Methods and devices for micro-isolation, extraction, and/or analysis of microscale components

Abstract

Provided herein are devices and methods for the micro-isolation of biological cellular material. A micro-isolation apparatus described can comprise a photomask that protects regions of interest against DNA-destroying illumination. The micro-isolation apparatus can further comprise photosensitive material defining access wells following illumination and subsequent developing of the photosensitive material. The micro-isolation apparatus can further comprise a chambered microfluidic device comprising channels providing access to wells defined in photosensitive material. The micro-isolation apparatus can comprise a chambered microfluidic device without access wells defined in photosensitive material where valves control the flow of gases or liquids through the channels of the microfluidic device. Also included are methods for selectively isolating cellular material using the apparatuses described herein, as are methods for biochemical analysis of individual regions of interest of cellular material using the devices described herein. Further included are methods of making masking arrays useful for the methods described herein.

What is claimed is: 
     
         1 . A micro-isolation apparatus comprising:
 a support suitable for mounting a biological sample; and   a mask capable of being sealed by a seal or laminated over the biological sample and positioned on the support, wherein the mask comprises at least one access well.   
     
     
         2 . The micro-isolation apparatus of  claim 1 , wherein the at least one access well is positioned to correspond, in use, to a region of interest of the biological sample. 
     
     
         3 . The micro-isolation apparatus of  claim 1 , wherein the mask further comprises a transparent or visually exposed region. 
     
     
         4 . The micro-isolation apparatus of  claim 3 , wherein the transparent region corresponds to the at least one access well. 
     
     
         5 . The micro-isolation apparatus of  claim 4 , wherein the transparent region is configured to allow passage of a light. 
     
     
         6 . The micro-isolation apparatus of  claim 4 , wherein the transparent region is configured to allow visualization of the region of interest. 
     
     
         7 . The micro-isolation apparatus of  claim 4 , wherein the transparent region is configured to allow access to the region of interest. 
     
     
         8 . The micro-isolation apparatus of  claim 1 , wherein the mask further comprises a plurality of access wells positioned to correspond, in use, to a plurality of regions of interest of the biological sample. 
     
     
         9 . The micro-isolation apparatus of  claim 8 , wherein the plurality of access wells are interconnected through a series of channels in the microfluidic device. 
     
     
         10 . The micro-isolation apparatus of  claim 1 , wherein the at least one channel further comprises an input channel and an output channel. 
     
     
         11 . The micro-isolation apparatus of  claim 1 , wherein the at least one access well comprises a reaction mixture. 
     
     
         12 . The micro-isolation apparatus of  claim 11 , wherein the reaction mixture comprises one or more reagents for PCR, real time PCR, RT-PCR, flow cytometry, fluorescent labeling, FRET, DNA sequencing, RNA sequencing, protein-protein interaction assays, immunoassays, protein-nucleic acid assays. 
     
     
         13 . The micro-isolation apparatus of  claim 1 , wherein the support is a glass slide, a quartz slide, a transparent polymer slide or a non-transparent polymer slide. 
     
     
         14 . The micro-isolation apparatus of  claim 1 , wherein the support is a membrane. 
     
     
         15 . The micro-isolation apparatus of  claim 1 , further comprising a chambered microfluidic device fluidly coupled to the mask comprising at least one channel that provides access to the at least one access well. 
     
     
         16 . The microfluidic apparatus of  claim 15 , wherein the microfluidic device is capable of being sealed by a seal or laminated. 
     
     
         17 . The microfluidic device of  claim 15 , wherein the mask further comprises a plurality of access wells positioned to correspond, in use, to a plurality of regions of interest of the biological sample and the chambered microfluidic device fluidly coupled to the mask further comprises a plurality of channels that provide access to the plurality of access wells. 
     
     
         18 . The micro-isolation apparatus of  claim 15 , wherein the at least one access well and the at least one channel comprise a reaction mixture. 
     
