Fluidic apparatus and methods useful for chemical and biological reactions

1. A method of performing a nucleic acid sequencing reaction, comprising:

(a) coupling a reagent cartridge to a detection apparatus;

wherein the reagent cartridge comprises a plurality of reagent reservoirs and a main channel;

(b) coupling the reagent cartridge to a pump;

(c) delivering sequencing reagents from the reagent cartridge to a flow cell, wherein the plurality of reagent reservoirs contains the sequencing reagents, and wherein the sequencing reagents comprise a nucleic acid sample for the sequencing reaction; and

(d) detecting the sequencing reaction in the flow cell using the detection apparatus,

wherein the pump is coupled to the reagent cartridge separately from the detection apparatus;

wherein the pump is a separate component from the reagent cartridge and the detection apparatus;

wherein the reagent cartridge interacts transiently with the detection apparatus; and

wherein the flow cell is an integral component of the detection apparatus such that the flow cell is coupled to the reagent cartridge during coupling of the reagent cartridge to the detection apparatus.

2. A sequencing system, comprising:

(a) a reagent cartridge coupled to a detection apparatus;

wherein the reagent cartridge comprises a plurality of reagent reservoirs and a main channel, and wherein the plurality of reagent reservoirs contain sequencing reagents; and

(b) a pump coupled to the reagent cartridge;

wherein the pump is fluidically coupled to the reagent cartridge separately from the detection apparatus;

wherein the pump is a separate component from the reagent cartridge and the detection apparatus;

wherein the reagent cartridge interacts transiently with the detection apparatus; and

wherein a flow cell is an integral component of the detection apparatus such that the flow cell is coupled to the reagent cartridge during coupling of the reagent cartridge to the detection apparatus;

wherein the system is configured to deliver sequencing reagents from the reagent cartridge to the flow cell.

3. The method of claim 1 , wherein at least in step (c), each reagent reservoir of the plurality of reagent reservoirs is connected to the main channel of the reagent cartridge via an individual valve such that each reagent reservoir fluidically communicates with the flow cell.

4. The method of claim 1 , wherein at least in step (c), the flow cell is connected to the main channel via a first passage at a first end of the main channel and a second passage at a second end of the main channel.

5. The method of claim 1 , wherein at least in step (c), the pump applies pressure to the main channel at a region that is between a first master valve and a second master valve, thereby allowing fluids to move through the main channel.

6. The method of claim 5 , wherein the delivering sequencing reagents from the reagent cartridge to the flow cell comprises opening a first reagent valve of a first reagent reservoir and the first master valve, thereby delivering a first sequencing reagent in the first reagent reservoir to the flow cell in a first direction.

7. The method of claim 6 , wherein the delivering sequencing reagents from the reagent cartridge to the flow cell further comprises opening a second reagent valve of a second reagent reservoir and the second master valve and closing the first reagent valve and the first master valve, thereby delivering a second sequencing reagent in the second reagent reservoir to the flow cell in a second direction that is opposite the first direction.

8. The method of claim 1 , wherein the flow cell of step (c) and (d) comprises a solid support having an array of features.

9. The method of claim 1 , further comprising (e) regulating flow of the sequencing reagents from the flow cell to a waste reservoir, wherein the regulating comprises opening a waste valve, and wherein the reagent cartridge comprises a waste reservoir and a waste valve in the main channel.

10. The method of claim 1 , wherein at least in step (c), the pump alternatively applies positive and negative pressure to the main channel.

11. The method of claim 1 , wherein the pump is a syringe pump.

12. The method of claim 1 , further comprising real-time monitoring of DNA polymerase activity with zeromode waveguides.

13. The system of claim 2 , wherein each reagent reservoir of the plurality of reagent reservoirs is connected to the main channel of the reagent cartridge via an individual valve such that each reagent reservoir fluidically communicates with the flow cell.

14. The system of claim 2 , wherein the flow cell is connected to the main channel via a first passage at a first end of the main channel and a second passage at a second end of the main channel.

15. The system of claim 2 , wherein the pump applies pressure to the main channel at a region that is between a first master valve and a second master valve, thereby allowing fluids to move through the main channel.

16. The system of claim 15 , wherein a first reagent reservoir of the plurality of reagent reservoirs comprises a first reagent valve, and when the first reagent valve and the first master valve are open a first sequencing reagent in the first reagent reservoir is delivered to the flow cell in a first direction.

17. The system of claim 16 , wherein a second reagent reservoir of the plurality of reagent reservoirs comprises a second reagent valve, and when the second reagent valve and the second master valve are open and the first reagent valve and the first master valve are closed, a second sequencing reagent in the second reagent reservoir is delivered to the flow cell in a second direction that is opposite the first direction.

18. The system of claim 2 , wherein the reagent cartridge comprises a waste reservoir and a waste valve in the main channel.

19. The system of claim 18 , wherein the system is configured to regulate flow of the sequencing reagents from the flow cell to the waste reservoir by opening the waste valve.

20. The system of claim 2 , wherein the pump alternatively applies positive and negative pressure to the main channel.

21. The system of claim 2 , wherein the pump is a syringe pump.

22. The system of claim 2 , wherein the flow cell comprises a solid support having an array of features.