Anomalously slow diffusion of single molecules near a patterned surface

Two-dimensional hexagonal arrays of micrometer-sized spheroidal cavities were fabricated from poly(vinyl alcohol) films on microscope cover glasses. The patterned surfaces in contact with solution and another regular cover glass were used to contain single molecules. Bursts of fluorescence from a series of single molecules entering and leaving the beam focus were observed. The molecules were all rotating rapidly compared with the fastest binning time of 100 mus. The fluorescence anisotropy decayed on the nanosecond time scale. The fluorescence spectra of mixtures of dyes confirmed that the bursts separated by time intervals of several to tens of seconds are from different molecules, while those bursts spanning intervals of several to tens of milliseconds are from the same molecule continually reentering the focus. The autocorrelation function of the time-resolved fluorescence intensity suggests a translational diffusion coefficient of 1.7 x 10(-8) cm(2) s(-1) for 6-carboxyrhodamine 6G hydrochloride molecules near the pattern, which is similar to260 times smaller than that in free solution. The mechanism of slowing the transverse diffusion process of single molecules near the pattern was further elucidated by total internal reflection microscopy, from which the molecules were observed to be avoiding the cavities.