High resolution DNA detection methods and devices

Abstract

The present invention provides methods and devices for detecting a target nucleic acid molecule. A set of oligonucleotide probes integrated into an electric circuit, where the oligonucleotide probes are positioned such that they can not come into contact with one another, are contacted with a sample. If the sample contains a target nucleic acid molecule, one which has sequences complimentary to both probes, the target nucleic acid molecule can bridge the gap between the probes. The resulting bridge can then carry electrical current between the two probes, indicating the presence of the target nucleic acid molecule.

1 . A method for detecting a target nucleic acid molecule, comprising, 
 providing a device for detecting the presence of a target nucleic acid molecule, comprising: 
 two electronic leads, where an end of a first lead is located near an end of a second lead but where the leads are not in contact, and  
 one or more sets of two oligonucleotide probes attached to the electronic leads, where the oligonucleotide probes are positioned such that the probes can not come into contact with one another and such that a target nucleic acid molecule, which has two sequences, a first sequence complimentary to a first probe attached to the first lead and a second sequence complimentary to a second probe attached to the second lead, can bind to both probes concurrently; and  
   contacting the probes with a sample which may have the target nucleic acid molecule under selective hybridization conditions, and    determining if an electrical current can be carried between the probes, said electrical current between the probes indicating the presence of the target nucleic acid molecule in the sample which has sequences complimentary to the probes.    
   
   
       2 . The method according to  claim 1 , wherein the nucleic acid molecule is DNA.  
   
   
       3 . The method according to  claim 1 , wherein the nucleic acid molecule is RNA.  
   
   
       4 . The method according to  claim 1 , further comprising: 
 coating a target nucleic acid molecule which is attached to the probes with a conductor.    
   
   
       5 . The method according to  claim 4 , wherein the conductor is silver.  
   
   
       6 . The method according to  claim 4 , wherein the conductor is gold.  
   
   
       7 . The method according to  claim 1 , further comprising: 
 contacting the target nucleic acid molecule with nucleases after binding with the probes.    
   
   
       8 . The method according to  claim 1 , further comprising: 
 contacting the target nucleic acid molecule with ligase after binding with the probes, and    heating the target nucleic acid molecule to a temperature high enough to denature a non-ligated target nucleic acid molecule from the probes.    
   
   
       9 . The method according to  claim 1 , wherein the probes are complimentary to sequences from the genetic material of a pathogenic bacteria.  
   
   
       10 . The method according to  claim 1 , wherein the pathogenic bacteria is a biowarfare agent.  
   
   
       11 . The method according to  claim 1 , wherein the pathogenic bacteria is a food borne pathogen.  
   
   
       12 . The method according to  claim 1 , wherein the probes are complimentary to sequences from the genetic material of a virus.  
   
   
       13 . The method according to  claim 1 , wherein the probes are complimentary to sequences from the genetic material of a human.  
   
   
       14 . The method according to  claim 1 , wherein one or both of the probes has a sequence which is complimentary to a sequence having a polymorphism, where the base or bases complimentary to the polymorphism are located at the end of the probe.  
   
   
       15 . A device for detecting the presence of a target nucleic acid molecule, comprising: 
 two electronic leads, where an end of a first lead is located near an end of a second lead but where the leads are not in contact, and    one or more sets of two oligonucleotide probes attached to the electronic leads, where the oligonucleotide probes are positioned such that the probes can not come into contact with one another and such that a target nucleic acid molecule, which has two sequences, a first sequence complimentary to a first probe attached to the first lead and a second sequence complimentary to a second probe attached to the second lead, can bind to both probes concurrently.    
   
   
       16 . The device according to  claim 15 , further comprising: 
 a chamber for treating a sample to release nucleic acid molecules from a sample.    
   
   
       17 . The device according to  claim 15 , wherein the device contains proteins for processing the sample.  
   
   
       18 . The device according to  claim 17 , wherein the protein is selected from the group consisting of a ligase, protease, restriction endonuclease, nuclease, or nucleic acid binding protein.  
   
   
       19 . The device according to  claim 17 , wherein the protein is a thermostable protein.  
   
   
       20 . The device according to  claim 15 , wherein the nucleic acid molecule is DNA.  
   
   
       21 . The device according to  claim 15 , wherein the nucleic acid molecule is RNA.  
   
   
       22 . The device according to  claim 1 , further comprising: 
 a chamber having a solution for coating a target nucleic acid molecule which is attached to the probes with a conductor.    
   
   
       23 . The device according to  claim 22 , wherein the conductor is silver.  
   
   
       24 . The device according to  claim 22 , wherein the conductor is gold.  
   
   
       25 . The device according to  claim 15 , further comprising: 
 a chamber containing nucleases for contacting the target nucleic acid after binding with the probes.    
   
   
       26 . The device according to  claim 15 , further comprising: 
 heating elements for heating the sample.    
   
   
       27 . The device according to  claim 15 , wherein the probes are complimentary to sequences from the genetic material of a pathogenic bacteria.  
   
   
       28 . The device according to  claim 27 , wherein the pathogenic bacteria is a biowarfare agent.  
   
   
       29 . The device according to  claim 27 , wherein the pathogenic bacteria is a food borne pathogen.  
   
   
       30 . The device according to  claim 15 , wherein the probes are complimentary to sequences from the genetic material of a virus.  
   
   
       31 . The device according to  claim 15 , wherein the probes are complimentary to sequences from the genetic material of a human.  
   
   
       32 . The device according to  claim 31 , wherein one or both of the probes has a sequence which is complimentary to a sequence having a polymorphism, where the base or bases complimentary to the polymorphism are located at the end of the probe.