Single T4-DNA molecules were confined in rectangular-shaped channels with adepth of 300 nm and a width in the range 150-300 nm casted in apoly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA moleculeswere measured with fluorescence microscopy as a function of the ionic strengthand composition of the buffer as well as the DNA intercalation level by theYOYO-1 dye. The data were interpreted with scaling theory for a wormlikepolymer in good solvent, including the effects of confinement, charge, andself-avoidance. It was found that the elongation of the DNA molecules withdecreasing ionic strength can be interpreted in terms of an increase of thepersistence length. Self-avoidance effects on the extension are moderate, dueto the small correlation length imposed by the channel cross-sectionaldiameter. Intercalation of the dye results in an increase of the DNA contourlength and a partial neutralization of the DNA charge, but besides effects ofelectrostatic origin it has no significant effect on the bare bending rigidity.In the presence of divalent cations, the DNA molecules were observed tocontract, but they do not collapse into a condensed structure. It is proposedthat this contraction results from a divalent counterion mediated attractiveforce between the segments of the DNA molecule.
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