Devices and methods for immobilizing nucleic acids

Abstract

The present invention generally relates to devices and methods for immobilizing nucleic acids on a substrate. In certain embodiments, devices of the invention include a voltage source, and a substrate coupled to the voltage source, in which hydrophobicity of the substrate changes in response to an applied electric field and a surface of the substrate is coated with a substance that retains nucleic acids.

What is claimed is: 
     
         1 . A device for elongating a nucleic acid, the device comprising:
 a voltage source; and   a substrate coupled to the voltage source, wherein hydrophobicity of the substrate changes in response to an applied electric field and a surface of the substrate is coated with a substance that retains nucleic acids.   
     
     
         2 . The device according to  claim 1 , wherein the substrate is a channel. 
     
     
         3 . The device according to  claim 1 , wherein the substrate comprises glass. 
     
     
         4 . The device according to  claim 3 , wherein the glass is coated with silanes. 
     
     
         5 . The device according to  claim 4 , wherein the substrate further comprises metal. 
     
     
         6 . The device according to  claim 1 , further comprising at least one reservoir fluidically coupled to the substrate. 
     
     
         7 . A method for elongating a nucleic acid on a substrate, the method comprising:
 temporarily applying an electric field to temporarily decrease hydrophobicity of a charged substrate, thereby causing a sample fluid comprising a nucleic acid to temporarily flow onto the charged substrate; and   maintaining the electric field for a time sufficient to allow the nucleic acid to interact with the charged substrate and become elongated and fixed on the substrate.   
     
     
         8 . The method according to  claim 7 , wherein the nucleic acid is DNA. 
     
     
         9 . The method according to  claim 7 , wherein the nucleic acid is from a microorganism. 
     
     
         10 . The method according to  claim 9 , wherein the microorganism is a bacterium. 
     
     
         11 . A method for characterizing a nucleic acid, the method comprising:
 temporarily applying an electric field to temporarily decrease hydrophobicity of a charged substrate, thereby causing a sample fluid comprising a nucleic acid to temporarily flow onto the charged substrate;   maintaining the electric field for a time sufficient to allow the nucleic acid to interact with the charged substrate and become elongated and fixed on the substrate so that the nucleic acid remains accessible for enzymatic reactions;   intermittently re-applying the electric field to cause reagents to flow to and from the substrate to wash, enzymatically digest, and stain the nucleic acid to obtain one or more restriction digests of the nucleic acid; and   imaging the restriction digests, thereby characterizing the nucleic acid.   
     
     
         12 . The method according to  claim 11 , further comprising constructing an optical map from the restriction digests. 
     
     
         13 . The method according to  claim 11 , wherein the nucleic acid is DNA. 
     
     
         14 . The method according to  claim 11 , wherein the nucleic acid is from a microorganism. 
     
     
         15 . The method according to  claim 14 , wherein the microorganism is a bacterium. 
     
     
         16 . The method according to  claim 15 , wherein the bacterium is at least one species selected from the group consisting of  E. coli  and  S. aureus.    
     
     
         17 . The method according to  claim 16 , wherein the  S. aureus  is a community-acquired methicillin-resistant strain of  S. aureus.    
     
     
         18 . The method according to  claim 16 , wherein the  S. aureus  is a hospital-acquired methicillin-resistant strain of  S. aureus.    
     
     
         19 . The method according to  claim 15 , wherein the nucleic acid comprises substantially all genomic DNA of the bacterium. 
     
     
         20 . The method according to  claim 15 , wherein the nucleic acid comprises a transcriptome of the bacterium.