Detection and identification of single dye labeled mononucleotide molecules released from an optical fiber in a microcapillary: First steps towards anew single molecule DNA sequencing technique

We present efficient detection of single dye labeled mononucleotide molecul es released from an optical fiber in a cone shaped microcapillary with an i nner diameter of 0.5 mu m at the small end. A 3 mu m diameter streptavidin coated optical fiber was doped with dye labeled mononucleotide molecules an d positioned about 400 mu m in front of the detection area. The flow of the negatively charged analyte molecules towards the detection area was establ ished by electrokinetic forces. Adsorption of the dye labeled mononucleotid e molecules on the capillary walls as well as the electroosmotic (EOF) flow could be drastically reduced using a 3% polyvinylpyrrolidone (PVP) matrix. We studied bursts of fluorescence photons from single fluorescently labele d mononucleotide molecules Cy5-dCTP and MR121-dUTP. The conjugates were exc ited by a short-pulse diode laser emitting at a wavelength of 638 nm with a repetition rate of 57 MHz. The setup consists essentially of a confocal mi croscope for time-correlated single-photon counting (TCSPC). Detection was performed by a single-photon avalanche-photodiode in combination with a PC plug-in card for TCSPC. The time-resolved fluorescence signals of individua l molecules were analyzed and identified by a maximum Likelihood estimator (MLE). We obtain an overall classification probability of about 96% for the time-resolved identification of Cy5-dCTP and MR121-dUTP via their characte ristic fluorescence decay times of 1.42 +/- 0.21 ns (Cy5-dCTP) and 2.41 +/- 0.32 ns (MR121-dUTP). In addition we report on detection and identificatio n of single Cy5-dCMP and MR121-dUMP molecules degraded enzymatically with t he 3' --> 5' proofreading activity of T4-DNA-polymerase from statistically labeled DNA strands bound to the optical fiber. The technique presented per mits counting and identification of fluorescently labeled mononucleotide mo lecules cleaved from DNA strands with counting rates > 200 nucleotides s(-1 ) and represents a suitable alternative for single molecule sequencing.