The fluorescent tagging of biomolecules can have substantial effects on the charge distribution and translocation of the molecules through nanochannels. We show that the diffusion and calculated flux of translocating protein molecules through nanochannels are strong functions of the tags used. The size of the nanopore channels of a membrane also affect whether the channels provide facilitated transport or act just like affinity chromatography. These findings have important implications on micro/nanofluidic based biophysical studies that greatly discount the effects of tagged dyes on molecular transport and their mechanics.
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