Monte Carlo Simulations and Analysis of Single-Molecule Detection and Imaging

Computer modeling and analysis methods are developed for two modes of operation of an instrument for sensitive fluorescence detection of individual dye-labeled molecules in solution. First, Monte Carlo simulations of experiments for single-molecule imaging (SMI) are extended to include effects of sample flow, sticking of molecules to surfaces, and the finite depth-of-focus of the optics. The results have a bearing on a patented method for high-speed single-molecule DNA sequencing. They indicate that the imaging of freely moving fluorescent labels within a microfluidic flowcell will be considerably more involved than that of immobilized molecules at a surface, which is the usual situation in SMI experiments. Second, the detection of single molecules as they pass through a tightly focused laser beam is discussed, with an emphasis on fluorescence correlation spectroscopy and the analysis of the autocorrelation function of the photon counts. Analysis methods are developed and applied to data from a collaborative experimental study within the topic of RNA transcription. The methods are extended to the case of flowing solution, for ongoing research with application to high-throughput pharmaceutical drug screening.