Substrate preparation process

Abstract

The present invention provides novel processes for the large scale preparation of arrays of polymer sequences wherein each array includes a plurality of different, positionally distinct polymer sequences having known monomer sequences. The methods of the invention combine high throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.

1 . A method of forming an array of polymers on a surface of a substrate, comprising: 
 providing a substrate having a first surface coated with functional groups protected with a photolabile protecting group, and a second surface having a layer disposed thereon, said layer including one or more of an index matching compound, a light absorbing compound and an antireflective compound; and    sequentially activating and coupling monomers in different selected regions of said substrate to form a plurality of different polymer sequences in different known locations on said surface of said substrate, wherein said activating step comprises directing an activation radiation at said first surface of said substrate.    
     
     
         2 - 49 . (canceled)  
     
     
         50 . A method for synthesizing a plurality of biopolymers on the surface of a support, said method comprising: (a) placing said support into a reaction chamber and applying to said surface said biopolymers or precursors of said biopolymers, (b) removing said support from said reaction chamber and placing said support into a flow chamber, (c) introducing a liquid reagent for conducting said synthesis into said flow chamber, (d) removing said liquid reagent from said flow chamber wherein the pressure in said chamber is maintained substantially atmospheric during said removing. (e) removing said support from said flow chamber and (f) repeating steps (a)-(e) to form said plurality of biopolymers on the surface of said support.  
     
     
         51 . A method according to  claim 50  wherein liquid reagent is removed from said flow chamber under vacuum.  
     
     
         52 . A method according to  claim 50  wherein liquid reagent is removed from said flow chamber by simultaneously venting and applying a vacuum to said flow chamber.  
     
     
         53 . A method according to  claim 52  wherein said venting and said applying a vacuum are carried out at opposite ends of said flow chamber.  
     
     
         54 . A method according to  claim 50  wherein said method further comprises holding said liquid reagent in said flow chamber for a predetermined period of time.  
     
     
         55 . A method according to  claim 50  wherein said support is glass.  
     
     
         56 . A method according to  claim 50  further comprising introducing a pressurized inert gas into said flow chamber after step (c) and simultaneously evacuating said flow chamber.  
     
     
         57 . A method according to  claim 50  wherein said biopolymers are polynucleotides.  
     
     
         58 . A method according to  claim 50  wherein said liquid reagent for conducting said synthesis comprises an oxidizing agent or an agent for removing a protecting group.  
     
     
         59 . A method according to  claim 50  wherein said biopolymers are synthesized on said surface in multiple arrays and said support is subsequently diced into individual arrays of biopolymers on a support.  
     
     
         60 . A method according to  claim 59  further comprising exposing the array to a sample and reading the array.  
     
     
         61 . A method according to  claim 60  comprising forwarding data representing a result obtained from a reading of the array.  
     
     
         62 . A method according to  claim 61  wherein the data is transmitted to a remote location.  
     
     
         63 . A method according to  claim 62  comprising receiving data representing a result of an interrogation obtained by the reading of the array.  
     
     
         64 . A method for synthesizing an array of biopolymers on the surface of a support wherein said synthesis comprises a plurality of monomer additions, said method comprising after each of said monomer additions: (a) placing said support into a flow chamber, (c) introducing a liquid reagent for conducting said synthesis into said flow chamber, (d) removing said reagent from said flow chamber by simultaneously venting said chamber and applying a vacuum to the interior of said chamber, (e) removing said support from said flow chamber and (f) repeating steps (a)-(e) to form said plurality of biopolymers on the surface of said support.  
     
     
         65 . A method according to  claim 64  wherein said venting and said applying a vacuum are carried out at opposite ends of said flow chamber.  
     
     
         66 . A method according to  claim 64  wherein said method further comprises holding said liquid reagent in said flow chamber for a predetermined period of time.  
     
     
         67 . A method according to  claim 64  wherein said support is glass.  
     
     
         68 . A method according to  claim 64  further comprising introducing a pressurized inert gas into said flow chamber after step (d) and simultaneously evacuating said flow chamber.  
     
     
         69 . A method according to  claim 64  wherein said biopolymers are polynucleotides.  
     
     
         70 . A method according to  claim 64  wherein said liquid reagent for conducting said synthesis is an oxidizing agent or an agent for removing a protecting group.  
     
     
         71 . A method according to  claim 64  wherein said biopolymers are synthesized on said surface in multiple arrays and said support is subsequently diced into individual arrays of biopolymers on a support.  
     
     
         72 . A flow cell assembly for conducting at least one reaction in the synthesis of an array of biopolymers on the surface of a support, said flow cell comprising: (a) a flow cell chamber, (b) a manifold in fluid communication with said chamber, said manifold comprising at least a wash reagent inlet, an inlet for a reagent for conducting a step of said synthesis, and a vent, and (c) a vacuum source in fluid communication with said flow cell chamber.  
     
     
         73 . A flow cell assembly according to  claim 72  further comprising a fluid level sensor and a controller for controlling said inlets, said vent and said vacuum source.  
     
     
         74 . A flow cell assembly according to  claim 72  further comprising a gas inlet.  
     
     
         75 . An apparatus for synthesizing an array of biopolymers on the surface of a support, said apparatus comprising: (a) one or more flow cell assemblies of  claim 72 , (b) one or more fluid dispensing stations in fluid communication with one or more of said plurality of flow cell assemblies, (c) a station for monomer addition to said surface of said support, and (d) a mechanism for moving a support to and from said station for monomer addition and a flow cell and from one flow cell to another flow cell.  
     
     
         76 . An apparatus according to  claim 75  further comprising a controller for controlling the movement of said mechanism.  
     
     
         77 . An apparatus according to  claim 75  wherein said mechanism is a robotic arm.  
     
     
         78 . A method comprising using an array, prepared by an apparatus according to  claim 75 , by exposing the array to a sample and reading the array.  
     
     
         79 . A method according to  claim 78  comprising forwarding data representing a result obtained from a reading of the array.  
     
     
         80 . A method according to  claim 79  wherein the data is transmitted to a remote location.  
     
     
         81 . A method according to  claim 80  comprising receiving data representing a result of an interrogation obtained by the reading of the array.