Nanowire-based system for analysis of nucleic acids

Abstract

A method for sequencing a nucleic acid template includes forming a nanowire assembly including a semiconductor nanowire and a probe covalently bound to the semiconductor nanowire; contacting the nanowire assembly with a template nucleic acid; contacting the nucleic acid duplexes with an extension nucleic acid, the extension nucleic acid joined to the probe; disrupting the nucleic acid duplexes; and measuring an electrical characteristic of a nanowire assembly of the set of nanowire assemblies.

1 - 20 . (canceled) 
     
     
         21 . A method for sequencing a nucleic acid template, the method comprising:
 forming a set of nanowire assemblies, each nanowire assembly of the set of nanowire assemblies including a semiconductor nanowire and a nucleic acid probe covalently bound to the semiconductor nanowire, the semiconductor nanowire connected at a first end to a first electrode and at a second end to a second electrode, a detector connected to the first and second electrodes to detect an electrical characteristic of the semiconductor nanowire;   contacting the set of nanowire assemblies with a template polynucleotide, the template polynucleotide at least partially complementary to the nucleic acid probe and forming a nucleic acid duplex with the nucleic acid probe;   contacting the nucleic acid duplexes with an extension nucleic acid and a ligase enzyme, the extension nucleic acid complementary to a portion of the template polynucleotide; and   measuring an electrical characteristic of a nanowire assembly.   
     
     
         22 . The method of  claim 21 , wherein the nucleic acid probe is connected to a first binding member and the semiconductor nanowire is connected to a second binding member that specifically binds to the first binding member. 
     
     
         23 . The method of  claim 22 , wherein the first binding member or the second binding member is streptavidin and the second binding member or the first binding member is biotin. 
     
     
         24 . The method of  claim 22 , wherein the nucleic acid probe is connected to two of the first binding members at sites spaced along the first nucleic acid. 
     
     
         25 . The method of  claim 24 , wherein the first binding members are spaced at opposite ends of the nucleic acid probe. 
     
     
         26 . The method of  claim 21 , further comprising, prior to measuring an electrical characteristic, disrupting the nucleic acid duplexes to render less stable nucleic acid duplexes single stranded. 
     
     
         27 . The method of  claim 26 , wherein disrupting includes changing a temperature of the set of nanowire assemblies. 
     
     
         28 . The method of  claim 26 , wherein disrupting includes adjusting an ionic strength of a solution surrounding the set of nanowire assemblies. 
     
     
         29 . The method of  claim 26 , wherein disrupting includes changing the concentration of an organic solvent. 
     
     
         30 . The method of  claim 26 , wherein disrupting includes enzymatically disrupting. 
     
     
         31 . The method of  claim 30 , wherein enzymatically disrupting includes adding nuclease. 
     
     
         32 . The method of  claim 26 , wherein disrupting includes changing an electric field of a nucleic acid assembly. 
     
     
         33 . The method of  claim 21 , wherein the step of measuring includes a step of measuring substantially no change in the electrical characteristic of a select nanowire assembly, thereby indicating that the extension nucleic acid is not added to an associated probe. 
     
     
         34 . The method of  claim 21 , wherein the step of measuring determines a change in the electrical characteristic correlating the joining of the extension nucleic acid to the nucleic acid probe. 
     
     
         35 . The method of  claim 21 , wherein the nucleic acid probe is a probe of a set of different probes that include regions of nucleotide sequence variation in a population. 
     
     
         36 . The method of  claim 35 , wherein a variation in the region is disposed at or near an end of the probe. 
     
     
         37 . The method of  claim 35 , wherein the nucleotide sequence variation corresponds to a polymorphism in a population. 
     
     
         38 . The method of  claim 35 , wherein each nanowire assembly includes a probe of the set of different probes that is different from another probe of another nanowire assembly of the set of nanowire assemblies. 
     
     
         39 . The method of  claim 35 , wherein the template polynucleotide includes a polymorphic region corresponding to a probe of the set of probes. 
     
     
         40 . The method of  claim 21 , further comprising forming a second nanowire assembly including a second semiconductor nanowire and a second nucleic acid probe covalently bound to the second semiconductor nanowire, wherein the nucleic acid assembly includes the nucleic acid probe having a first region with a first nucleotide sequence variation and the second nucleic acid assembly includes the second nucleic acid probe having the region with a second nucleotide sequence variation.