Methods and systems for monitoring multiple optical signals from a single source

Abstract

Methods and systems for monitoring a plurality of different optical signals from a single source of such signals, where each such different optical signal is spatially separated from other such signals and directed to different detectors or locations upon a single detector, which direction is generally accomplished through the use of a small number of optical components and/or manipulations.

1 - 40 . (canceled) 
   
   
       41 . A method of identifying nucleotides in a nucleic acid sequence, comprising:
 providing a plurality of polymerization complexes within a plurality of confined reaction environments, wherein each complex comprises a polymerase enzyme, and a template nucleic acid;   contacting the plurality of complexes with a plurality of types of nucleotide analogs labeled with distinguishable fluorescent labels under conditions suitable for polymerization;   transmitting fluorescent signals associated with incorporation of a nucleotide analog to a detector, wherein location of the fluorescent signals on the detector is indicative of an individual confined reaction environment and a type of nucleotide incorporated;   identifying a nucleotide in a nucleic acid sequence based upon the type of nucleotide incorporated and the confined reaction environment.   
   
   
       42 . The method of  claim 41 , wherein the transmitting step comprises collecting fluorescent signals from the plurality of confined reaction environments and passing the fluorescent signals through an optical train that directs different spectral components of the fluorescent signals to different locations on the detector. 
   
   
       43 . The method of  claim 42 , wherein the optical train comprises a dispersive optical element selected from a prism and an optical grating. 
   
   
       44 . The method of  claim 41 , wherein the confined reaction environments comprise zero mode waveguides. 
   
   
       45 . The method of  claim 41 , wherein fluorescent signals associated with incorporation of a plurality of nucleotide analogs in a complex are transmitted to the detector, and a plurality of nucleotides in the nucleic acid sequence are identified. 
   
   
       46 . The method of  claim 41 , wherein the optical train comprises at least a first prism to direct spectrally different fluorescent signals to different locations on the detector. 
   
   
       47 . The method of  claim 46 , further comprising at least a second prism, configured to adjust relative spectral separation for different fluorescent signal components. 
   
   
       48 . The method of  claim 47 , wherein the second prism is provided to be rotatable on its optical axis. 
   
   
       49 . A method of identifying nucleotides incorporated in polymerase mediated, template dependent nucleic acid synthesis reactions comprising:
 providing a plurality template nucleic acid/polymerase complexes on a substrate;   contacting the plurality of complexes with a plurality of nucleotide analogs having spectrally distinct fluorescent labels, wherein incorporation of nucleotides produces characteristic incorporation signals;   directing incorporation signals to a single detector, wherein a location of a signal on the detector is indicative of a complex incorporating the nucleotide and a type of nucleotide incorporated; and   identifying the nucleotide incorporated into a template mediated nucleic acid synthesis reaction from the location of the signal on the detector.   
   
   
       50 . The method of  claim 49 , wherein the directing step comprises passing optical signals through dispersive optical element to separate signals from the spectrally distinct labels and image the signals onto different regions of the single detector. 
   
   
       51 . The method of  claim 49 , wherein the complexes are individually optically resolvable. 
   
   
       52 . The method of  claim 49 , wherein the plurality of complexes are optically confined. 
   
   
       53 . The method of  claim 52 , wherein the plurality of complexes are disposed within an array of zero mode waveguides. 
   
   
       54 . A method of analyzing a reaction, comprising:
 providing a first reactant immobilized on a substrate;   contacting the first reactant with a second reactant and a third reactant, each bearing a spectrally distinct label;   directing signals from the spectrally distinct labels that are characteristic of interaction of the first reactant with one of the second and third reactants to a location on a first detector, wherein the location on the detector is indicative of the first reactant location on the substrate and the second or third reactant with which the first reactant interacted;   identifying the first reactant and the second or third reactant with which the first reactant interacted.   
   
   
       55 . The method of  claim 54 , wherein the first reactant comprises at least a first nucleic acid. 
   
   
       56 . The method of  claim 55 , wherein the first reactant further comprises a polymerase enzyme. 
   
   
       57 . The method of  claim 55 , wherein the second and third reactants comprise second and third nucleic acids, respectively. 
   
   
       58 . The method of  claim 56 , wherein the second and third reactants comprise first and second nucleotide analogs, respectively 
   
   
       59 . The method of  claim 57 , wherein the second and third nucleic acids each comprise a spectrally distinct fluorescent label. 
   
   
       60 . The method of  claim 58 , wherein the first and second nucleotide analogs each comprises a spectrally distinct fluorescent label.