Patent ID: 8241573

Claim:
A system for detecting fluorescence emitted from nucleic acids, wherein the nucleic acids comprise fluorescent labels, the system comprising: a) a stage configured to hold a solid substrate having the nucleic acids; b) a fluid direction system for controllably moving one or more reagents into contact with the nucleic acids; c) an illumination system for exciting the fluorescent labels via total internal reflection (TIR), the illumination system comprising a mode scrambler and a multimode optical fiber that provides a fluorescent-excitation illumination beam having multiple propagating modes, the mode scrambler scrambling the modes of the illumination beam to provide a substantially uniform illumination footprint to excite the fluorescent labels, wherein the illumination beam is directed to be incident on the solid substrate so that the footprint excites the fluorescent labels through TIR; and d) a detector component for detecting fluorescence produced from excitation of the fluorescent labels by the footprint.