Devices and methods for measuring nanometer level binding reactions

Abstract

Systems and methods for measuring nanometer level binding reactions are described herein. In some embodiments, the disclosed subject matter is directed to a device comprising (a) a substrate having a surface and (b) an ordered array of posts, pits, or patches over the surface, wherein the posts, pits, or patches are capable of binding a protein or small molecule ligand, and wherein the pitch between adjacent posts, pits, or patches is less than about 100 nm. In some other embodiments, the disclosed subject matter is also directed to methods for identifying the presence of an analyte in a fluid and to methods for measuring relative binding specificity or affinity between an analyte in a fluid and the posts, pits, or patches, using the device of the disclosed subject matter.

1 . A device for measuring nanometer level binding reactions, the device comprising: 
 (a) a surface; and    (b) an ordered array of posts, pits, or patches on the surface, wherein the posts, pits, or patches are capable of binding a protein or small molecule ligand, wherein the pitch between adjacent posts, pits, or patches is less than about 100 nm, and wherein each post consists essentially of titanium dioxide or gold-palladium alloy.    
     
     
         2 . The device of  claim 1 , wherein the device comprises a gradual change of pitch that varies from about 5 nm to about 100 nm.  
     
     
         3 . The device of  claim 1 , wherein the post, pit, or patch has affixed thereto at least one protein molecule.  
     
     
         4 . The device of  claim 3 , wherein one of the post, pit, or patch has affixed thereto exactly one protein molecule.  
     
     
         5 . The device of  claim 1 , wherein the protein molecule comprises at least a portion of a dynein heavy chain, a tubulin, a kinesin, a myosin, a cytoplasmic domain of an integrin, an actin, an extracellular matrix protein, a fibronectin, a collagen, a laminin, a DNA solenoid, a DNA, a histone-DNA complex, an RNA, an RNA-protein complexes, a bacterial coat proteins, an antibody, a lectin, an avidin, or any combination thereof.  
     
     
         6 . The device of  claim 1 , wherein the protein molecule comprises a full-length dynein heavy chain.  
     
     
         7 . The device of  claim 1 , wherein the protein molecule comprises a dynein motor domain.  
     
     
         8 . The device of  claim 7 , wherein the protein molecule comprises an N-terminal portion of the dynein motor domain.  
     
     
         9 . A method for measuring a nanometer level binding reaction, the method comprising 
 (a) providing a device comprising a surface; the surface comprising an ordered array of posts, pits, or patches, wherein the pitch between adjacent posts, pits, or patches is less than about 100 nm, wherein each post, pit, or patch is coated with ligand, and wherein each post consists essentially of titanium dioxide or gold-palladium alloy;    (b) contacting the surface of the device with a sample; and    (c) determining whether or not an analyte from the sample interacts or binds to a ligand-coated post, pit, or patch to measure the nanometer level binding reaction.    
     
     
         10 . The method of  claim 9 , further comprising isolating the analyte from the sample.  
     
     
         11 . The method of  claim 9 , wherein the device comprises a gradual change of pitch that varies from about 5 nm to about 100 nm.  
     
     
         12 . The method of  claim 9 , wherein the post, pit, or patch has affixed thereto at least one protein molecule.  
     
     
         13 . The method of  claim 12 , wherein one of the post, pit, or patch has affixed thereto exactly one protein molecule.  
     
     
         14 . The method of  claim 12 , wherein the protein molecule comprises at least a portion of a dynein heavy chain, a tubulin, a kinesin, a myosin, a cytoplasmic domain of an integrin, an actin, an extracellular matrix protein, a fibronectin, a collagen, a laminin, a DNA solenoids, a DNA, histone-DNA complex, an RNA, an RNA-protein complex, a bacterial coat protein, an antibody, a lectin, an avidin, or any combination thereof.  
     
     
         15 . The method of  claim 12 , wherein the protein molecule comprises a full-length dynein heavy chain.  
     
     
         16 . The method of  claim 12 , wherein the protein molecule comprises a dynein motor domain.  
     
     
         17 . The method of  claim 16 , wherein the protein molecule comprises an N-terminal portion of the dynein motor domain.