Author: Stefan Michael Giovan
Publisher:
ISBN:
Category : DNA repair
Languages : en
Pages : 212
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Book Description
A complex connection exists between the 3 dimensional topological state of DNA in living organisms and biological processes including gene expression, DNA replication, recombination and repair. A significant limitation in developing a detailed, quantitative understanding of this connection is due to a lack of rigorous methods to calculate statistical mechanical properties of DNA molecules with complex topologies, including supercoiling, looping and knotting. This dissertation's main focus is on developing such methods and applying them to realistic DNA and nucleoprotein models. In chapter 2, a method is presented to calculate free energies and J factors of protein mediated DNA loops by normal mode analysis (NMA). This method is similar to calculations performed previously but with several significant advances. We apply the method to the specific case of DNA looping mediated by Cre recombinase protein. J factors calculated by our method are compared to experimental measurements to extract geometric and elastic properties of the Cre-DNA synaptic complex. In particular, the results suggest the existence of a synaptic complex that is more flexible than previously expected and may be explained by a stable intermediate in the reaction pathway that deviates significantly from the planar crystal structure. Calculating free energies of DNA looping is difficult in general, especially when considering intermediate length scales such as plasmid sized DNA which may readily adopt multiple topological states. In chapter 3, a novel method is presented to obtain free energies of semiflexible biopolymers with fixed topologies and arbitrary ratios of contour length L to persistence length P. High accuracy is demonstrated by calculating free energies of specific DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.
Author: Luke Czapla
Publisher:
ISBN:
Category : DNA-protein interactions
Languages : en
Pages : 126
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Book Description
There are many challenges involved in the simulation of DNA. In this work, novel Monte Carlo techniques are developed and applied to understanding the biophysical properties of DNA. A coarse-grained model is applied to feasibly simulate long DNA chains of hundreds to thousands of base pairs, using a reduced base-pair step representation of the DNA. Using this model, a canonical Monte Carlo simulation of DNA is developed to characterize the structure and flexibility of double-helical DNA. By applying a unique algorithm for generating uncorrelated DNA conformations a priori, limitations of the original Metropolis Monte Carlo algorithm are avoided. Furthermore, there is developing experimental evidence that non-specifically associating proteins that induce DNA bending modulate the in-vivo flexibility of DNA. To investigate the effect of these proteins, a grand canonical Monte Carlo simulation technique is developed, extending the model of free DNA to incorporate non-specific protein-DNA interactions. In this technique, DNA chains are simulated with varying numbers of bound proteins. Ubiquitous DNA architectural proteins such as the prokaroytic nucleoid protein HU and the eukaryotic HMG-box proteins are investigated with this technique. By incorporating structural information from the protein-DNA complexes currently available in the Nucleic Acid Database, models of these DNA-binding proteins are constructed and used in this method. The results predict an enhancement of DNA flexibility due to non-specific binding of these proteins, and calculations of the cyclization (ring-closure) properties and force-extension responses of protein-bound DNA chains compared to free DNA chains are presented. In addition, the effects of these proteins on the topological properties of closed circular DNA and on the looping properties of DNA constrained by binding to the Lac repressor protein assembly are characterized in large-scale parallel simulations. Coordination of protein binding on circular and looped DNA and induction of negative supercoiling of DNA by DNA architectural proteins is predicted, with important biological implications for chromosome organization and transcription regulation.
Author: Alexander Vologodskii
Publisher: CRC Press
ISBN: 135135583X
Category : Medical
Languages : en
Pages : 192
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Book Description
Topology and Physics of Circular DNA presents comprehensive coverage of the physical properties of circular DNA. The author examines how topological constraints arising from cyclization of DNA lead to distinctive properties that make closed molecules radically different from linear DNA. The phenomenon of supercoiling, its geometric and topological analysis, and the formation of noncanonical structures in circular DNA under the influence of supercoiling are emphasized. The combination of consistent theoretical analysis and detailed treatment of major experimental approaches make Topology and Physics of Circular DNA an important reference volume for biophysicists, biochemists, molecular biologists, and researchers and students who want to expand their understanding of circular DNA.
