Chemical amplification based on fluid partitioning

Abstract

A system for nucleic acid amplification of a sample comprises partitioning the sample into partitioned sections and performing PCR on the partitioned sections of the sample. Another embodiment of the invention provides a system for nucleic acid amplification and detection of a sample comprising partitioning the sample into partitioned sections, performing PCR on the partitioned sections of the sample, and detecting and analyzing the partitioned sections of the sample.

The invention claimed is: 
     
       1. An apparatus for nucleic acid amplification of a sample, comprising:
 means for partitioning said sample into partitioned sections, wherein said means for partitioning said sample into partitioned sections comprises an injection orifice, and   means for performing PCR on said partitioned sections of said sample.   
     
     
       2. The apparatus for nucleic acid amplification of a sample of  claim 1  wherein said injection orifice is an injection orifice that produces microdroplets. 
     
     
       3. The apparatus for nucleic acid amplification of a sample of  claim 1  wherein said injection orifice is an injection orifice that injects said sample and a PCR reagent. 
     
     
       4. The apparatus for nucleic acid amplification of a sample of  claim 1  wherein said means for performing PCR on said partitioned sections of said sample comprises a continuous tube for circulating said partitioned sections of said sample through a heater to perform PCR. 
     
     
       5. The apparatus for nucleic acid amplification of a sample of  claim 1  wherein said means for performing PCR on said partitioned sections of said sample comprises a continuous tube for circulating said partitioned sections of said sample through a heater and cooler to perform PCR. 
     
     
       6. The apparatus for nucleic acid amplification of a sample of  claim 1  wherein said means for performing PCR on said partitioned sections of said sample comprises a pump, a continuous tube, and a heater. 
     
     
       7. The apparatus for nucleic acid amplification of a sample of  claim 1  including means for detection and analysis of said partitioned sections of said sample comprising a laser and a detector. 
     
     
       8. The apparatus for nucleic acid amplification of a sample of  claim 1  including means for detection and analysis of said partitioned sections of said sample comprising a blue laser and a detector. 
     
     
       9. The apparatus for nucleic acid amplification of a sample of  claim 1  wherein said means for partitioning said sample into partitioned sections comprises means for separating said sample into immiscible slugs. 
     
     
       10. A method of nucleic acid amplification of a sample, comprising the steps of:
 partitioning said sample into partitioned sections, wherein said step of partitioning said sample into partitioned sections comprises flowing said sample through an injection orifice, and   subjecting said partitioned sections of said sample to PCR.   
     
     
       11. A method of nucleic acid amplification of a sample, the method comprising the steps
 a. providing an aqueous solution, wherein the aqueous solution comprises components for performing nucleic acid amplification and an input sample comprising a plurality of nucleic acids;   b. providing an immiscible partitioning fluid;   c. providing a solid substrate, wherein the solid substrate comprises a two-dimensional array of small indentations;   d. contacting the aqueous solution with the immiscible partitioning fluid on the solid substrate, wherein the immiscible partitioning fluid is less dense than the aqueous solution, wherein the solid substrate is configured such that the contacting the aqueous solution with the immiscible partitioning fluid partitions the input sample comprising the plurality of nucleic acids into one or more microdroplets, and wherein the one or more microdroplets are further partitioned into and held by the two-dimensional array of small indentations; and   e. performing nucleic acid amplification of the one or more microdroplets held by the two-dimensional array of small indentations.   
     
     
       12. The method of claim 11, wherein the solid substrate is hydrophobic. 
     
     
       13. The method of claim 11, wherein the nucleic acid amplification step comprises alternately heating and cooling the solid substrate. 
     
     
       14. The method of claim 11, wherein the nucleic acids comprise a target DNA. 
     
     
       15. The method of claim 12, wherein the one or more microdroplets contain, on average, a single template of the target DNA, and wherein the single template is amplified within the one or more microdroplets. 
     
     
       16. The method of claim 11, wherein the components for performing nucleic acid amplification comprise one or more polymerase chain reaction (PCR) reagents. 
     
     
       17. The method of claim 11, wherein the method further comprises detecting one or more products of the nucleic acid amplification. 
     
     
       18. The method of claim 17, wherein the detecting comprises optically detecting. 
     
     
       19. The method of claim 18, wherein the optically detecting comprises confocal imaging. 
     
     
       20. The method of claim 18, wherein the optically detecting comprises laser excitation. 
     
     
       21. The method of claim 18, wherein the optically detecting comprises fluorescent detection. 
     
     
       22. The method of claim 18, wherein the optically detecting comprises detecting a colorimetric indicator. 
     
     
       23. The method of claim 18, wherein the optically detecting comprises signaling the presence of a target nucleic acid. 
     
     
       24. The method of claim 11, wherein the nucleic acid amplification comprises multiple heating and cooling cycles. 
     
     
       25. The method of claim 24, wherein the number of cycles is sufficient to detect products of the nucleic acid amplification. 
     
     
       26. The method of claim 11, wherein the one or more microdroplets have a volume of about 5×10 −9  to 10 −12  liters.