Monte-Carlo Simulations of Gel-Electrophoresis of Dna Knots

Weber, Cédric; Fleurant, M.; Rios, Paolo De Los; Dietler, Giovanni

doi:10.1142/9789812703460_0008

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“…Therefore, it is to be expected that unknotted DNA molecules should show higher electrophoretic mobility than knotted molecules starting from some critical field strength. However, below this critical strength knots should migrate more quickly as they are more compact and therefore show smaller hydrodynamic friction and are also less likely to encounter gel fibres [35]. When a gel fibre is encountered by migrating molecules the detachment of knots and unknots is very similar in the low field regime (compare figures 2 with 4).…”

Section: Resultsmentioning

confidence: 95%

Simulations of electrophoretic collisions of DNA knots with gel obstacles

Weber¹,

Rios

Dietler

et al. 2006

J. Phys.: Condens. Matter

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Gel electrophoresis can be used to separate nicked circular DNA molecules of equal length but forming different knot types. At low electric fields, complex knots drift faster than simpler knots. However, at high electric field the opposite is the case and simpler knots migrate faster than more complex knots. Using Monte Carlo simulations we investigate the reasons of this reversal of relative order of electrophoretic mobility of DNA molecules forming different knot types. We observe that at high electric fields the simulated knotted molecules tend to hang over the gel fibres and require passing over a substantial energy barrier to slip over the impeding gel fibre. At low electric field the interactions of drifting molecules with the gel fibres are weak and there are no significant energy barriers that oppose the detachment of knotted molecules from transverse gel fibres.

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Section: Resultsmentioning

confidence: 95%