Oxide Layers on Silicone Substrates for Effective Confocal Laser Microscopy

Abstract

Methods of performing confocal laser microscopy on a polymer array disposed on a silicon wafer substrate, the method comprising the steps of providing a silicon wafer substrate having a top side and a bottom side, coating the top side of the silicon wafer with an oxide coating to provide an oxide coated wafer, covalently coupling a plurality of probes to the top side of the coated wafer to provide a fixed polymer array, hybridizing the fixed polymer array with a plurality of labeled ligands, and assaying for one or more hybridized ligands using confocal laser fluorescence microscopy to detect hybridization are provided.

1 . A method of performing confocal laser microscopy on a polymer array disposed on a silicon wafer substrate, said method comprising the steps of:
 providing a silicon wafer substrate having a top side and a bottom side;   coating said top side of said silicon wafer with an oxide coating to provide an oxide coated wafer;   covalently coupling a plurality of probes to said top side of said coated wafer to provide a fixed polymer array;   hybridizing said fixed polymer array with a plurality of labeled ligands; and   assaying for one or more hybridized ligands using confocal laser fluorescence microscopy to detect hybridization.   
     
     
         2 . The method of  claim 1 , further comprising applying BisB to said oxide coating. 
     
     
         3 . A method of performing confocal laser microscopy on a polymer array disposed on a silicon wafer substrate, said method comprising the steps of:
 providing a silicon wafer substrate having a top side and a bottom side;   coating said top side of said substrate with a transparent oxide layer to provide an oxide coated wafer;   depositing a reactive functional group comprising a labile protecting group substantially uniformly across the transparent oxide layer;   selectively removing one or more of said labile protecting groups from predefined regions of said wafer to provide exposed functional groups in said predefined regions;   reacting said exposed functional groups with a monomer comprising a reactive functional group and a labile protecting group;   repeating the steps of selectively removing and reacting to produce said polymer array;   hybridizing said polymer array with a plurality of ligands; and   assaying for one or more hybridized ligands using a confocal laser fluorescence microscopy to detect hybridization.   
     
     
         4 . The method of  claim 3 , wherein said oxide layer has a thickness of at least 3,500 angstroms. 
     
     
         5 . The method of  claim 3 , wherein said oxide layer has a thickness of at least 35,000 angstroms. 
     
     
         6 . The method of  claim 3 , wherein said labile protecting group is an acid labile protecting group. 
     
     
         7 . The method of  claim 6 , wherein said acid labile protecting group is a dimethoxytrityl group. 
     
     
         8 . The method of  claim 6 , wherein said acid labile protecting group is removed by activating a photoacid generator with light of an appropriate wavelength to produce acid. 
     
     
         9 . The method of  claim 8 , wherein said photoacid generator is an ionic photoacid generator or a non-ionic photoacid generator. 
     
     
         10 . The method of  claim 9 , wherein said photoacid generator is an ionic photoacid generator. 
     
     
         11 . The method of  claim 9 , wherein said photoacid generator is a non-ionic photoacid generator. 
     
     
         12 . The method of  claim 11 , wherein said non-ionic photoacid generator is 2,6-dinitrobenzyl tosylate. 
     
     
         13 . The method of  claim 10 , wherein said ionic photoacid generator is an onium salt. 
     
     
         14 . The method of  claim 13 , wherein said onium salt is bis-(4-t-butyl phenyl) iodonium PF 6   − . 
     
     
         15 . The method of  claim 3 , wherein said labile protective group is a photolabile protecting group. 
     
     
         16 . The method of  claim 3 , wherein said monomer is selected from the group consisting of a nucleotide, a nucleic acid, an amino acid and a peptide. 
     
     
         17 . The method of  claim 3 , wherein said monomer is a nucleic acid and said labile protecting group is MeNPOC. 
     
     
         18 . The method of  claim 3 , wherein said monomer is a nucleic acid and said labile protecting group is NNPOC or MBPMOC.