Nanouidic Compaction of DNA by Like-Charged Protein

Abstract

The effects of the like-charged proteins bovine serum albumin and hemoglobin on the conformation and compaction of single DNA molecules confined in rectangular nanochannels were investigated with fluorescence microscopy. The channels have lengths of 50 μm and cross-sectional diameters in the range of 80-300 nm. In the wider channels, the DNA molecules are compressed and eventually condense into a compact form with increasing concentration of protein. In the narrow channels, no condensation was observed. The threshold concentration for condensation depends on the channel cross-sectional diameter as well as the ionic strength of the supporting medium. The critical values for full compaction are typically less than one-tenth of a millimolar. In the bulk phase and in the same environmental conditions, no condensation was observed. Anisotropic nanoconfinement hence facilitates compaction of DNA by negatively charged protein. We tentatively interpret this behavior in terms of enhanced depletion interaction between segments of the DNA molecule due to orientation order imposed by the channel walls.