Giovanni Zocchi
- Published in print:
- 2018
- Published Online:
- January 2019
- ISBN:
- 9780691173863
- eISBN:
- 9781400890064
- Item type:
- chapter
- Publisher:
- Princeton University Press
- DOI:
- 10.23943/princeton/9780691173863.003.0002
- Subject:
- Physics, Soft Matter / Biological Physics
DNA is a deformable molecule. The term “deformable” implies phenomena rooted in the collective behavior of many atoms, and a description based on concepts of continuum and statistical mechanics. Long ...
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DNA is a deformable molecule. The term “deformable” implies phenomena rooted in the collective behavior of many atoms, and a description based on concepts of continuum and statistical mechanics. Long DNA molecules are an excellent experimental system to study the equilibrium conformations and dynamics of long, flexible molecules. This chapter discusses the following: DNA melting, the zipper model, experimental melting curves, base pairing and base stacking as separate, Hamiltonian formulation of the zipper model, 2 × 2 model, nearest neighbor model, connection to nonlinear dynamics, linear and nonlinear elasticity of DNA, bending modulus and persistence length, measurements of DNA elasticity (short and long molecules), the Euler instability, and the DNA yield transition.Less
DNA is a deformable molecule. The term “deformable” implies phenomena rooted in the collective behavior of many atoms, and a description based on concepts of continuum and statistical mechanics. Long DNA molecules are an excellent experimental system to study the equilibrium conformations and dynamics of long, flexible molecules. This chapter discusses the following: DNA melting, the zipper model, experimental melting curves, base pairing and base stacking as separate, Hamiltonian formulation of the zipper model, 2 × 2 model, nearest neighbor model, connection to nonlinear dynamics, linear and nonlinear elasticity of DNA, bending modulus and persistence length, measurements of DNA elasticity (short and long molecules), the Euler instability, and the DNA yield transition.
Frederic Lawrence Holmes
- Published in print:
- 2001
- Published Online:
- October 2013
- ISBN:
- 9780300085402
- eISBN:
- 9780300129663
- Item type:
- chapter
- Publisher:
- Yale University Press
- DOI:
- 10.12987/yale/9780300085402.003.0004
- Subject:
- History, History of Science, Technology, and Medicine
This chapter discusses the responses proposed by others to the challenge posed by Max Delbruck's provocative paper on the DNA replication problem. This occurred while Meselson and Stahl attended to ...
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This chapter discusses the responses proposed by others to the challenge posed by Max Delbruck's provocative paper on the DNA replication problem. This occurred while Meselson and Stahl attended to more immediate tasks. At the time, responses appeared on two widely divergent levels. On an abstract plane that appealed particularly to physicists, there appeared topographical models suggesting alternatives to Delbruck's scheme for resolving the unwinding dilemma. On an experimental plane, some of the members of the phage network sought to trace the patterns of distribution of parental DNA molecules into progeny DNA. Somewhere between these levels, Jim Watson himself took Delbruck's objections seriously enough to think about alternative structures for DNA that might obviate the unwinding problem altogether.Less
This chapter discusses the responses proposed by others to the challenge posed by Max Delbruck's provocative paper on the DNA replication problem. This occurred while Meselson and Stahl attended to more immediate tasks. At the time, responses appeared on two widely divergent levels. On an abstract plane that appealed particularly to physicists, there appeared topographical models suggesting alternatives to Delbruck's scheme for resolving the unwinding dilemma. On an experimental plane, some of the members of the phage network sought to trace the patterns of distribution of parental DNA molecules into progeny DNA. Somewhere between these levels, Jim Watson himself took Delbruck's objections seriously enough to think about alternative structures for DNA that might obviate the unwinding problem altogether.
David Bensimon, Vincent Croquette, Jean-François Allemand, Xavier Michalet, and Terence Strick
- Published in print:
- 2018
- Published Online:
- February 2019
- ISBN:
- 9780198530923
- eISBN:
- 9780191864711
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/oso/9780198530923.001.0001
- Subject:
- Physics, Soft Matter / Biological Physics
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 ...
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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.Less
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.
Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Stéphane Vialette
- Published in print:
- 2009
- Published Online:
- August 2013
- ISBN:
- 9780262062824
- eISBN:
- 9780262258753
- Item type:
- book
- Publisher:
- The MIT Press
- DOI:
- 10.7551/mitpress/9780262062824.001.0001
- Subject:
- Mathematics, Mathematical Biology
From one cell to another, from one individual to another, and from one species to another, the content of DNA molecules is often similar. The organization of these molecules, however, differs ...
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From one cell to another, from one individual to another, and from one species to another, the content of DNA molecules is often similar. The organization of these molecules, however, differs dramatically, and the mutations that affect this organization are known as genome rearrangements. Combinatorial methods are used to reconstruct putative rearrangement scenarios in order to explain the evolutionary history of a set of species, often formalizing the evolutionary events that can explain the multiple combinations of observed genomes as combinatorial optimization problems. This book offers a comprehensive survey of this rapidly expanding application of combinatorial optimization. It can be used as a reference for experienced researchers or as an introductory text for a broader audience. Genome rearrangement problems have proved so interesting from a combinatorial point of view that the field now belongs as much to mathematics as to biology. The book takes a mathematically oriented approach, but provides biological background when necessary. It presents a series of models, beginning with the simplest (which is progressively extended by dropping restrictions), each constructing a genome rearrangement problem. The book also discusses an important generalization of the basic problem known as the median problem, surveys attempts to reconstruct the relationships between genomes with phylogenetic trees, and offers a collection of summaries and appendixes with additional information.Less
From one cell to another, from one individual to another, and from one species to another, the content of DNA molecules is often similar. The organization of these molecules, however, differs dramatically, and the mutations that affect this organization are known as genome rearrangements. Combinatorial methods are used to reconstruct putative rearrangement scenarios in order to explain the evolutionary history of a set of species, often formalizing the evolutionary events that can explain the multiple combinations of observed genomes as combinatorial optimization problems. This book offers a comprehensive survey of this rapidly expanding application of combinatorial optimization. It can be used as a reference for experienced researchers or as an introductory text for a broader audience. Genome rearrangement problems have proved so interesting from a combinatorial point of view that the field now belongs as much to mathematics as to biology. The book takes a mathematically oriented approach, but provides biological background when necessary. It presents a series of models, beginning with the simplest (which is progressively extended by dropping restrictions), each constructing a genome rearrangement problem. The book also discusses an important generalization of the basic problem known as the median problem, surveys attempts to reconstruct the relationships between genomes with phylogenetic trees, and offers a collection of summaries and appendixes with additional information.
Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Steéphane Vialette
- Published in print:
- 2009
- Published Online:
- August 2013
- ISBN:
- 9780262062824
- eISBN:
- 9780262258753
- Item type:
- chapter
- Publisher:
- The MIT Press
- DOI:
- 10.7551/mitpress/9780262062824.003.0001
- Subject:
- Mathematics, Mathematical Biology
This introductory chapter first discusses the molecular evolution and the birth of the combinatorics of genome rearrangements. It then describes the genome rearrangement problem; the scope of the ...
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This introductory chapter first discusses the molecular evolution and the birth of the combinatorics of genome rearrangements. It then describes the genome rearrangement problem; the scope of the present survey; an overview of the models; and the organization of the book.Less
This introductory chapter first discusses the molecular evolution and the birth of the combinatorics of genome rearrangements. It then describes the genome rearrangement problem; the scope of the present survey; an overview of the models; and the organization of the book.
