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Relevant bibliographies by topics / DNA unzipping

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Academic literature on the topic 'DNA unzipping'

Author: Grafiati

Published: 14 March 2023

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Journal articles on the topic "DNA unzipping"

1

Krautbauer, Rupert, Matthias Rief, and Hermann E. Gaub. "Unzipping DNA Oligomers." Nano Letters 3, no. 4 (April 2003): 493–96. http://dx.doi.org/10.1021/nl034049p.

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Chakrabarti, Buddhapriya, and David R. Nelson. "Shear Unzipping of DNA†." Journal of Physical Chemistry B 113, no. 12 (March 26, 2009): 3831–36. http://dx.doi.org/10.1021/jp808232p.

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Kafri, Y., D. Mukamel, and L. Peliti. "Melting and unzipping of DNA." European Physical Journal B - Condensed Matter 27, no. 1 (May 1, 2002): 135–46. http://dx.doi.org/10.1140/epjb/e20020138.

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Amnuanpol, Sitichoke. "Physical origin of DNA unzipping." Journal of Biological Physics 42, no. 1 (August 26, 2015): 69–82. http://dx.doi.org/10.1007/s10867-015-9393-0.

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Lubensky, David K., and David R. Nelson. "Pulling Pinned Polymers and Unzipping DNA." Physical Review Letters 85, no. 7 (August 14, 2000): 1572–75. http://dx.doi.org/10.1103/physrevlett.85.1572.

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Volkov, S. N., and A. V. Solov’yov. "The mechanism of DNA mechanical unzipping." European Physical Journal D 54, no. 3 (June 30, 2009): 657–66. http://dx.doi.org/10.1140/epjd/e2009-00194-5.

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CALVO, J., J. NIETO, J. SOLER, and M. O. VÁSQUEZ. "ON A DISPERSIVE MODEL FOR THE UNZIPPING OF DOUBLE-STRANDED DNA MOLECULES." Mathematical Models and Methods in Applied Sciences 24, no. 03 (December 29, 2013): 495–511. http://dx.doi.org/10.1142/s0218202513500577.

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The paper deals with the analysis of a nonlinear Fokker–Planck equation modeling the mechanical unzipping of double-stranded DNA under the influence of an applied force. The dependent variable is the probability density of unzipping m base pairs. The nonlinear Fokker–Planck equation we propose here is obtained when we couple the model proposed in [D. K. Lubensky and D. R. Nelson, Pulling pinned polymers and unzipping DNA, Phys. Rev. Lett.85 (2000) 1572–1575] with a transcendental equation for the applied force. The resulting model incorporates nonlinear effects in a different way than the usual models in kinetic theory. We show the well-posedness of this model. For that we require a combination of techniques coming from second-order kinetic equations and compensated compactness arguments in conservation laws.

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Mathé, Jérôme, Hasina Visram, Virgile Viasnoff, Yitzhak Rabin, and Amit Meller. "Nanopore Unzipping of Individual DNA Hairpin Molecules." Biophysical Journal 87, no. 5 (November 2004): 3205–12. http://dx.doi.org/10.1529/biophysj.104.047274.

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Viasnoff, V., N. Chiaruttini, J. Muzard, and U. Bockelmann. "Force fluctuations assist nanopore unzipping of DNA." Journal of Physics: Condensed Matter 22, no. 45 (October 29, 2010): 454122. http://dx.doi.org/10.1088/0953-8984/22/45/454122.

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Li, Xinqiong, Guiqin Song, Linqin Dou, Shixin Yan, Ming Zhang, Weidan Yuan, Shirong Lai, et al. "The structure and unzipping behavior of dumbbell and hairpin DNA revealed by real-time nanopore sensing." Nanoscale 13, no. 27 (2021): 11827–35. http://dx.doi.org/10.1039/d0nr08729g.

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Dissertations / Theses on the topic "DNA unzipping"

1

Baldazzi, Valentina. "Statistical mechanics of unzipping : Bayesian inference of DNA sequence." Université Louis Pasteur (Strasbourg) (1971-2008), 2006. https://publication-theses.unistra.fr/public/theses_doctorat/2005/BALDAZZI_Valentina_2005.pdf.

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Herskowitz, Lawrence J. "Kinetic and statistical mechanical modeling of DNA unzipping and kinesin mechanochemistry." THE UNIVERSITY OF NEW MEXICO, 2011. http://pqdtopen.proquest.com/#viewpdf?dispub=3440145.

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Marenduzzo, Davide. "Phases of Polymers and Biopolymers." Doctoral thesis, SISSA, 2002. http://hdl.handle.net/20.500.11767/4581.

