Mathematics of DNA structure, function and interactions

Stephen D. Levene, Lynn Zechiedrich (auth.), Craig John Benham, Stephen Harvey, Wilma K. Olson, De Witt Sumners, David Swigon (eds.)144190669X, 9781441906694

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 and 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.

Table of contents :
Front Matter….Pages i-xi
Nick Cozzarelli: A Personal Remembrance….Pages 1-5
Mathematical Methods in Dna Topology: Applications to Chromosome Organization and Site-Specific Recombination….Pages 7-36
Conformational Statistics of Dna and Diffusion Equations on The Euclidean Group….Pages 37-52
Perspectives On DNA Looping….Pages 53-71
Differences Between Positively and Negatively Supercoiled DNA that Topoisomerases May Distinguish….Pages 73-121
Calibration of Tethered Particle Motion Experiments….Pages 123-138
Difference Topology: Analysis of High-Order DNA-Protin Assemblies….Pages 139-158
Useful Intrusions of DNA Topology Into Experiments on Protein-DNA Geometry….Pages 159-175
Topological Analysis of DNA-Protein Complexes….Pages 177-194
Closing the Loop on Protein-DNA Interactions: Interplay Between Shape and Flexibility in Nucleoprotein Assemblies Having Implications for Biological Regulation….Pages 195-212
Four-Way Helical Junctions in DNA Molecules….Pages 213-224
Micromechanics of Single Supercoiled DNA Molecules….Pages 225-249
Flexibility Of Nucleosomes On Topologically Constrained DNA….Pages 251-291
The Mathematics of DNA Sturcture, Mechanics, and Dynamics….Pages 293-320
Paradox Regained: a Topological Coupling of Nuclesomal DNA Wrapping and Chromatin Fibre Coiling….Pages 321-329
Statistical-Mechanical Analysis of Enzymatic Topological Transformations in DNA Molecules….Pages 331-346
Back Matter….Pages 1-8