Studies of molecular motions by fluorescence microscopy at single molecule and single fiber levels

Abstract

In this dissertation, state-of-the-art fluorescence microscopy techniques are employed to probe unique nanoscale phenomena in poly(dimethylsiloxane) (PDMS) films and on single carbon nanofibers. In one study, the mobility and physical entrapment of single dye molecules in dry and solvent-loaded PDMS films is explored. Experiments are performed under dry nitrogen and at various levels of isopropyl alcohol (IPA) loading from the vapor phase, as monitored by a PDMS-coated quartz-crystal microbalance. Single molecules are shown to be predominantly immobile under dry conditions and mostly mobile under IPA-saturated conditions. FCS is used to measure the apparent diffusion coefficient, yielding a mean that is virtually independent of IPA loading and sample class. An increase in the population of mobile molecules under high IPA conditions is attributed to the filling of film micropores with solvent, rather than by incorporation of molecularly dispersed solvent into the PDMS.

In a second study, the molecular mobility of both neutral and cationic molecules in cured PDMS films is studied as a function of oligomer extraction. Cross correlation and Bayesian burst analysis methods were used to quantify the populations of fixed and total molecules, respectively. The results show that the total concentration of dye increases with increased oligomer extraction, while the relative populations of fixed and mobile molecules decrease and increase, respectively. These results are relevant to the use of PDMS in microfluidics, nanofiltration and pervaporation membranes and solid phase microextraction fibers.

In a final study, molecular beacons (MBs) were immobilized onto the ends of single, sol-gel encapsulated vertically-alligned carbon nanofibers (VACNFs) attached to a silicon electrode. MB fluorescence was monitored as a function of the potential applied to the VACNF in a three-electrode electrochemical cell. Application of positive potentials attracts the negatively charged backbone of the MB, causing hybridization of the stem and a reduction in beacon fluorescence. Negative potentials cause dehybridization of the stem, and an increase in MB fluorescence. This study presents the first measurement of potential-dependent dehybridization/rehybridization of MBs attached directly to the end of a single VACNF. These studies will help to characterize the mechanism by which future lab-on-a-chip devices will detect harmful bio-organisms.