Nanowire-based system for analysis of nucleic acids

Abstract

System for detection and/or analysis of nucleic acids using nanowires to detect covalent modification of nucleic acids.

1 . A method of detecting and/or analyzing a nucleic acid, comprising: 
 contacting a nanowire assembly including a nanowire coupled to a nucleic acid analyte with at least one reagent for covalent modification of nucleic acids based on nucleic acid structure; and    measuring an electrical characteristic of the nanowire assembly to determine whether or not the at least one reagent produced a covalent modification of the nanowire assembly, thereby providing structural information about the nucleic acid analyte.    
     
     
         2 . The method of  claim 1 , wherein the step of contacting is performed on an array of such nanowire assemblies disposed in fluid communication.  
     
     
         3 . The method of  claim 2 , wherein the nanowire assemblies are coupled to different nucleic acid analytes, and wherein the step of measuring provides structural information about each of the different nucleic acid analytes.  
     
     
         4 . The method of  claim 1 , wherein the step of measuring includes a step of measuring substantially no change in the electrical characteristic, thereby indicating that the nucleic acid analyte lacks structure capable of directing covalent modification by the at least one reagent.  
     
     
         5 . The method of  claim 1 , wherein the step contacting is performed on a nanowire assembly including a nucleic acid probe that is attached to the nanowire and that pairs selectively with the nucleic acid analyte to couple the nucleic acid analyte to the nanowire.  
     
     
         6 . The method of  claim 5 , wherein the nucleic acid probe is configured as a primer of nucleic acid synthesis with the nucleic acid analyte as a template, and wherein the step of contacting includes a step of contacting the primer and the template with a polymerase and a nucleotide substrate for the polymerase.  
     
     
         7 . The method of  claim 6 , wherein the step of measuring determines an amount of change in the electrical characteristic, if any, the method further comprising a step of correlating the amount to a number of nucleotide subunits linked to the primer by the step of contacting.  
     
     
         8 . The method of  claim 6 , wherein the steps of contacting and measuring are repeated individually for each of four different nucleotide substrates corresponding to the nucleotides guanosine, adenosine, thymidine, and cytidine.  
     
     
         9 . The method of  claim 8 , wherein the steps of contacting and measuring are repeated over two or more cycles of contacting individually with the four different nucleotide substrates.  
     
     
         10 . The method of  claim 1 , wherein the step of contacting includes a step of contacting with a reagent having ligation activity, and wherein the step of measuring includes a step of determining whether or not nucleic acid ligation occurred.  
     
     
         11 . The method of  claim 1 , wherein the step of contacting includes a step of contacting with a reagent for cleavage of nucleic acids, and wherein the step of measuring includes a step of determining whether or not nucleic acid cleavage occurred.  
     
     
         12 . The method of  claim 1 , further comprising a step of adjusting a stringency for nucleic acid hybridization.  
     
     
         13 . The method of  claim 12 , wherein the step of adjusting a stringency is performed by adjusting at least one of a temperature, an electric field, and a fluid composition associated with the nanowire assembly.  
     
     
         14 . The method of  claim 1 , wherein the step of contacting is performed with a nanowire coupled to a nucleic acid at two or more spaced positions along the nucleic acid.  
     
     
         15 . The method of  claim 1 , wherein the nanowire functions as a field effect transistor.  
     
     
         16 . A system for detecting and/or analyzing nucleic acids, comprising: 
 a nanowire assembly including a nanowire coupled to a nucleic acid template base-paired with a primer;    a reagent delivery system capable of contacting the nanowire assembly sequentially with different reagents for extension of the primer based on the nucleic acid template;    an electrical detector configured to measure an electrical characteristic of the nanowire assembly; and    a controller in communication with the reagent delivery system and the electrical detector and configured to collect data corresponding to changes in the electrical characteristic in response to contact with the different reagents, thereby providing sequence information about the nucleic acid template    
     
     
         17 . The system of  claim 16 , wherein the nanowire assembly is a plurality of nanowire assemblies coupled to different templates, and wherein the controller is configured to collect data for each of the plurality of nanowire assemblies, thereby providing sequence information about each of the different templates.  
     
     
         18 . The system of  claim 16 , wherein the nanowire assembly functions as a field effect transistor.  
     
     
         19 . The system of  claim 16 , wherein the different reagents provide selective addition of guanosine, adenosine, thymidine, and cytidine to the primer.  
     
     
         20 . The system of  claim 16 , further comprising a heater configured to apply heat to the nanowire assembly.