MULTI-CAPILLARY OPTICAL WAVE-GUIDES FOR DNA-SEQUENCING

Cylindrial capillaries can be used as optical elements in a waveguide, where refraction will confine an appropriately focused light beam to pass through the interiors of successive capillaries in a flat paralle l array. Such a capillary waveguide allows efficient illumination of s amples in multiple capillaries with relatively little laser power. Ana lytical expressions derived under paraxial and thin-lens approximation s provide guidance in selecting the capillary sizes and the refractive indices that will produce the waveguiding effect, but accurate predic tions require exact ray tracing. Small reflective losses as the light passes through the capillary surfaces cause cumulative intensity decre ases, but the resulting lack of uniformity can be compensated to a con siderable extent by illuminating the capillary array from both sides. A 12-capillary waveguide illuminated from both sides in air has a diff erence of less than 10% from the strongest to the weakest illumination . By increasing the refractive index of both the external medium and t he contents of the capillaries, a 96-capillary waveguide for DNA seque ncing could be produced that would also provide nearly uniform illumin ation. A 12-capillary, bi-directionally illuminated waveguide system f or DNA sequencing has been constructed. The two focused laser beams ar e delivered by integrated fiber optic transmitters (IFOTs), and fluore scence is collected by a set of optical fibers whose spacing exactly m atches that of the capillaries in the waveguide. The system is easy to align and provides sensitive detection of fluorescence with minimal c ross-talk between channels.