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 contribution presents 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
attention paid to the elastic and topological properties of DNA.
Finally, advances in the understanding of electrophoresis, a
technique of crucial importance in everyday molecular biology, are
exposed in T. Duke's contribution.
The third section presents provides an overview of the main
computational approaches to integrate, analyse and simulate
molecular and genetic networks. First, J. van Helden introduces a
series of statistical and computational methods allowing the
identification of short nucleic fragments putatively involved in
the regulation of gene expression from sets of promoter sequences
controlling co-expressed genes. Next, the chapter by Samsonova et
al. connects this issue of transcriptional regulation with that of
the control of cell differentiation and pattern formation during
embryonic development. Finally, H. de Jong and D. Thieffry review a
series of mathematical approaches to model the dynamical behaviour
of complex genetic regulatory networks. This contribution includes
brief descriptions and references to successful applications of
these approaches, including the work of B. Novak, on the dynamical
modelling of cell cycle in different model organisms, from yeast to
mammals.
. Provides a comprehensive overview of the structure and function
of DNA and RNA at the interface between physics, biology and
information science.
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