Device and method for pressure-driven plug transport and reaction

Abstract

The present invention provides microfabricated substrates and methods of conducting reactions within these substrates. The reactions occur in plugs transported in the flow of a carrier-fluid.

1 .- 15 . (canceled) 
     
     
         16 . A system comprising:
 a microfluidic device comprising a substrate having a plurality of traps in fluidic communication with a channel, each trap comprises an opening along a side of the channel shaped and/or sized to accommodate a partition of a sample fluid within; and   a detector to detect, monitor, or analyze each partition of sample fluid retained within a corresponding trap, the detector to detect emissions from one or more detectable markers associated with a target molecule in response to the occurrence of a polymerase-chain reaction (PCR) reaction in one or more partitions of sample fluid.   
     
     
         17 . The system of  claim 16 , further comprising a plurality of partitions of sample fluid positioned within the plurality of traps in response to flow of an immiscible fluid through the channel. 
     
     
         18 . The system of  claim 17 , wherein each of the plurality of partitions of sample fluid is at least partially surrounded by the immiscible fluid. 
     
     
         19 . The system of  claim 18 , wherein each of the plurality of partitions of sample fluid is separated from one another and retained within a respective trap via the immiscible fluid positioned over the opening of each trap. 
     
     
         20 . The system of  claim 17 , wherein the immiscible fluid is an oil. 
     
     
         21 . The system of  claim 16 , wherein the target molecule is a biological molecule. 
     
     
         22 . The system of  claim 21 , wherein the sample fluid comprises at least one biological molecule and one or more chemical reagents for conducting a biological reaction with the at least one biological molecule resulting in the formation of a reaction product upon undergoing the PCR reaction. 
     
     
         23 . The system of  claim 22 , wherein the detector measures at least one property associated with a partition of sample fluid based on detection of emissions from the one or more detectable markers. 
     
     
         24 . The system of  claim 23 , wherein the detector is at least one of an optical detector and a fluorescence detector. 
     
     
         25 . The system of  claim 24 , wherein the detector detects an intensity of a fluorescent signal emitted from a detectable marker associated with a reaction product in one or more of the partitions of sample fluid for quantitative analysis and/or captures one or more images of a fluorescent signal emitted from a detectable marker associated with a reaction product in one or more of the partitions of sample fluid for quantitative analysis. 
     
     
         26 . A method comprising:
 a microfluidic device comprising a substrate having a plurality of traps in fluidic communication with a channel, each trap comprises an opening along a side of the channel shaped and/or sized to accommodate a partition of a sample fluid within;   introducing a sample fluid into the channel of the device via an inlet, the sample fluid comprising a target molecule;   introducing a fluid immiscible with the sample fluid into the channel via the inlet;   positioning a plurality of partitions of sample fluid within the plurality of traps in response to flow of the immiscible fluid through the channel and displacement of the sample fluid; and   monitoring each partition of sample fluid retained within a corresponding trap, wherein monitoring comprises detecting emissions from one or more detectable markers associated with a target molecule in response to the occurrence of a polymerase-chain reaction (PCR) reaction in one or more partitions of sample fluid.   
     
     
         27 . The method of  claim 26 , wherein each of the plurality of partitions of sample fluid is at least partially surrounded by the immiscible fluid. 
     
     
         28 . The method of  claim 27 , wherein each of the plurality of partitions of sample fluid is separated from one another and retained within a respective trap via the immiscible fluid positioned over the opening of each trap. 
     
     
         29 . The method of  claim 26 , wherein the immiscible fluid is an oil. 
     
     
         30 . The method of  claim 26 , wherein the target molecule is a biological molecule. 
     
     
         31 . The method of  claim 30 , wherein the biological molecule is DNA or RNA. 
     
     
         32 . The method of  claim 30 , wherein the sample fluid comprises at least one biological molecule and one or more chemical reagents for conducting a biological reaction with the at least one biological molecule resulting in the formation of a reaction product upon undergoing the PCR reaction. 
     
     
         33 . The method of  claim 32 , wherein monitoring each partition of sample fluid comprises measuring at least one property associated with a partition of sample fluid based on detection of emissions from the one or more detectable markers, wherein measuring at least one property comprises detecting, with a detector, a signal emitted from a detectable marker. 
     
     
         34 . The method of  claim 33 , wherein the detector is at least one of an optical detector and a fluorescence detector. 
     
     
         35 . The method of  claim 34 , further comprising:
 detecting, via a fluorescence detector, an intensity of a fluorescent signal emitted from a detectable marker associated with a reaction product in one or more of the partitions of sample fluid for quantitative analysis; and/or   capturing, via an optical detector, one or more images of a fluorescent signal emitted from a detectable marker associated with a reaction product in one or more of the partitions of sample fluid for quantitative analysis.