Polarization Anisotropy of DNA in Nanochannels

Studies of DNA in nanoscale confinement, where the dynamics and statics of the DNA extension or position is investigated as a function of e.g. DNA contour length, degree and shape of the confinement as well as buffer conditions, has yielded new insight in the physical properties of DNA. Our work extends this field by not only studying the location of fluorescent dyes along a confined DNA molecule but also monitor the orientation of the dyes by measuring the polarization of the fluorescence emission. By choosing a dye which fluorescence polarization is related to the DNA backbone and measuring the emission that is polarized parallel and perpendicular to the extension axis of the stretched DNA, information on the local spatial distribution of the DNA backbone can be obtained. The result is analogous to linear dichroism (LD) on a single-molecule level, and obtained in a highly parallel fashion.