Devices and processes for analyzing nucleic acid damage and repair using electrophoresis

Abstract

Systems, methods, and devices are provided for assessing DNA damage and repair in cells by measuring DNA migration under electrophoresis. In one exemplary embodiment, a microarray configured to hold cells in a predetermined spatial relationship is employed to improve accuracy, speed, and reliability of such measurements. In another embodiment, a self-contained cassette having a matrix material disposed therein can be used to create a substantially uniform environment for analyzing DNA damage and repair. Fluid can be circulated through the cell to assist in creating spatial patterns on the matrix material, or alternatively, the matrix material can already include a microarray pattern disposed thereon. Various methods and systems that take advantage of such microarrays and cassettes are also provided.

1 . A self-contained electrophoresis assay cassette, comprising:
 a housing defining at least one inner cavity;   a matrix material disposed within the cavity, the matrix material comprising a plurality of cell assay locations; and   an opening for introducing cells into the cavity, whereby upon introduction of cells into the cavity, a plurality of cells will be distributed to the cell assay locations.   
     
     
         2 . The device of  claim 1 , wherein the opening is a fluid delivery inlet port and the cassette further comprises a fluid delivery outlet port coupled to the inlet port, wherein the inlet port is configured to receive a fluid into the cavity and the outlet port is configured to remove a fluid from the cavity. 
     
     
         3 . The device of  claim 1 , wherein the opening further comprises a removable portion of the housing. 
     
     
         4 . The device of  claim 1 , wherein the matrix material has a generally uniform thickness. 
     
     
         5 . The device of  claim 1 , wherein the housing further comprises a plurality of layers with at least one gasket disposed therebetween. 
     
     
         6 . The device of  claim 1 , wherein the housing further comprises a plurality of layers with a membrane disposed therebetween. 
     
     
         7 . The device of  claim 1 , wherein the matrix material further comprises one or more cell capture sites. 
     
     
         8 . The device of  claim 1 , wherein a height of the housing ranges from about 25 micrometers to about 1 millimeter. 
     
     
         9 . The device of  claim 1 , wherein a thickness of the matrix material ranges from about 10 micrometers to about 500 micrometers. 
     
     
         10 . The device of  claim 1 , further comprising at least one divider that separates the matrix material into at least two regions. 
     
     
         11 . The device of  claim 1 , wherein the self-contained electrophoresis assay cassette further comprises first and second electrode terminals for applying an electric current to the matrix material. 
     
     
         12 . A system for nucleic acid analysis, comprising:
 the self-contained electrophoresis assay cassette of  claim 1 ;   a first applicator for applying a first reagent to at least a portion of the matrix material; and   a second applicator for applying a second reagent to at least another portion of the matrix material.   
     
     
         13 . The system of  claim 12 , wherein the matrix material further comprises one or more cell capture sites. 
     
     
         14 . The system of  claim 13 , wherein the second applicator is configured to apply the second reagent to a portion of the matrix material distinct from the portion to which the first reagent is applied. 
     
     
         15 . The system of  claim 12 , wherein the second applicator is configured to apply the second reagent to a portion of the matrix material that at least partially overlays the portion to which the first reagent is applied. 
     
     
         16 . The system of  claim 12 , further comprising a shunt coupled to the cassette and configured to receive a cell containing fluid. 
     
     
         17 . A system for nucleic acid analysis, comprising:
 the self-contained electrophoresis assay cassette of  claim 1 ;   an overlay disposed above matrix material and configured to apply at least one reagent to at least a portion of the plurality of cell assay locations.   
     
     
         18 . The system of  claim 17 , wherein the overlay further comprises a plurality of macrowells. 
     
     
         19 . The system of  claim 18 , wherein the overlay further comprises one or more drug-bearing hydrogels disposed in the macrowells. 
     
     
         20 . A system for determining multiple exposure conditions, comprising:
 the self-contained electrophoresis assay cassette of  claim 1 ;   a template disposed above the matrix material and configured to selectively regulate exposures of the plurality of cell assay locations to one or more conditions.   
     
     
         21 . The system of  claim 20 , wherein the template is a moveable shield. 
     
     
         22 . The system of  claim 20 , wherein the one or more conditions are created, at least in part, by an electromagnetic radiation source. 
     
     
         23 . A method for analyzing a nucleic acid, comprising:
 obtaining a matrix material capable of receiving a plurality of cells;   disposing at least one cell in each of a plurality of cell assay locations;   exposing the cells to at least one reagent;   performing electrophoresis on the plurality of cells; and   analyzing parameters resulting from performing electrophoresis.   
     
     
         24 . The method of  claim 23 , wherein the matrix material is disposed in a self-contained electrophoresis assay cassette. 
     
     
         25 . The method of  claim 24 , further comprising introducing a fluid into the cassette to diffuse the plurality of cells across at least a portion of the matrix material. 
     
     
         26 . The method of  claim 25 , further comprising evacuating the fluid from the cassette. 
     
     
         27 . The method of  claim 23 , further comprising:
 obtaining a second matrix material; and   adding the second matrix material to the first matrix material after disposing at least one cell in each of a plurality of cell assay locations.   
     
     
         28 . The method of  claim 23 , wherein the plurality of cell assay locations are one or more cell capture sites. 
     
     
         29 . The method of  claim 23 , further comprising:
 placing a divider over the matrix material; and   adding a second matrix material having a plurality of cells disposed therein above the divider.