     
         19 . A method to analyze a biological sample, the method comprising:
 positioning the biological sample on a support suitable for mounting a biological sample;   applying a mask comprising at least one access well and capable of being sealed by a seal or laminated over the biological sample and positioned on the support;   providing a reaction mixture for a desired reaction or series of reactions to the at least one access well, the reaction mixture mixing with analytes from the biological sample;   allowing sufficient time for the desired reaction or series of reactions to occur; and   performing an analysis of the biological sample or a portion thereof following the desired reaction or series of reactions.   
     
     
         20 . The method of  claim 19 , further comprising sealing or laminating the mask following applying the mask over the biological sample and providing a reaction mixture. 
     
     
         21 . The method of  claim 19 , further comprising performing an analysis of the biological sample or a portion thereof during the desired reaction or series of reactions. 
     
     
         22 . The method of  claim 19 , wherein performing an analysis of the biological sample or a portion thereof comprises visualizing the biological sample or a portion thereof. 
     
     
         23 . The method of  claim 19 , further comprising recapturing the reaction mixture following the desired reaction or series of reactions for further processing. 
     
     
         24 . The method of  claim 19 , wherein the providing a reaction mixture comprises soaking the mask in a bulk solution comprising the reaction mixture such that soaking the mask in the bulk solution allows for the reaction mixture to enter the at least one access well. 
     
     
         25 . The method of  claim 19 , wherein the biological sample is a biological tissue section, an emulsion containing biological cells, a gel containing biological cells, or a polymer matrix containing biological cells. 
     
     
         26 . The method of  claim 19 , wherein the analysis performed is PCR analysis. 
     
     
         27 . The method of  claim 19 , wherein the analysis performed is in preparation for sequencing. 
     
     
         28 . The method of  claim 19 , wherein the analysis performed is measurement of an optical signal. 
     
     
         29 . The method of  claim 19 , wherein providing a reaction mixture comprises using a supply chip comprising a plurality of chambers matching the mask. 
     
     
         30 . The method of  claim 19 , wherein the wherein the mask further comprises a plurality of access wells positioned to correspond, in use, to a plurality of regions of interest of the biological sample. 
     
     
         31 . The method of  claim 30 , wherein the plurality of access wells are positioned in a series of rows and columns. 
     
     
         32 . The method of  claim 31 , wherein the providing a reaction mixture comprises adding a first reaction mixture to a first row of access wells and adding a second reaction mixture to a second row of access wells such that the first row of access wells and the second row of access wells comprise distinct reaction mixtures. 
     
     
         33 . The method of  claim 31 , wherein the providing a reaction mixture comprises adding a first reaction mixture to a first column of access wells and adding a second reaction mixture to a second column of access wells such that the first column of access wells and the second column of access wells comprise distinct reaction mixtures. 
     
     
         34 . The method of  claim 30 , wherein the plurality of access wells are configured such that there is no fluidic connection between any two access wells in the mask. 
     
     
         35 . The method of  claim 30 , further comprising creating a virtual matrix from results from the analysis of the plurality of regions of interest, the virtual matrix created such that results from the analysis of the plurality of regions of interest are positioned in a topological location within the virtual matrix corresponding to a topological location of the plurality of regions of interest on the support. 
     
     
         36 . The method of  claim 35 , wherein the virtual matrix is used to create an analytical map of the biological sample. 
     
     
         37 . A method to analyze a biological sample, the method comprising:
 positioning the biological sample on a support suitable for mounting a biological sample;   applying a mask over the biological sample and positioned on the support, wherein the mask comprises at least one access well;   applying a chambered microfluidic device to the mask comprising at least one channel that provides access to the at least one access well, the chambered microfluidic device capable of being sealed by a seal or laminated;   providing a reaction mixture for a desired reaction or series of reactions to the at least one access well;   allowing sufficient time for the desired reaction or series of reactions to occur; and   performing an analysis of the biological sample or a portion thereof following the desired reaction or series of reactions.   
     
     
         38 . The method of  claim 37 , further comprising recapturing the reaction mixture following the desired reaction or series of reactions for further processing. 
     
     
         39 . The method of  claim 37 , wherein the providing a reaction mixture comprises
 providing the reaction mixture to the at least one channel of the chambered microfluidic;   applying a chambered microfluidic device to the mask; and   transferring the reaction mixture from the at least one channel to the at least one access well by centrifugation or capillary action.