Computational Studies of RNA and DNA - download pdf or read online

By Bohdan Schneider, Helen M. Berman (auth.), J. à poner, F. Lankaš (eds.)

ISBN-10: 1402047940

ISBN-13: 9781402047947

ISBN-10: 1402048513

ISBN-13: 9781402048517

Computational reviews of RNA and DNA

Jiri Sponer and Filip Lankas

Computational experiences of RNA and DNA comprises, in an built-in approach, smooth computational stories of nucleic acids, starting from complicated digital constitution quantum chemical calculations via particular solvent molecular dynamics (MD) simulations as much as mesoscopic modelling, with the main target given to the MD box. It offers an equivalent emphasis to the major tools and functions whereas successes in addition to pitfalls of the computational concepts are discussed.

The structures and difficulties studied include:

  • Accurate calculations of base pairing energies
  • Electronic houses of nucleic acids and electron move, via quite a few varieties of nucleic acid
  • Calculating DNA elasticity

This booklet is ideal to teachers and researchers in natural and computational chemistry in addition to biochemistry and especially these attracted to the molecular modelling of nucleic acids.

Besides the state-of-the artwork technology, the ebook additionally offers introductory info to non-specialists to go into and comprehend this field.

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Additional resources for Computational Studies of RNA and DNA

Example text

1994). Crystal Structure of a Four-Stranded Intercalated DNA: d(C4). Biochemistry 33, 13540-13546. 55. W. -H. (1978). Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement. Biol. 123, 607-630. 56. M. B. (1994). Three-dimensional structure of a hammerhead ribozyme. Nature 372, 68-74. 57. R. A. (1996). Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 273, 1678-1685. 58. V. L. (1982). The Anatomy of A-, B-, and Z-DNA. Science 216, 475-485.

Chem. 2, 287-303. 33. , Swaminathan, S. & Karplus, M. (1983). CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. Chem. 4, 187-217. 34. B. & Westhof, E. (2001). Geometric nomenclature and classification of RNA base pairs. RNA 7, 499-512. 35. , Jurecka, P. & Hobza, P. (2004). Accurate interaction energies of hydrogenbonded nucleic acid base pairs. Soc. 126, 10142-10151. 36. -J. B. (1989). Definitions and nomenclature of nucleic acid structure parameters. EMBO J.

Most nucleic acid self-recognition interactions are driven by “direct readout” of one nucleotide sequence by another. Direct readout is best conceptualized as interactions via hydrogen bonds of nucleic acid bases. In this sense, direct readout is recognition of digital sequence. Indirect readout is the analogous readout of features not directly connected to nucleotide sequence. All structural characteristics used for indirect readout are ultimately sequence dependent, but consist of features like groove dimensions and backbone conformations that are much less sequence dependent than the hydrogen bonding potential of base edges.

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Computational Studies of RNA and DNA by Bohdan Schneider, Helen M. Berman (auth.), J. à poner, F. Lankaš (eds.)


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