Systems and Methods for Containing Biological Samples

Abstract

An article for holding a plurality of biological samples includes a substrate a substrate comprising a first surface and an opposing second surface and a plurality of reaction sites in the substrate. Each of the reaction sites extends from an opening in the first surface to an opening in the second surface. The reaction sites comprise a hexagonal shape and are configured to provide sufficient surface tension by capillary action to hold respective biological samples. The reaction sites have a density over at least a portion of the surfaces that is at least 170 holes per square millimeter. At least one of the surfaces may have a surface roughness characterized by an arithmetic average roughness (Ra) that is less than or equal to 5 nanometers.

1 . An article for holding a plurality of biological samples, the article comprising:
 a substrate comprising a first surface and an opposing second surface; and   a plurality of reaction sites in the substrate, each of the reaction sites extending from an opening in the first surface to an opening in the second surface, the reaction sites being configured to provide sufficient surface tension by capillary action to hold respective biological samples;   wherein a density of reaction sites over at least a portion of one of surfaces is at least 170 holes per square millimeter.   
     
     
         2 . The article of  claim 1 , wherein at least one of the surfaces has a surface roughness characterized by one or more of an arithmetic average roughness (Ra) that is less than or equal to 5 nanometers, a maximum valley depth roughness (Rv) that is less than or equal to 15 nanometers, a maximum peak height roughness (Rp) that is less than or equal to 9 nanometers, or a maximum peak to trench roughness (Rt) that is less than or equal to 24 nanometers. 
     
     
         3 . (canceled) 
     
     
         4 . The article of  claim 1 , wherein two or more of the reaction sites comprise a hexagonal shape at one of the surfaces or at each of the surfaces. 
     
     
         5 - 7 . (canceled) 
     
     
         8 . The article of  claim 1 , wherein the openings of each surface are arranged in a close-packed hexagonal matrix. 
     
     
         9 - 11 . (canceled) 
     
     
         12 . The article of  claim 1 , wherein each of the walls of the two or more of the reaction sites is tapered between the surfaces. 
     
     
         13 . (canceled) 
     
     
         14 . The article of  claim 1 , wherein each of the walls of the two or more of the reaction sites includes a chamfer located at one of the surfaces or at each of the surfaces. 
     
     
         15 . (canceled) 
     
     
         16 . The article of  claim 1 , wherein at least some of the reaction sites have a volume between the opposing surfaces that is less than or equal to 1 nanoliter. 
     
     
         17 - 18 . (canceled) 
     
     
         19 . The apparatus of  claim 1 , wherein a reaction site volume of at a first plurality of the reaction sites is different than a reaction site volume of at a second plurality of the reaction sites. 
     
     
         20 - 27 . (canceled) 
     
     
         28 . The article of  claim 1 , wherein the substrate comprises a photo-structured glass ceramic material. 
     
     
         29 . The article of  claim 1 , wherein the substrate comprises a silicon material. 
     
     
         30 . The apparatus of  claim 1 , further comprising a fiducial disposed on at least one of the surfaces. 
     
     
         31 . An article for holding biological samples for analysis, the article comprising:
 a substrate having a pair of opposing surfaces; and   a plurality of reaction sites in the substrate, each of the reaction sites extending from an opening in one of the opposing surfaces of the substrate to an opening in the other one of the opposing surfaces, the reaction sites being configured to provide sufficient surface tension by capillary action to hold respective biological samples;   wherein at least some of the reaction sites have a volume between the opposing surfaces that is less than or equal to 1 nanoliter.   
     
     
         32 . An apparatus, comprising:
 the article of  claim 1 ; and   a carrier comprising:
 a first cover comprising a bottom surface; and 
 a second cover comprising a top surface; 
   wherein the article is disposed between the top surface and the bottom surface;   wherein there is a space between the first surface of the substrate and the top surface;   wherein there is a space between the second surface of the substrate and the bottom surface.   
     
     
         33 . (canceled) 
     
     
         34 . The apparatus of  claim 32 , further comprising a PDMS material disposed within the spaces. 
     
     
         35 . (canceled) 
     
     
         36 . The article of  claim 32 , wherein the carrier comprises an aperture disposed perpendicular to the surfaces and sized to allow passage of the substrate, wherein the aperture comprises a piercable membrane that is broken when the substrate is moved into the carrier. 
     
     
         37 - 39 . (canceled) 
     
     
         40 . A system comprising:
 the apparatus of  claim 32 ;   a light source configured to provide an excitation beam;   a photodetector configured to receive emission light from two or more of the reaction sites when the excitation beam interacts with a biological solution contained in the two or more of the reaction sites;   an optical system comprising an excitation optical system configured to deliver at least a portion of the excitation beam to the two or more of the reaction sites and emission optical system to deliver at least some of the emission light from the two or more of the reaction sites to the detector.   
     
     
         41 . The system of  claim 40 , further comprising a thermal control unit to control a temperature of the substrate or within the substrate. 
     
     
         42 - 45 . (canceled) 
     
     
         46 . A method of making an article for holding biological samples for analysis, the method comprising:
 providing a substrate comprising glass and having a first surface and an opposing second surface;   covering the glass with a mask comprising a pattern;   passing an ultraviolet beam through the mask and onto at least portions of the substrate;   exposing the at least portion of the substrate to a corrosive agent;   removing material to provide a plurality of reaction sites extending from one of the surfaces of the substrate to the other one of the surfaces;   subsequently exposing the substrate to an ultraviolet beam so as to change a characteristic of the glass;   
     
     
         47 - 54 . (canceled) 
     
     
         55 . A method of making an article for holding biological samples for analysis, the method comprising:
 providing a substrate comprising silicon and having a first surface and an opposing second surface;   applying a pattern to one of the surfaces;   etching a plurality of wells the first surface;   removing material from the second surface to form at least one through-hole from a corresponding well of the plurality of wells;   forming a surface roughness on at least one of the surfaces, the surface roughness characterized by one or more of an arithmetic average roughness (Ra) that is less than or equal to 5 nanometers, a maximum valley depth roughness (Rv) that is less than or equal to 15 nanometers, a maximum peak height roughness (Rp) that is less than or equal to 9 nanometers, or a maximum peak to trench roughness (Rt) that is less than or equal to 24 nanometers.   
     
     
         56 . (canceled) 
     
     
         57 . A method of preparing a plurality of biological samples, the method comprising:
 providing the article of  claim 1 ;   providing a carrier comprising:
 a first cover comprising a bottom surface; and 
 a second cover comprising a top surface; 
 an aperture sized to receive the article; 
   providing an insertion tool comprising:
 a U-shaped body; 
 a pair of arms configured to slideably engage the carrier; 
   attaching the article within the U-shaped body;   sliding the insertion tool by an amount sufficient to dispose the article between the covers;   
     
     
         58 - 63 . (canceled)