Static conformation and dynamics of single DNA molecules confined in nanoslits

Nearly thirty years ago, Daoud and de Gennes derived the scaling predictions for the linear polymer chains trapped in a slit with dimension close to the Kuhn length; however, these predictions have yet to be compared with experiments. We have fabricated nanoslits with vertical dimension similar to the Kuhn length of ds-DNA (110 nm) using standard photolithography techniques. Fluorescently labeled single DNA molecules with contour lengths L ranging from 4 to 75 mu m were successfully injected into the slits and the chain molecules undergoing Brownian motions were imaged by fluorescence microscopy. The distributions of the chain radius of gyration and the two-dimensional asphericity were measured. It is found that the DNA molecules exhibit highly anisotropic shape and the mean asphericity is chain length independence. The shape anisotropy of DNA in our measurements is between two and three dimensions (2D and 3D). The static scaling law of the chain extension and the radius of gyration < R-parallel to >,< R-g >similar to L-nu were observed with nu(R parallel to)=0.65 +/- 0.02 and nu(Rg)=0.68 +/- 0.05. These results are close to the average value between two (nu(R parallel to,Rg)=0.75) and three (nu(R parallel to,Rg)=0.6) -dimensional theoretical value. The scaling of the extensional and rotational relaxation time are between Rouse model in nanoslits and Zimm model in the bulk solution, respectively. We show that the conformation and chain relaxation of DNA confined in a slit close to Kuhn length exhibit the quasi-two-dimensional behavior.