Gel electrophoresis of nucleic acids: Difference between revisions - Wikipedia

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The biased reptation model has also been used to explain the mobility of DNA in PFGE. The orientation of the DNA is progressively built up by reptation after the onset of a field, and the time it reached the steady state velocity is dependent on the size of the molecule. When the field is changed, larger molecules take longer to reorientate, it is therefore possible to discriminate between the long chains that cannot reach its steady state velocity from the short ones that travel most of the time in steady velocity.<ref name=viovy>{{cite journal |journal=Reviews of Modern Physics |volume= 72 |pages= 813–872 |year=2000 |title=Electrophoresis of DNA and other polyelectrolytes: Physical mechanisms|author=Jean-Louis Viovy |doi=10.1103/RevModPhys.72.813 |bibcode=2000RvMP...72..813V}}</ref> Other models, however, also exist.

Real-time fluorescence microscopy of stained molecules showed more subtle dynamics during electrophoresis, with the DNA showing considerable elasticity as it alternately stretching in the direction of the applied field and then contracting into a ball, or becoming hooked into a U-shape when it gets caught on the polymer fibres.<ref>{{cite journal |authorvauthors=Smith, S.B.SB, Aldridge, P.K.PK, &Callis Callis,JB J.B. |title=Observation of individual DNA molecules undergoing gel electrophoresis |journal=Science |volume=243 |issue=4888 |pages=203–206 |year=1989 |pmid= 2911733 |doi=10.1126/science.2911733|bibcode = 1989Sci...243..203S }}</ref><ref>{{cite journal |journal=Nature |year=1989|volume=338 |issue=6215|pages=520–2 |title=Conformational dynamics of individual DNA molecules during gel electrophoresis |vauthors=Schwartz DC, Koval M |pmid=2927511 |doi=10.1038/338520a0|bibcode = 1989Natur.338..520S }}</ref> This observation may be termed the "caterpillar" model.<ref>{{citation |title=Physical Biochemistry: Principles and Applications |author= David Sheehan |url=http://books.google.co.uk/books?id=AxxbYlsuZrwC&pg=PT352&f=false#v=onepage&q&f=false |page=181|publisher=Wiley-Blackwell |edition=2nd |year=2009 |isbn= 978-0470856031 }}</ref> Other model proposes that the DNA gets entangled with the polymer matrix, and the larger the molecule, the more likely it is to become entangled and its movement impeded.<ref>{{cite journal |journal=Electrophoresis |year=2009 |volume=30 |issue=12 |pages=2014–24 | doi=10.1002/elps.200900264 |title=DNA migration mechanism analyses for applications in capillary and microchip electrophoresis |vauthors=Forster RE, Hert DG, Chiesl TN, Fredlake CP, Barron AE |pmid=19582705 |pmc=2762034 }}</ref>

==Visualization==