive charting of neuronal and glial epigenomes. This includes DNA cytosine and adenine methylation, hundred(s) of residue-specific post-translational histone modifications and histone variants, transcription factor occupancies, and chromosomal conformations and loopings. Epigenome mappings provide an important avenue to assign function to many risk-associated DNA variants and mutations that do not affect protein-coding sequences. Powerful novel single cell technologies offer the opportunity to understand genome function in context of the vastly complex cellular heterogeneity and neuroanatomical diversity of the human brain.
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Book chapters on the topic "DNA looping"

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Finzi, Laura. "Perspectives On DNA Looping." In Mathematics of DNA Structure, Function and Interactions, 53–71. New York, NY: Springer New York, 2009. http://dx.doi.org/10.1007/978-1-4419-0670-0_4.

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Shoura, Massa J., and Stephen D. Levene. "Understanding DNA Looping Through Cre-Recombination Kinetics." In Discrete and Topological Models in Molecular Biology, 405–18. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-40193-0_19.

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Finzi, Laura, Carlo Manzo, Chiara Zurla, Haowei Wang, Dale Lewis, Sankar Adhya, and David Dunlap. "DNA Looping in Prophage Lambda: New Insight from Single-Molecule Microscopy." In Biological and Medical Physics, Biomedical Engineering, 193–212. New York, NY: Springer New York, 2010. http://dx.doi.org/10.1007/978-0-387-92808-1_9.

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Paro, Renato, Ueli Grossniklaus, Raffaella Santoro, and Anton Wutz. "Biology of Chromatin." In Introduction to Epigenetics, 1–28. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-68670-3_1.

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AbstractThis chapter provides an introduction to chromatin. We will examine the organization of the genome into a nucleosomal structure. DNA is wrapped around a globular complex of 8 core histone proteins, two of each histone H2A, H2B, H3, and H4. This nucleosomal arrangement is the context in which information can be established along the sequence of the DNA for regulating different aspects of the chromosome, including transcription, DNA replication and repair processes, recombination, kinetochore function, and telomere function. Posttranslational modifications of histone proteins and modifications of DNA bases underlie chromatin-based epigenetic regulation. Enzymes that catalyze histone modifications are considered writers. Conceptually, erasers remove these modifications, and readers are proteins binding these modifications and can target specific functions. On a larger scale, the 3-dimensional (3D) organization of chromatin in the nucleus also contributes to gene regulation. Whereas chromosomes are condensed during mitosis and segregated during cell division, they occupy discrete volumes called chromosome territories during interphase. Looping or folding of DNA can bring regulatory elements including enhancers close to gene promoters. Recent techniques facilitate understanding of 3D contacts at high resolution. Lastly, chromatin is dynamic and changes in histone occupancy, histone modifications, and accessibility of DNA contribute to epigenetic regulation.
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Zong, Chenghang. "Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) for the Analysis of DNA Copy Number Variation." In Neuromethods, 133–42. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7280-7_7.

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"DNA Looping." In Encyclopedia of Genetics, Genomics, Proteomics and Informatics, 528. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6754-9_4666.

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"Looping of DNA." In Encyclopedia of Genetics, Genomics, Proteomics and Informatics, 1122. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6754-9_9572.

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Manzo, Carlo, and Laura Finzi. "Quantitative Analysis of DNA-Looping Kinetics from Tethered Particle Motion Experiments." In Methods in Enzymology, 199–220. Elsevier, 2010. http://dx.doi.org/10.1016/s0076-6879(10)75009-6.

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Lucchesi, John C. "The basic mechanism of gene transcription." In Epigenetics, Nuclear Organization & Gene Function, 17–32. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198831204.003.0003.

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Transcription is initiated by factors that interact with RNA polymerases and recruit them to specific sites, unwind the DNA molecules and allow the synthesis of RNA transcripts complementary to one of the single DNA strands. RNA polymerase II (RNAPII) transcribes genes that encode proteins and some non-coding RNAs; RNAPI transcribes ribosomal RNA genes; RNAPIII transcribes genes that encode tRNAs and other non-coding RNAs. The transcription process starts with a pre-initiation complex (PIC), its activation and promoter clearance. Activation involves chromatin looping, usually promoted by the large multiprotein Mediator complex. RNAPII often makes a promoter-proximal pause, then resumes productive elongation of the transcript. Transition through the different phases of transcription is orchestrated by the phosphorylation of the main subunit of RNAPII. The 5´ end of many transcripts is protected by a methylated guanosine “cap,” and the 3´ end by the addition of a chain of adenosine monophosphates (polyadenylation). Many transcripts undergo splicing to remove regions that interrupt the coding sequence.
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Wu, Hai-Young, and Leroy F. Liu. "[20] Topological approaches to studies of protein-mediated looping of DNA in vivo." In Methods in Enzymology, 346–51. Elsevier, 1992. http://dx.doi.org/10.1016/0076-6879(92)12022-i.

