Analysis of the fluctuations of a single-tethered, quantum-dot labeled DNA molecule in shear flow

A novel technique for analyzing the conformational fluctuations of a single, surface-tethered DNA molecule by fluorescence microscopy is reported. Attaching a nanometer-sized fluorescent quantum dot to the free end of a λ-phage DNA molecule allows us to study the fluctuations of a native DNA molecule without the mechanical properties being altered by fluorescent dye staining. We report on the investigation of single-tethered DNA in both the unperturbed and the shear flow induced stretched state. The dependence of the observed fractional extension and the magnitude of fluctuations on the shear rate can be qualitatively interpreted by Brochard's stem-and-flower model. The cyclic dynamics of a DNA molecule is directly observed in the shear flow experiment.