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In this thesis we develop coarse grained models aiming at understanding physical problems arising from phase transitions which occur at the single molecule level. The thesis will consist of two parts, grossly related to and motivated by the two subjects dealt with above. In the first half, we will focus on critical phenomena in stretching experiments, namely in DNA unzipping and polymer stretching in a bad solvent. In the second part, we will develop a model of thick polymers, with the goal of understanding the origin of the protein folds and the physics underlying the folding ‘transition’, as well as with the hope of shedding some light on some of the fundamental questions highlighted in this Introduction. In the first part of the thesis we will introduce a simple model of self-avoiding walks for DNA unzipping. In this way we can map out the phase diagram in the force vs. temperature plane. This reveals the present of an interesting cold unzipping transition. We then go on to study the dynamics of this coarse grained model. The main result which we will discuss is that the unzipping dynamics below the melting temperature obeys different scaling laws with respect to the opening above thermal denaturation, which is governed by temperature induced fluctuating bubbles. Motivated by this and by recent results from other theoretical groups, we move on to study the relation to DNA unzipping of the stretching of a homopolymer below the theta point. Though also in this case a cold unzipping is present in the phase diagram, this situation is richer from the theoretical point of view because the physics depends crucially on dimension: the underlying phase transition indeed is second order in two dimensions and first order in three. This is shown to be intimately linked to the failure of mean field in this phenomena, unlike for DNA unzipping. In particular, the globule unfolds via a series (hierarchy) of minima. In two dimensions they survive in the thermodynamic limit whereas if the dimension, d, is greater than 2, there is a crossover and for very long polymers the intermediate minima disappear. We deem it intriguing that an intermediate step in this minima hierarchy for polymers of finite length in the three-dimensional case is a regular mathematical helix, followed by a zig-zag structure. This is found to be general and almost independent of the interaction potential details. It suggests that a helix, one of the well-known protein secondary structure, is a natural choice for the ground state of a hydrophobic protein which has to withstand an effective pulling force. In the second part, we will follow the inverse route and ask for a minimal model which is able to account for the basic aspects of folding. By this, we mean a model which contains a suitable potential which has as its ground state a protein-like structure and which can account for the known thermodynamical properties of the folding transition. The existing potential which are able to do that[32] are usually constructed ‘ad hoc’ from knowledge of the native state. We stress that our procedure here is completely different and the model which we propose should be built up starting from minimal assumptions. Our main result is the following. If we throw away the usual view of a polymer as a sequence of hard spheres tethered together by a chain (see also Chapter 1) and substitute it with the notion of a flexible tube with a given thickness, then upon compaction our ’thick polymer’ or ’tube’ will display a rich secondary structure with protein-like helices and sheets, in sharp contrast with the degenerate and messy crumpled collapsed phase which is found with a conventional bead-and-link or bead-and-spring homopolymer model. Sheets and helices show up as the polymer gets thinner and passes from the swollen to the compact phase. In this sense the most interesting regime is a ‘twilight’ zone which consists of tubes which are at the edge of the compact phase, and we thus identify them as ‘marginally compact strucures’. Note the analogy with the result on stretching, in which the helices were in the same way the ‘last compact’ structures or the ‘first extended’ ones when the polymer is being unwinded by a force. After this property of ground states is discussed, we proceed to characterize the thermodynamics of a flexible thick polymer with attraction. The resulting phase diagram is shown to have many of the properties which are usually required from protein effective models, namely for thin polymers there is a second order collapse transition (O collapse) followed, as the temperature is lowered, by a first order transition to a semicrystalline phase where the compact phase orders forming long strands all aligned preferentially along some direction. For thicker polymers the transition to this latter phase occurs directly from the swollen phase, upon lowering T, through a first order transition resembling the folding transition of short proteins.

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Books on the topic "DNA unzipping"

1

Regenerative Processes Involving the CAMP Unzipping of DNA: Synthesis of Proteins Integrating Plasticity and Longevity. Nova Science Publishers, Incorporated, 2017.

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2

Bensimon, David, Vincent Croquette, Jean-François Allemand, Xavier Michalet, and Terence Strick. Single-Molecule Studies of Nucleic Acids and Their Proteins. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198530923.001.0001.