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Conference papers on the topic "DNA looping"

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Kandinov, Alan, Krishnan Raghunathan, and Jens-Christian Meiners. "Using DNA looping to measure sequence dependent DNA elasticity." In SPIE NanoScience + Engineering, edited by Kishan Dholakia and Gabriel C. Spalding. SPIE, 2012. http://dx.doi.org/10.1117/12.945930.

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Lillian, Todd D., N. C. Perkins, and S. Goyal. "Computational Elastic Rod Model Applied to DNA Looping." In ASME 2007 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2007. http://dx.doi.org/10.1115/detc2007-34956.

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DNA is a long flexible biopolymer containing genetic information. Proteins often take advantage of DNA’s inherent flexibility to perform their cellular functions. Here we present selected results from our computational studies of the mechanical looping of DNA by the Lactose repressor protein. The Lactose repressor resides in the bacterium E. coli and deforms DNA into a loop as a means of controlling the production of enzymes necessary for digesting lactose. We examine this looping process using a computational rod model [1–3] to understand the strain energy and geometry for the resultant DNA loops. Our model captures the multiple looped conformations of the molecule arising from both multiple boundary conditions and geometric nonlinearities. In addition, the model captures the periodic variation of strain energy with base-pair length as suggested by repression experiments (see, for example, [4, 5]).
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Wilson, David P., Todd Lillian, Sachin Goyal, Alexei V. Tkachenko, Noel C. Perkins, and Jens-Christian Meiners. "Understanding the role of thermal fluctuations in DNA looping." In SPIE Fourth International Symposium on Fluctuations and Noise, edited by Sergey M. Bezrukov. SPIE, 2007. http://dx.doi.org/10.1117/12.724717.

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Milstein, J. N., Yih-Fan Chen, and Jens-Christian Meiners. "Protein-mediated DNA looping in a fluctuating micromechanical environment." In SPIE NanoScience + Engineering, edited by Kishan Dholakia and Gabriel C. Spalding. SPIE, 2010. http://dx.doi.org/10.1117/12.860048.

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Anderson, L. Meadow, and Haw Yang. "A simplified model for lysogenic regulation through DNA looping." In 2008 30th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2008. http://dx.doi.org/10.1109/iembs.2008.4649226.

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Smith, Douglas E., Gregory J. Gemmen, and Rachel Millin. "DNA looping and cleavage by restriction enzymes studied by manipulation of single DNA molecules with optical tweezers." In SPIE Optics + Photonics, edited by Kishan Dholakia and Gabriel C. Spalding. SPIE, 2006. http://dx.doi.org/10.1117/12.681504.

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Lillian, Todd D. "An Elastic Rod Representation for the LacI-DNA Loop Complex." In ASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2011. http://dx.doi.org/10.1115/detc2011-47407.

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The well-recognized Lac repressor protein (LacI) regulates transcription by bending DNA into a loop. In addition to the known role of DNA flexibility, there is accumulating evidence suggesting that the flexibility of LacI also plays a role in this gene regulation. Here we extend our elastic rod model for DNA (previously used to model DNA only) to represent LacI. Specifically, we represent sites of concentrated flexibility in the protein with flexible elastic rod domains; and we represent relatively rigid domains of the protein with stiff elastic rod domains. Our analysis shows the sensitivity of looping energetics to the degree of flexibility within the protein over a large range of DNA lengths. In addition, we show that the predicted energetically dominant binding topology (A) remains upon introducing protein flexibility.
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Blumberg, Seth, Arivalagan Gajraj, Matthew Pennington, Alexei Tkachenko, and Jens-Christian Meiners. "The role of thermal fluctuations and mechanical constraints in protein-mediated DNA looping." In SPIE Third International Symposium on Fluctuations and Noise, edited by Nigel G. Stocks, Derek Abbott, and Robert P. Morse. SPIE, 2005. http://dx.doi.org/10.1117/12.609496.

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Kajino, Taisuke, Teppei Shimamura, Shuyi Gong, Kiyoshi Yanagisawa, Masahiro Nakatochi, Sebastian Griesing, Yukako Shimada, et al. "Abstract 2464: Divergent lncRNAMYMLRregulates MYC by eliciting DNA looping and promoter-enhancer interaction." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-2464.

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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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