Author: Craig John Benham
Publisher: Springer Science & Business Media
ISBN: 1441906711
Category : Medical
Languages : en
Pages : 359
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Book Description
Propelled by the success of the sequencing of the human and many related genomes, molecular and cellular biology has delivered significant scientific breakthroughs. Mathematics (broadly defined) continues to play a major role in this effort, helping to discover the secrets of life by working collaboratively with bench biologists, chemists and physicists. Because of its outstanding record of interdisciplinary research and training, the IMA was an ideal venue for the 2007-2008 IMA thematic year on Mathematics of Molecular and Cellular Biology. The kickoff event for this thematic year was a tutorial on Mathematics of Nucleic Acids, followed by the workshop Mathematics of Molecular and Cellular Biology, held September 15--21 at the IMA. This volume is dedicated to the memory of Nicholas R. Cozzarelli, a dynamic leader who fostered research and training at the interface between mathematics and molecular biology. It contains a personal remembrance of Nick Cozzarelli, plus 15 papers contributed by workshop speakers. The papers give an overview of state-of-the-art mathematical approaches to the understanding of DNA structure and function, and the interaction of DNA with proteins that mediate vital life processes.
Author: Carol R. Lamberson
Publisher:
ISBN:
Category :
Languages : en
Pages : 308
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Book Description
The synthesis and DNA binding properties of three macrocyclic diacridines (31, 32 and 33) is discussed. The two acridines are connected by linker chains at the 4- and 9-positions. Macrocycles 31 and 32 are linked via spermine at the 9-position and have been shown to bind to DNA by bisintercalation using absorption spectroscopy titrations, thermal denaturation studies, and viscometric titrations 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 the macrocycle binds to DNA by formation of a catenated complex in which one linking chain is located in opposite grooves of the DNA. The NMR studies and absorption spectral titrations suggest that 31 binds by insertion of the acridines on each side of one base pair in violation of the neighbor exclusion principle. Macrocycle 33 has a diamide linker chain at the 9-position of the acridine rings. This molecule binds to DNA by intercalation as evident from its ability to remove and reverse the supercoils in closed circular DNA. However, the results are inconclusive as to whether it binds by mono- or bisintercalation. The mono-linked diacridine 34 has been shown to bind to DNA by bisintercalation. The preliminary synthetic results for a novel trisintercalator are discussed. Trimer 35 consists of a naphthalene diimide as the central chromophore and two 9-aminoacridines as the terminal chromophores. Trimer 35 was synthesized from 1,4,5,8-naphthalene dianhydride which was reacted with the mono-Boc protected diamine to give the N,N$spprime$-disubstituted naphthalene diimide. After deprotection, the diimide was reacted with two moles of 9-phenoxyacridine to produce 35. The dimer 36 containing a naphthalene diimide and one 9-aminoacridine was synthesized in a similar manner.
Author: Wan Yuan Beatrice Soh
Publisher:
ISBN:
Category :
Languages : en
Pages : 222
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Book Description
Over two decades ago, with advances in microfabrication techniques and fluorescence microscopy, single-molecule studies emerged as a powerful approach to investigate polymer dynamics at the molecular level. By providing a platform for the direct observation and precise manipulation of individual polymer molecules, single-molecule studies allow for the probing of microscopic interactions that give rise to the macroscopic properties of the polymer system. Single molecule studies have been widely used to investigate the static and dynamic properties of double-stranded deoxyribonucleic acid (DNA) as a model polymer. Such studies not only help to develop a fundamental understanding of key topics in polymer physics that cannot be easily accessed via traditional bulk experimental methods, but also facilitate the development of emerging DNA mapping and sequencing techniques. The majority of single-molecule studies to date have involved linear DNA molecules. It is known that topological constraints on the molecular level have a signicant influence on polymer dynamics. A nascent area in the field of polymer physics is the study of polymers with complex topologies. In this thesis, we present a series of single-molecule experiments and Brownian dynamics simulations used to investigate the polymer physics of topologically complex DNA. Specically, we focus on knotted polymers, ring polymers and catenated polymer networks. To investigate the impact of a knot on polymer dynamics, we employ a combined approach of single-molecule experiments and Brownian dynamics simulations. We study experimentally the steady-state behavior of knotted polymers in planar