Mathematics of DNA Structure, Function and Interactions

by Benham, Craig John; Harvey, Stephen; Olson, Wilma K.; Sumners, De Witt L.; Swigon, David

• ISBN13: 9781441906694
• ISBN10: 144190669X
• Format: Hardcover
• Copyright: 2009-09-29
• Publisher: Springer Verlag

Summary

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 onMathematics 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 vitallife processes.

Table of Contents

Foreword	p. v
Preface	p. vii
Nick Cozzarelli: A personal remembrance	p. 1
Mathematical methods in DNA topology: Applications to chromosome organization and site-specific recombination	p. 7
Conformational statistics of DNA and diffusion equations on the Euclidean group	p. 37
Perspectives on DNA looping	p. 53
Differences between positively and negatively supercoiled DNA that topoisomerases may distinguish	p. 73
Calibration of tethered particle motion experiments	p. 123
Difference topology: Analysis of high-order DNA-protein assemblies	p. 139
Useful intrusions of DNA topology into experiments on protein-DNA geometry	p. 159
Topological analysis of DNA-protein complexes	p. 177
Closing the loop on protein-DNA interactions: Interplay between shape and flexibility in nucleoprotein assemblies having implications for biological regulation	p. 195
Four-way helical junctions in DNA molecules	p. 213
Micromechanics of single supercoiled DNA molecules	p. 225
Flexibility of nucleosomes on topologically constrained DNA	p. 251
The mathematics of DNA structure, mechanics, and dynamics	p. 293
Paradox regained: a topological coupling of nucleosomal DNA wrapping and chromatin fibre coiling	p. 321
Statistical-mechanical analysis of enzymatic topological transformations in DNA molecules	p. 331
List of workshop participants	p. 347
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