Multi‐capillary optical waveguides 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 parallel array. Such a capillary waveguide allows efficient illumination of samples in multiple capillaries with relatively little laser power. Analytical expressions derived under paraxial and thin‐lens approximations provide guidance in selecting the capillary sizes and the refractive indices that will produce the waveguiding effect, but accurate predictions require exact ray tracing. Small reflective losses as the light passes through the capillary surfaces cause cumulative intensity decreases, but the resulting lack of uniformity can be compensated to a considerable extent by illuminating the capillary array from both sides. A 12‐capillary waveguide illuminated from both sides in air has a difference of less than 10% from the strongest to the weakest illumination. By increasing the refractive index of both the external medium and the contents of the capillaries, a 96‐capillary waveguide for DNA sequencing could be produced that would also provide nearly uniform illumination. A 12‐capillary, bi‐directionally illuminated waveguide system for DNA sequencing has been constructed. The two focused laser beams are delivered by integrated fiber optic transmitters (IFOTs), and fluorescence is collected by a set of optical fibers whose spacing exactly matches that of the capillaries in the waveguide. The system is easy to align and provides sensitive detection of fluorescence with minimal cross‐talk between channels.

[1]  M. Quesada.  Replaceable polymers in DNA sequencing by capillary electrophoresis. , 1997, Current opinion in biotechnology.

[2]  James P. Landers,et al.  Handbook of Capillary Electrophoresis , 1993 .

[3]  J. Berka,et al.  Capillary electrophoresis with polymer matrices: DNA and protein separation and analysis. , 1996, Methods in enzymology.

[4]  Arthur W. Miller,et al.  DNA sequencing by capillary electrophoresis with replaceable linear polyacrylamide and laser-induced fluorescence detection. , 1993, Analytical chemistry.

[5]  N. Dovichi,et al.  Activation energy of the separation of DNA sequencing fragments in denaturing noncross‐linked polyacrylamide by capillary elecrophoresis , 1996, Electrophoresis.

[6]  M. Vilenchik,et al.  Influence of coiling on performance in capillary electrophoresis using open tubular and polymer network columns , 1992 .

[7]  Richard A. Mathies,et al.  Capillary array electrophoresis using laser-excited confocal fluorescence detection , 1992 .

[8]  M. Quesada,et al.  Multiple capillary DNA sequencer that uses fiber‐optic illumination and detection , 1996, Electrophoresis.

[9]  E. Yeung,et al.  Optimization of Excitation and Detection Geometry for Multiplexed Capillary Array Electrophoresis of DNA Fragments , 1995 .

[10]  H. Dhadwal,et al.  Design and characterization of coherent integrated fiber-optic imaging probes. , 1994, Applied optics.

[11]  S. Takahashi,et al.  A capillary array gel electrophoresis system using multiple laser focusing for DNA sequencing. , 1996, Analytical chemistry.

[12]  Arthur W. Miller,et al.  The use of elevated column temperature to extend DNA sequencing read lengths in capillary electrophoresis with replaceable polymer matrices , 1996, Electrophoresis.

[13]  Takashi Anazawa,et al.  Multiple Sheath-Flow Gel Capillary-Array Electrophoresis for Multicolor Fluorescent DNA Detection , 1994 .

[14]  N. Dovichi,et al.  Subattomole amino acid analysis by capillary zone electrophoresis and laser-induced fluorescence. , 1988, Science.

[15]  J. Berka,et al.  Rapid DNA sequencing of more than 1000 bases per run by capillary electrophoresis using replaceable linear polyacrylamide solutions. , 1996, Analytical chemistry.

[16]  A. Gerrard,et al.  Introduction to Matrix Methods in Optics , 1975 .

[17]  Edward S. Yeung,et al.  Simultaneous monitoring of DNA fragments separated by electrophoresis in a multiplexed array of 100 capillaries , 1994 .

[18]  R A Mathies,et al.  DNA sequencing using capillary array electrophoresis. , 1992, Analytical chemistry.