Sedimentation of macroscopic rigid knots and its relation to gel electrophoretic mobility of DNA knots.
We address the general question of the extent to which the hydrodynamic behaviour of microscopic freely fluctuating objects can be reproduced by macrosopic rigid objects. In particular, we compare the sedimentation speeds of knotted DNA molecules undergoing gel electrophoresis to the sedimentation speeds of rigid stereolithographic models of ideal knots in both water and silicon oil. We find that the sedimentation speeds grow roughly linearly with the average crossing number of the ideal knot configurations, and that the correlation is stronger within classes of knots. This is consistent with previous observations with DNA knots in gel electrophoresis.
King's College London, Materials and Molecular Modelling, The Strand, London, UK.
Cédric
C
Weber
Mathias
M
Carlen
Giovanni
G
Dietler
Eric J
EJ
Rawdon
Andrzej
A
Stasiak
D004270:DNA, Circular / Q000737:chemistry*; D004586:Electrophoresis / Q000379:methods; D005782:Gels / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D012825:Silicon; D014867:Water
D004270:DNA, Circular; D005782:Gels; D014867:Water; D012825:Silicon