DNA Molecular dynamics modeling involves simulations of DNA molecular geometry and topology changes with time as a result of both intra- and inter- molecular interactions of DNA. Whereas molecular models of Deoxyribonucleic acid molecules such as closely packed spheres made of plastic or metal wires for 'skeletal models' are useful representations of static DNA structures, their usefulness is very limited for representing complex DNA dynamics.

PropertyValue
dbpprop:abstract
  • DNA Molecular dynamics modeling involves simulations of DNA molecular geometry and topology changes with time as a result of both intra- and inter- molecular interactions of DNA. Whereas molecular models of Deoxyribonucleic acid molecules such as closely packed spheres made of plastic or metal wires for 'skeletal models' are useful representations of static DNA structures, their usefulness is very limited for representing complex DNA dynamics. Computer molecular modeling allows both animations and molecular dynamics simulations that are very important for understanding how DNA functions in vivo. An old standing dynamic problem is how DNA "self-replication" takes place in living cells that should involve transient uncoiling of supercoiled DNA fibers. Although DNA consists of relatively rigid, very large elongated biopolymer molecules called "fibers" or chains its molecular structure in vivo undergoes dynamic configuration changes that involve dynamically attached water molecules, ions or proteins/enzymes. Supercoiling, packing with histones in chromosome structures, and other such supramolecular aspects also involve in vivo DNA topology which is even more complex than DNA molecular geometry, thus turning molecular modeling of DNA dynamics into a series of challenging problems for biophysical chemists, molecular biologists and biotechnologists. Thus, DNA exists in multiple stable geometries and has a rather large number of configurational, quantum states which are close to each other in energy on the potential energy surface of the DNA molecule. Such varying molecular geometries can also be computed, at least in principle, by employing ab initio quantum chemistry methods that can attain high accuracy for small molecules, although claims that acceptable accuracy can be also achieved for polynuclelotides, as well as DNA conformations, were recently made on the basis of VCD spectral data. Such quantum geometries define an important class of ab initio molecular models of DNA whose exploration has barely started especially in connection with results obtained by VCD in solutions. More detailed comparisons with such ab initio quantum computations are in principle obtainable through 2D-FT NMR spectroscopy and relaxation studies of polynucleotide solutions or specifically labeled DNA, as for example with deuterium labels.
dbpprop:portalparProperty
  • Molecular and Cellular Biology
  • Portal.svg
dbpprop:reference
dbpprop:wikiPageUsesTemplate
rdfs:comment
  • DNA Molecular dynamics modeling involves simulations of DNA molecular geometry and topology changes with time as a result of both intra- and inter- molecular interactions of DNA. Whereas molecular models of Deoxyribonucleic acid molecules such as closely packed spheres made of plastic or metal wires for 'skeletal models' are useful representations of static DNA structures, their usefulness is very limited for representing complex DNA dynamics.
rdfs:label
  • DNA Dynamics
skos:subject
foaf:homepage
foaf:page