Transient intra-tube effects

The biased reptation model provides a good framework to discuss the experimental results of the various gel electrophoresis techniques used to separate nucleic acids. Although more experiments are needed to fully characterize these techniques, available results indicate that the simplified version of the model discussed in this paper is satisfactory when low-frequency pulsed fields are used, or when transient intra-tube effects are not dominant. This is the case in continuous fields, for small molecules in intermittent fields, and possibly also for crossed fields. However, intra-tube effects are observed to play a role in field-inversion electrophoresis, for long molecules in intermittent fields, and during the first stages of an experiment (where an orientation overshoot is observed). 

Although intra-tube effects may be expected to play a larger role in pulsed field techniques and transient effects, the form of the model which averages over these effects offers a good framework to discuss the experimental results even in these cases. The orientation overshoot observed with linear dichroism is a transient effect that occurs at a time which is smaller than the tube-renewal time we thus conclude... 

However, three remarks concerning the effects of short wavelength modes should be made here. First, the over- and under-shoot stretching phenomena clearly point out that some intra-tube DMA modes, neglected in the BRM, are excited if the field is applied on a truly random coil DNA. This transient effect does not seem to affect the overall reptative behaviour of DNA, but may be very important in pulsed field techniques where separation is increased by coupling the external pulsed field(s) to transient effects that may affect the molecular electrophoretic mobility. 

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See also in sourсe #XX -- [ ]

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