  Single T4-DNA molecules were confined in rectangular-shaped channels with a
depth of 300 nm and a width in the range 150-300 nm casted in a
poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules
were measured with fluorescence microscopy as a function of the ionic strength
and composition of the buffer as well as the DNA intercalation level by the
YOYO-1 dye. The data were interpreted with scaling theory for a wormlike
polymer in good solvent, including the effects of confinement, charge, and
self-avoidance. It was found that the elongation of the DNA molecules with
decreasing ionic strength can be interpreted in terms of an increase of the
persistence length. Self-avoidance effects on the extension are moderate, due
to the small correlation length imposed by the channel cross-sectional
diameter. Intercalation of the dye results in an increase of the DNA contour
length and a partial neutralization of the DNA charge, but besides effects of
electrostatic origin it has no significant effect on the bare bending rigidity.
In the presence of divalent cations, the DNA molecules were observed to
contract, but they do not collapse into a condensed structure. It is proposed
that this contraction results from a divalent counterion mediated attractive
force between the segments of the DNA molecule.
