Methods and systems for mask alignment in manufacturing process of arrays

Abstract

Provided herein are molecules and salts thereof, arrays containing molecules and salts thereof, solid supports containing molecules and salts thereof, kits containing molecules or salts thereof, and methods of determining alignment of photolithographic masks comprising molecules or salts thereof.

1 .- 20 . (canceled) 
     
     
         21 . A method comprising:
 a) deprotecting a subset of a plurality of protected molecules comprising a photoreactive or acid-sensitive protecting group to form a plurality of deprotected molecules; wherein the plurality of protected molecules is comprised in a first array region; wherein the plurality of deprotected molecules is comprised in a second array region; and wherein a distance from a boundary of the first array region to a boundary of the second array region is substantially uniform; and   b) detecting alignment of the second array region with the first array region, wherein the detecting alignment comprises detecting a chromophoric signal from at least one of the first array region and the second array region; and wherein the first array region and the second array region are substantially located in a space between two or more features on an array, wherein the array comprises the first array region and the second array region.   
     
     
         22 . The method of  claim 21 , wherein the two or more features on the first array region and the second array region are synthesized using solid phase peptide coupling. 
     
     
         23 . The method of  claim 21 , wherein each of the features is a region on a solid substrate ranging from about 0.5 μm to about 200 μm in diameter. 
     
     
         24 . The method of  claim 21 , wherein a center-to-center distance between the features ranges from about 1 μm to about 300 μm in diameter. 
     
     
         25 . The method of  claim 21 , wherein the array comprises at least one nucleoside, nucleotide, polynucleotide, peptide, peptoid, saccharide, aptamer, or antibody or fragment thereof. 
     
     
         26 . The method of  claim 21 , further comprising forming the first array region, wherein the forming the first array region comprises:
 i) forming an oxygen-silicon covalent bond between a solid substrate and a first molecule or salt thereof comprising a silicon at a first end and an epoxide at a second end; and   ii) forming a V-carbon covalent bond between a carbon atom of the epoxide and a second molecule or salt thereof comprising an amino group, thereby opening the epoxide;
 wherein V is nitrogen, oxygen, sulfur, or selenium; 
 wherein the epoxide and the silicon are linked by a group comprising an alkyl, alkylether, or alkylthioether, wherein each of alkyl, alkylether, or alkylthioether is optionally substituted with hydroxyl, thiol, amino, or halo, and 
 wherein the first array region further comprises coupling, wherein an amino acid or salt thereof is further coupled to: a protected biotin or salt thereof; or a protected serine or salt thereof; or a chromophoric dye, to form the plurality of protected molecules. 
   
     
     
         27 . The method of  claim 26 , wherein the coupling is via a covalent bond or a non-covalent bond. 
     
     
         28 . The method of  claim 21 , wherein the deprotecting comprises a photodeprotection reaction. 
     
     
         29 . The method of  claim 28 , wherein the photodeprotection reaction comprises a photoacid or photoacid generator. 
     
     
         30 . The method of  claim 21 , wherein the detecting alignment further comprises binding a detectably labeled probe to the plurality of deprotected molecules. 
     
     
         31 . The method of  claim 30 , wherein the detectably labeled probe comprises a chromophoric dye. 
     
     
         32 . The method of  claim 31 , wherein the chromophoric dye is a fluorescent dye or a phosphorescent dye. 
     
     
         33 . The method of  claim 30 , wherein the detectably labeled probe comprises a labeled polypeptide or a salt thereof. 
     
     
         34 . The method of  claim 33 , wherein the labeled polypeptide comprises streptavidin, neutravidin, or captavidin, or a salt thereof. 
     
     
         35 . The method of  claim 33 , wherein the labeled polypeptide or salt thereof is labeled with a chromophoric dye. 
     
     
         36 . The method of  claim 21 , wherein the detecting alignment further comprises a fluorescence scan. 
     
     
         37 . The method of  claim 21 , wherein the first array region is a peptide array. 
     
     
         38 . The method of  claim 26 , wherein the solid substrate comprises a wafer substrate. 
     
     
         39 . The method of  claim 21 , wherein the first array region comprises a density of amino groups of each of a plurality of molecules or salts thereof ranging from about 1×10 10  groups per cm 2  to about 1×10 15  amino groups per cm 2 . 
     
     
         40 . The method of  claim 21 , wherein the first array region is formed by a deposition reaction. 
     
     
         41 . The method of  claim 21 , wherein the first array region is formed in solution phase or in gas phase. 
     
     
         42 . An array comprising a plurality of molecules or salts thereof having the structure:
 (a)   
       
         
           
           
               
               
           
         
          or a salt thereof,
 wherein W is S or O; 
 X is S, O, or NH; 
 Y and Z are H, or wherein Y and Z are combined to form a S, O, or methylene; 
 R 1  is alkyl, alkenyl, alkynyl, aryl, heteroalkyl, heteroalkenyl, or heteroaryl; and
 wherein R 1  further comprises a solid support; 
 
 R 2  is hydrogen or alkyl; 
 R 3  is alkyl, alkenyl, aryl, heteroalkyl, heteroalkenyl, heteroaryl, or arylalkyl; 
 R 4  and R 5  are independently hydrogen or alkyl, alkenyl, aryl, heteroalkyl, heteroalkenyl, heteroaryl, or arylalkyl; wherein at least one of R 4  and R 5  is not hydrogen; 
 
         (b) 
       
       
         
           
           
               
               
           
         
          or a salt thereof,
 wherein W is S or O; 
 R 1  is alkyl, alkenyl, alkynyl, aryl, heteroalkyl, heteroalkenyl, or heteroaryl; and
 wherein R 1  further comprises a solid support; 
 
 R 2 , R 3 , and R 4  are independently hydrogen or alkyl;
 R 5  is alkyl, alkenyl, aryl, heteroalkyl, heteroalkenyl, heteroaryl, or arylalkyl; or 
 
 
         (c) 
       
       
         
           
           
               
               
           
         
          or a salt thereof,
 wherein W is S or O; 
 R 1  is alkyl, alkenyl, alkynyl, aryl, heteroalkyl, heteroalkenyl, or heteroaryl; and
 wherein R 1  further comprises a solid support; 
 
 R 2  hydrogen or alkyl; 
 R 14  and R 15  are the same or different and are independently hydrogen, halo, alkyl, alkenyl, aryl, heteroalkyl, arylalkyl, hydroxyarylalkyl, heteroarylalkyl, cycloalkyl, thioalkyl, selenoalkyl, hydroxyalkyl, or amino-substituted alkyl; 
 R 16  is H or alkyl; 
 A is a functional group comprising a chromophore.