Mixed-phase fluids for nucleic acid sequencing and other analytical assays

Abstract

An analytical system that includes a flow cell, a liquid delivery component, a gas delivery component and a bubble generator component, wherein the liquid delivery component is configured to deliver liquid from one or more reservoirs to the bubble generator component, wherein the gas delivery component is configured to deliver gas from one or more source to the bubble generator component, and wherein the bubble generator component is configured to mix liquids from the liquid delivery component with gas from the gas delivery component to deliver a fluid foam to the inside of the flow cell, wherein the fluid foam includes bubbles of the gas in the liquid.

What is claimed is: 
     
         1 . A method for sequencing a nucleic acid, comprising
 (a) providing a sequencing system comprising
 (i) a flow cell comprising a nucleic acid immobilized therein, 
 (ii) a bubble generator component that delivers gas bubbles to a liquid at a predefined rate; 
   (b) delivering a series of fluids to the inside of the flow cell to perform a cycle of a sequencing process, wherein at least one of the fluids is a fluid foam produced by the bubble generator component comprising gas bubbles in the liquid; and   (c) repeating step (b), thereby determining the sequence for the nucleic acid.   
     
     
         2 . The method of  claim 1 , wherein the nucleic acid is immobilized on a surface inside the flow cell. 
     
     
         3 . The method of  claim 2 , wherein the nucleic acid is present at a site in an array of nucleic acids immobilized on the surface. 
     
     
         4 . The sequencing system of  claim 3 , wherein the sequencing process comprises optically resolving the site from other sites in the array. 
     
     
         5 . The method of  claim 1 , wherein at least one of the fluids that is delivered to the flow cell is fluid foam containing a reversibly terminated nucleotide. 
     
     
         6 . The method of  claim 5 , wherein at least one of the fluids that is delivered to the flow cell is fluid foam containing a deblocking reagent. 
     
     
         7 . The method of  claim 1 , wherein at least one of the fluids that is delivered to the flow cell is fluid foam containing a fluorescently labeled nucleotide. 
     
     
         8 . The method of  claim 7 , wherein the fluorescently labeled nucleotide comprises a reversible terminator moiety. 
     
     
         9 . The method of  claim 1 , wherein at least one of the fluids that is delivered to the flow cell is fluid foam containing a polymerase. 
     
     
         10 . The method of  claim 9 , wherein the polymerase forms a stabilized ternary complex with a fluorescently labeled nucleotide and the nucleic acid in fluid foam. 
     
     
         11 . The method of  claim 10 , wherein the sequencing process comprises optical detection of the stabilized ternary complex. 
     
     
         12 . The method of  claim 9 , wherein the polymerase covalently adds a fluorescently labeled nucleotide to the nucleic acid in fluid foam. 
     
     
         13 . The method of  claim 12 , wherein the sequencing process comprises optical detection of the fluorescently labeled nucleotide added to the nucleic acid. 
     
     
         14 . The method of  claim 1 , wherein the optical detection comprises irradiating the inside of the flow cell and collecting luminescence emission from the inside of the flow cell. 
     
     
         15 . The method of  claim 1 , wherein the bubbles are substantially devoid of oxygen gas. 
     
     
         16 . The method of  claim 1 , wherein the bubble generator component comprises a filter membrane located at a junction through which the gas is delivered to the liquid. 
     
     
         17 . The method of  claim 16 , wherein the filter membrane comprises a hydrophobic material having a pattern of holes therein. 
     
     
         18 . The method of  claim 1 , wherein at least one of the fluids that is delivered to the flow cell is substantially devoid of bubbles. 
     
     
         19 . The method of  claim 18 , wherein the sequencing process comprises optical detection of the nucleic acid in the fluid that is devoid of bubbles. 
     
     
         20 . The method of  claim 1 , wherein the delivering comprises delivering at least a portion of the fluid foam into the flow cell, out of the flow cell and back into the flow cell. 
     
     
         21 . The method of  claim 1 , wherein the fluid foam comprises a volume fraction of bubbles that is at least 25% of the total volume of the fluid foam. 
     
     
         22 . The method of  claim 21 , wherein the average diameter of the bubbles is at most 95%, of the diameter of the inside of the flow cell. 
     
     
         23 . The method of  claim 1 , wherein the cross-sectional area of the inside of the flow cell is between 10 μm 2  and 100 mm 2 . 
     
     
         24 . The method of  claim 1 , wherein the volume of the inside of the flow cell is between 1 μl and 10 ml. 
     
     
         25 . The method of  claim 1 , wherein the bubbles in the fluid foam have an average diameter that is between 500 nm and 500 μm. 
     
     
         26 . A sequencing system, comprising
 a stage, a liquid delivery component, a gas delivery component and a bubble generator component,   wherein the stage is configured to accept a flow cell,   wherein the liquid delivery component is configured to deliver liquid from one or more reservoirs to the inside of the flow cell,   wherein the gas delivery component is configured to deliver gas from one or more source to the bubble generator component, and   wherein the bubble generator component is configured to introduce bubbles from the gas delivery component into liquid from the liquid delivery component to deliver a fluid foam to the inside of the flow cell, wherein the fluid foam comprises bubbles of the gas in the liquid.   
     
     
         27 . A flow cell comprising
 a stabilized ternary complex immobilized inside a flow cell, wherein the stabilized ternary complex comprises a polymerase, a primed template nucleic acid and a next correct nucleotide for the template; and   a fluid foam comprising a plurality of gas bubbles in a liquid, wherein the fluid foam is in contact with the stabilized ternary complex.