Articles having localized molecules disposed thereon and methods of producing same

Abstract

Methods of producing substrates having selected active chemical regions by employing elements of the substrates in assisting the localization of active chemical groups in desired regions of the substrate. The methods may include optical, chemical and/or mechanical processes for the deposition, removal, activation and/or deactivation of chemical groups in selected regions of the substrate to provide selective active regions of the substrate.

1 - 13 . (canceled) 
     
     
         14 . A method of preferentially localizing desired molecules within optical confinements disposed upon a substrate, comprising:
 depositing the desired molecules over the surface of the substrate; and   selectively removing the desired molecules from the surface of the substrate that is not within the optical confinements.   
     
     
         15 . The method of  claim 14 , wherein the substrate comprises an opaque layer on a transparent layer, and wherein the optical confinements comprise nanoscale wells disposed through the opaque layer and exposing part of the transparent layer. 
     
     
         16 . The method of  claim 15 , wherein the transparent layer comprises SiO 2 . 
     
     
         17 . The method of  claim 15 , wherein the opaque layer comprises a metal or metal oxide. 
     
     
         18 . The method of  claim 15 , wherein the opaque layer comprises aluminum and the transparent layer comprises SiO 2 . 
     
     
         19 . The method of  claim 14 , wherein the optical confinements comprise zero mode waveguides. 
     
     
         20 . The method of  claim 14 , wherein selectively removing the desired molecules from the surface of the substrate that is not within the optical confinements comprises contacting the substrate with a deactivation component coupled to an exclusionary component, which exclusionary component is at least partially excluded from entering into the optical confinements. 
     
     
         21 . The method of  claim 20 , wherein the deactivation component comprises an enzyme. 
     
     
         22 . The method of  claim 21 , wherein the enzyme is selected from the group consisting of a protease, a nuclease, and a carbohydrase. 
     
     
         23 . The method of  claim 21 , wherein the enzyme is a site-specific protease. 
     
     
         24 . The method of  claim 20 , wherein the exclusionary component is a large particle or a macromolecule. 
     
     
         25 . The method of  claim 24 , wherein the exclusionary component comprises a bead. 
     
     
         26 . The method of  claim 24 , wherein the exclusionary component comprises a rigid or semi-rigid elongated polymer. 
     
     
         27 . The method of  claim 24 , wherein the exclusionary component comprises a double-stranded nucleic acid molecule. 
     
     
         28 . The method of  claim 20 , wherein the deactivation component is a protease and the exclusionary component is a double-stranded DNA molecule. 
     
     
         29 . The method of  claim 20 , wherein the deactivation component is a protease and the exclusionary component is a bead. 
     
     
         30 . The method of  claim 14 , wherein the desired molecules are enzymes. 
     
     
         31 . The method of  claim 14 , wherein the desired molecules are polymerases. 
     
     
         32 . The method of  claim 14 , wherein the desired molecules comprise binding moieties. 
     
     
         33 . The method of  claim 32 , wherein the binding moieties are biotins.