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

Abstract

Methods and systems are described for determining information about template sequences by simultaneously providing excitation over time to a plurality of confined sources on a substrate, each confined source carrying out a template mediated addition of nucleotides with a polymerase enzyme. The nucleotides have different labels, each with a different emission wavelength profile. Optical elements direct optical signals from the different NTPs within each optical confinement to different detector locations. Observing the optical signals over time allows for obtaining sequence information about the template nucleic acids.

1 . An optical analysis method comprising:
 simultaneously providing excitation radiation over time to each of a plurality of confined sources on a substrate, wherein each confined source comprises a polymerase enzyme associated with a template nucleic acid sequence;   exposing the polymerase enzymes to polymerase reaction conditions including two or more differently fluorescently labeled types of NTPs, whereby each differently labeled type of NTP has a different emission wavelength profile;   passing the emitted light through an optical train such that for each confined source the optical signal from each type of NTP is directed along a different optical path than each other type of NTP, such that the optical signal from each type of NTP is directed to a different detector location;   observing the optical signals over time from each confined source to determine a time sequence of NTP incorporation, thereby obtaining information about the template nucleic acid sequences.   
     
     
         2 . The method of  claim 1  wherein the optical signals are detected using a single detector. 
     
     
         3 . The method of  claim 1  wherein the optical signals are detected using two or more discrete detectors or detector arrays. 
     
     
         4 . The method of  claim 1  wherein the optical train comprises one or more wedge prism or optical grating to direct the optical signals along different optical paths to different detector locations. 
     
     
         5 . The method of  claim 1  wherein the confined sources comprises reaction regions. 
     
     
         6 . The method of  claim 5  wherein the confined reaction regions comprise wells in a multiwell plate. 
     
     
         7 . The method of  claim 5  wherein confined reaction regions comprise features on a molecular array. 
     
     
         8 . The method of  claim 5 , wherein the confined reactions region comprise zero mode waveguides. 
     
     
         9 . The method of  claim 1  wherein the polymerase enzyme comprises a DNA polymerase. 
     
     
         10 . The method of  claim 1  wherein the two or more differently fluorescently labeled types of NTPs comprise four differently fluorescently labeled types on NTPs. 
     
     
         11 . The method of  claim 10  wherein the four differently fluorescently labeled types on NTPs correspond to A, T, G, and C. 
     
     
         12 . A system for performing optical analyses comprising:
 a substrate comprising a plurality of confined sources, wherein each confined source comprises a polymerase enzyme associated with a template nucleic acid sequence;   an excitation radiation source that provides excitation radiation to the plurality of confined sources on the substrate, whereby the confined sources are in contact with a solution comprising two or more differently fluorescently labeled types of NTPs, whereby each differently labeled type of NTP has a different emission wavelength profile;   an optical train that directs the optical signal from each type of NTP within each confined source along a different optical path than each other type of NTP, such that the optical signal from each type of NTP is directed to a different detector location, and   one or more detectors that measure the optical signals over time to determine a time sequence of NTP incorporation for the polymerases within each confined source, thereby obtaining information about the template nucleic acid sequence.   
     
     
         13 . The system of  claim 12  wherein the optical signals are detected using a single detector. 
     
     
         14 . The system of  claim 12  wherein the optical signals are detected using two or more discrete detectors or detector arrays. 
     
     
         15 . The system of  claim 12  wherein the optical train comprises one or more wedge prism or optical grating to direct the optical signals along different optical paths to different detector locations. 
     
     
         16 . The system of  claim 12  wherein the confined sources comprises reaction regions. 
     
     
         17 . The method of  claim 16  wherein the confined reaction regions comprise wells in a multiwell plate. 
     
     
         18 . The system of  claim 16  wherein confined reaction regions comprise features on a molecular array. 
     
     
         19 . The system of  claim 16 , wherein the confined reactions region comprise zero mode waveguides. 
     
     
         20 . The system of  claim 12  wherein the one or more detectors comprise one or more photodiode arrays. 
     
     
         21 . The system of  claim 12  wherein the one or more detectors comprise one or more charge coupled devices (CCDs).