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This book presents a comprehensive overview of the foundations of single-molecule studies, based on manipulation of the molecules and observation of these with fluorescent probes. It first discusses the forces present at the single-molecule scale, the methods to manipulate them, and their pros and cons. It goes on to present an introduction to single-molecule fluorescent studies based on a quantum description of absorption and emission of radiation due to Einstein. Various considerations in the study of single molecules are introduced (including signal to noise, non-radiative decay, triplet states, etc.) and some novel super-resolution methods are sketched. The elastic and dynamic properties of polymers, their relation to experiments on DNA and RNA, and the structural transitions observed in those molecules upon stretching, twisting, and unzipping are presented. The use of these single-molecule approaches for the investigation of DNA–protein interactions is highlighted via the study of DNA and RNA polymerases, helicases, and topoisomerases. Beyond the confirmation of expected mechanisms (e.g., the relaxation of DNA torsion by topoisomerases in quantized steps) and the discovery of unexpected ones (e.g., strand-switching by helicases, DNA scrunching by RNA polymerases, and chiral discrimination by bacterial topoII), these approaches have also fostered novel (third generation) sequencing technologies.

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Book chapters on the topic "DNA unzipping"

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Merstorf, Céline, Benjamin Cressiot, Manuela Pastoriza-Gallego, Abdel Ghani Oukhaled, Laurent Bacri, Jacques Gierak, Juan Pelta, Loïc Auvray, and Jérôme Mathé. "DNA Unzipping and Protein Unfolding Using Nanopores." In Methods in Molecular Biology, 55–75. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-773-6_4.

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Cissé, Ismaïl, Pierre Mangeol, and Ulrich Bockelmann. "DNA Unzipping and Force Measurements with a Dual Optical Trap." In Single Molecule Analysis, 45–61. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-282-3_3.

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3

delToro, Damian J., and Douglas E. Smith. "Measuring Unzipping and Rezipping of Single Long DNA Molecules with Optical Tweezers." In Methods in Molecular Biology, 371–92. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8556-2_19.

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Bensimon, David, Vincent Croquette, Jean-François Allemand, Xavier Michalet, and Terence Strick. "Structural Transitions in DNA." In Single-Molecule Studies of Nucleic Acids and Their Proteins, 105–18. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198530923.003.0005.

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In this chapter we discuss the various structural transitions observed on dsDNA upon twisting and stretching: the transition to denatured DNA at negative twist and to P-DNA at positive twist; the transition to S-DNA at large force and its relation with DNA melting. We discuss mechanical unzipping of DNA and show how DNA rehybridization under tension in the presence of complementary oligonucleotides can be used to sequence the molecule.

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Li, Ming, and Michelle D. Wang. "Unzipping Single DNA Molecules to Study Nucleosome Structure and Dynamics." In Methods in Enzymology, 29–58. Elsevier, 2012. http://dx.doi.org/10.1016/b978-0-12-391938-0.00002-1.

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Conference papers on the topic "DNA unzipping"

1

Lubensky, David K. "Unzipping DNA: From Pulling to Pores and Back Again." In UNSOLVED PROBLEMS OF NOISE AND FLUCTUATIONS: UPoN 2002: Third International Conference on Unsolved Problems of Noise and Fluctuations in Physics, Biology, and High Technology. AIP, 2003. http://dx.doi.org/10.1063/1.1584908.

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Ye, Fan, James T. Inman, and Michelle D. Wang. "Mechanical unzipping of DNA molecules in parallel using nanophotonic tweezers." In Optical Trapping and Optical Micromanipulation XVII, edited by Kishan Dholakia and Gabriel C. Spalding. SPIE, 2020. http://dx.doi.org/10.1117/12.2570629.

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Neuman, Keir C., and Yeonee Seol. "Untwisting and Unzipping: Magnetic Tweezers Based Measurements of DNA Processing Enzymes." In Optical Trapping Applications. Washington, D.C.: OSA, 2015. http://dx.doi.org/10.1364/ota.2015.otw3e.1.

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4

Singh, Amar, and Navin Singh. "Role of chain stiffness and end entropy in the unzipping of DNA chain." In PROCEEDING OF INTERNATIONAL CONFERENCE ON RECENT TRENDS IN APPLIED PHYSICS AND MATERIAL SCIENCE: RAM 2013. AIP, 2013. http://dx.doi.org/10.1063/1.4810670.

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Wang, Michelle D., Steven J. Koch, Alla Shundrovsky, and Benjamin C. Jantzen. "Unzipping force analysis of protein association (UFAPA): a novel technique to probe protein-DNA interactions." In SPIE's First International Symposium on Fluctuations and Noise, edited by Sergey M. Bezrukov, Hans Frauenfelder, and Frank Moss. SPIE, 2003. http://dx.doi.org/10.1117/12.500332.

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