Ultra-high throughput rotary capillary array electrophoresis scanner for fluorescent DNA sequencing and analysis

We have constructed a rotary confocal fluorescence scanner and capillary ar ray electrophoresis system that is designed to analyze over 1000 DNA sequen cing or fragment sizing separations in parallel. Capillaries are arranged a round the surface of a cylinder and a rotating objective in the middle of t he cylinder excites and collects fluorescence from labeled DNA fragments as they pass the capillary detection window. The capillaries are pressure-fil led with a replaceable matrix and the samples are electrokinetically inject ed in parallel from a stainless steel microtiter plate at the cathode end. We demonstrate that the instrument is capable of producing four-color data from all capillaries at a scan rate of 4 Hz (corresponding to a linear scan velocity of 121 cm/s). M13 sequencing data were obtained using a 128 capil lary array mounted in half of the first quadrant of the scanner. In this in itial run, read lengths greater than 500 bases were obtained in over 60% of the capillaries.