New PDF release: Multiple aspects of DNA and RNA from biophysics to

By Chatenay D., et al. (eds.)

ISBN-10: 0444520813

ISBN-13: 9780444520814

This e-book is devoted to the a number of points, that's, organic, actual and computational of DNA and RNA molecules. those molecules, primary to very important procedures, were experimentally studied by way of molecular biologists for 5 a long time because the discovery of the constitution of DNA by way of Watson and Crick in 1953. fresh progresses (e.g. use of DNA chips, manipulations on the unmarried molecule point, availability of big genomic databases...) have printed an imperious desire for theoretical modelling. extra progresses will essentially no longer be attainable with no an built-in figuring out of all DNA and RNA features and studies.The ebook is meant to be a laptop reference for complex graduate scholars or younger researchers prepared to obtain a extensive interdisciplinary knowing of the a number of points of DNA and RNA. it really is divided in 3 major sections:The first part includes an advent to biochemistry and biology of nucleic acids. The constitution and serve as of DNA are reviewed in R. Lavery's bankruptcy. the following contribution, by way of V. Fritsch and E. Westhof, concentrates at the folding houses of RNA molecules. The mobile approaches regarding those molecules are reviewed by way of J. Kadonaga, with targeted emphasis at the legislation of transcription. those chapters doesn't require any initial wisdom within the box (except that of simple biology and chemistry).The moment part covers the biophysics of DNA and RNA, beginning with fundamentals in polymer physics within the contribution via R. Khokhlov. a wide house is then dedicated to the presentation of modern experimental and theoretical progresses within the box of unmarried molecule reviews. T. Strick's contribution provides a close description of many of the micro-manipulation ideas, and studies fresh experiments at the interactions among DNA and proteins (helicases, topoisomerases, ...). The theoretical modeling of unmarried molecules is gifted by way of J. Marko, with a different cognizance paid to the elastic and topological homes of DNA. ultimately, advances within the realizing of electrophoresis, a strategy of the most important value in daily molecular biology, are uncovered in T. Duke's contribution.The 3rd part provides offers an summary of the most computational techniques to combine, examine and simulate molecular and genetic networks. First, J. van Helden introduces a chain of statistical and computational equipment permitting the id of brief nucleic fragments putatively inquisitive about the rules of gene expression from units of promoter sequences controlling co-expressed genes. subsequent, the bankruptcy by way of Samsonova et al. connects this factor of transcriptional law with that of the regulate of phone differentiation and trend formation in the course of embryonic improvement. eventually, H. de Jong and D. Thieffry overview a chain of mathematical techniques to version the dynamical behaviour of advanced genetic regulatory networks. This contribution contains short descriptions and references to winning functions of those techniques, together with the paintings of B. Novak, at the dynamical modelling of mobilephone cycle in several version organisms, from yeast to mammals. . offers a finished evaluation of the constitution and serve as of DNA and RNA on the interface among physics, biology and data technology.

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Extra info for Multiple aspects of DNA and RNA from biophysics to bioinformatics

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In the first group we find bond length, valence angle and dihedral terms which depend respectively on the relative positions of two, three or four linearly bonded atoms. The first two of these terms are generally quadratic functions, while the third is based on a cosine function. Each must be parameterized to reproduce the appropriate experimental (or quantum chemically calculated) value of the bond length, valence angle or dihedral (or set of symmetrically equivalent dihedrals) and be associated with an appropriate force constant determining the flexibility of the corresponding value.

The results of this study, which concern a 13 bp fragment of DNA with the sequence CGCATGAGTACGC, enable us to break down the helix-coil transition into two steps, the passage from a double-stranded helix (ds) into two helical single strands (s1 and s2) and then the passage of each of these strands to a disordered coil. mol−1 , but that this number actually hides opposing enthalpy and entropy changes which are roughly five times larger. mol−1 (almost exclusively due to base stacking). This term is however almost exactly compensated by the entropic loss associated with helical ordering.

25. The very best crystals diffract to roughly 1 Å and yield electron density maps that enable individual atoms, including hydrogens, to be distinguished. Although X-ray diffraction is undoubtedly the best technique available for determining the fine structure of DNA, the very process of forming crystals does run the risk of deforming the oligomers. Such deformations can notably affect helix bending and these problems have hindered the use of crystallography as DNA structure, dynamics and recognition 17 a means for understanding sequence-induced structural changes in the double helix.

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Multiple aspects of DNA and RNA from biophysics to bioinformatics by Chatenay D., et al. (eds.)

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