elongational fields and nd that the presence of a knot leads to a faster relaxation time and, accordingly, a shift in the coilstretch transition for the molecule. In consequence, the untying of a knot near the coilstretch transition can give rise to dramatic changes in chain conformation. We use Brownian dynamics simulations to study in detail the impact of the knot untying process on polymer dynamics in planar elongational fields and complement the simulations with experimental results. As a knot moves o the chain in an elongational field, the knot size changes due to the non-uniform tension prole along the chain and causes a change in the eective Weissenberg number, which in turn leads to a change in chain extension. With the use of simulations, we further investigate the knot untying process by probing the topological pathway of an untying knot. We study the distributions of knot conformational states and knot untying pathways on uniformly tensioned chains and chains subjected to elongational fields, and demonstrate that external fields can be used to influence how a knot unties from a chain. Next, we shift focus to ring polymers. We use single-molecule experiments to study the dynamics of self-entangled circular DNA. Our results demonstrate that ring polymers can self-entangle by forming self-threadings, and that such threadings can lead to a signicant slowdown in polymer dynamics. It seems counterintuitive that self-entanglements can arise in ring polymers, which lack chain ends. To delve into the physics of self-entanglements on circular chains, we implement a macroscopic system that allows for the direct visualization of chain conformation. We investigate the formation of self-entanglements on granular chains subjected to a tumbling motion, and use the well-studied self-entanglements on linear chains as a framework for interpreting self-entanglements on circular chains. We develop a method to characterize the self-entanglements on circular chains with known topological descriptors from knot theory and propose a general mechanism for the self-entanglement of circular chains. Finally, we consider the deformation dynamics of catenated DNA networks. A kinetoplast is a complex network of catenated DNA rings that resembles a two-dimensional polymeric system. We perform single-molecule experiments to study the deformation response of kinetoplasts in a planar elongational field. Our results demonstrate that kinetoplasts deform in a stagewise fashion and undergo transient deformation at large strains, as a result of conformational rearrangements from a metastable state. In contrast to linear polymers that display a coil-stretch transition, kinetoplasts do not exhibit an abrupt transition between the non-deformed and deformed states.
Author: Victor A. Bloomfield
Publisher: Sterling Publishing Company
ISBN: 9780935702491
Category : Science
Languages : en
Pages : 854
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Book Description
Providing a comprehensive account of the structures and physical chemistry properties of nucleic acids, with special emphasis on biological function, this text has been organized to meet the needs of those who have only a basic understanding of physical chemistry and molecular biology.
Author: Remus T. Dame
Publisher: Springer Nature
ISBN: 1071639307
Category :
Languages : en
Pages : 654
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Book Description
Author:
Publisher:
ISBN:
Category : Medicine
Languages : en
Pages : 1498
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Book Description
Author: Roderick D.M. Page
Publisher: John Wiley & Sons
ISBN: 1444313363
Category : Science
Languages : en
Pages : 352
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Book Description
The study of evolution at the molecular level has given the subject of evolutionary biology a new significance. Phylogenetic 'trees' of gene sequences are a powerful tool for recovering evolutionary relationships among species, and can be used to answer a broad range of evolutionary and ecological questions. They are also beginning to permeate the medical sciences. In this book, the authors approach the study of molecular evolution with the phylogenetic tree as a central metaphor. This will equip students and professionals with the ability to see both the evolutionary relevance of molecular data, and the significance evolutionary theory has for molecular studies. The book is accessible yet sufficiently detailed and explicit so that the student can learn the mechanics of the procedures discussed. The book is intended for senior undergraduate and graduate students taking courses in molecular evolution/phylogenetic reconstruction. It will also be a useful supplement for students taking wider courses in evolution, as well as a valuable resource for professionals. First student textbook of phylogenetic reconstruction which uses the tree as a central metaphor of evolution. Chapter summaries and annotated suggestions for further reading. Worked examples facilitate understanding of some of the more complex issues. Emphasis on clarity and accessibility.
