Titel: Multiple Aspects of DNA and Rna: From Biophysics to Bioinformatics: Lecture Notes of the Les Houches Summer School 2004
Herausgegeben von Didier Chatenay, Simona Cocco, Remi Monasson
ELSEVIER SCIENCE & TECHNOLOGY
November 2005 - gebunden - 354 Seiten
This book is dedicated to the multiple aspects, that is, biological, physical and computational of DNA and RNA molecules. These molecules, central to vital processes, have been experimentally studied by molecular biologists for five decades since the discovery of the structure of DNA by Watson and Crick in 1953. Recent progresses (e.g. use of DNA chips, manipulations at the single molecule level, availability of huge genomic databases...) have revealed an imperious need for theoretical modelling. Further progresses will clearly not be possible without an integrated understanding of all DNA and RNA aspects and studies.
The book is intended to be a desktop reference for advanced graduate students or young researchers willing to acquire a broad interdisciplinary understanding of the multiple aspects of DNA and RNA. It is divided in three main sections:
The first section comprises an introduction to biochemistry and biology of nucleic acids. The structure and function of DNA are reviewed in R. Lavery's chapter. The next contribution, by V. Fritsch and E. Westhof, concentrates on the folding properties of RNA molecules. The cellular processes involving these molecules are reviewed by J. Kadonaga, with special emphasis on the regulation of transcription. These chapters does not require any preliminary knowledge in the field (except that of elementary biology and chemistry).
The second section covers the biophysics of DNA and RNA, starting with basics in polymer physics in the contribution by R. Khokhlov. A large space is then devoted to the presentation of recent experimental and theoretical progresses in the field of single molecule studies. T. Strick's contributionpresents a detailed description of the various micro-manipulation techniques, and reviews recent experiments on the interactions between DNA and proteins (helicases, topoisomerases, ...). The theoretical modeling of single molecules is presented by J. Marko, with a special atten
Chapter 1 - R. Lavery: DNA Structure, Dynamics and Recognition Chapter 2 - V. Fritsch and E. Westhof: Introduction to non-Watson-Crick Base Pairs and RNA Folding Chapter 3 - J.T. Kadonaga: Regulation of Transcrption by RNA Polymerase II Chapter 4 - A.R. Khokhlov, E. Yu Kramarenko: Basic Concepts of Statistical Physics of Polymers Chapter 5 - T.A.J. Duke: The Physics of DNA Electrophoresis Chapter 6 - T.R. Strick: Single-Molecule Studies of DNA Mechanics and DNA/Protein Interactions Chapter 7 - J.F. Marko: Introduction to Single-DNA Micromechanics Chapter 8 - J. van Helden: The Analysis of Regulatory Sequences Chapter 9 - M.G. Samsonova: A Survey of Gene Circuit Approach Applied to Modelling of Segment Determination in Fruit Fly Chapter 10 - H. de Jong and D. Thieffry: Modeling, Analysis, and Simulation of Genetic Regulatory Networks: From Differential Equations to Logical Models
Didier Chatenay activities since 1995 is devoted to experimental research at the frontiers between physics and biology. His first contributions were in the field of single molecule experiments and particulary in the micromanipulation of single nucleic acid molecules (DNA, RNA). In particular he evidenced new structural transitions of a single DNA molecule submitted to an external force. Simona Cocco's research activity since 2001 is devoted to the applications of statistical physics to biophysics. Her main contributions on the latter issue, in collaboration with Remi Monasson, are related to the modeling of single molecule experiments, in particular the structural transtitions of the DNA and RNA molecules under mechanical stress. Remi Monasson's research activity since 1995 is devoted to the applications of statistical physics to interdisciplinary fields as computer science and biophysics. His main contributions on the latter issue, in collaboration with Simona Cocco, are related to the modeling of single molecule experiments, in particular the structural transitions of the DNA and RNA molecules under mechanical stress. The research of Denis Thieffry focuses on the development of qualitative tools for the integration, the modeling and the dynamical analysis of biological regulatory networks. These tools are currently applied to the dynamical modeling of gene networks involved in development, cell cycle and cancer. Jean Dalibard works in the field of atomic physics and quantum optics. His recent activities is centered on the physics of cold quantum gases, in particular Bose-Einstein condensation.