Sensor arrays and nucleic acid sequencing applications

Abstract

Embodiments of the present invention provide devices methods for sequencing DNA using arrays of reaction regions containing electronic sensors to monitor changes in solutions contained in the reaction regions. Test and fill reaction schemes are disclosed that allow DNA to be sequenced. By sequencing DNA using parallel reactions contained in large arrays, DNA can be rapidly sequenced.

What is claimed is: 
     
         1 . A sensor comprising a plurality of reaction cavities for holding reactants, the cavities having DNA molecules to be sequenced with each of the cavities having statistically one DNA molecule to be sequenced, each of the cavities having a surface for attachment of the one DNA molecule to be sequenced and a coupled optical sensor for detecting changes resulting from a chemical reaction in each of the cavities, furthermore each of the cavities comprises a DNA oligo, the DNA oligo comprising a first nuclease-resistant nucleotide or a first nuclease-resistant nucleotide analog at the 3′-end of the DNA oligo,
 wherein the sensor is configured to perform: 
 repeated nucleotide addition and excision reactions without cleavage of the first nuclease-resistant nucleotide or the first nuclease-resistant nucleotide analog; 
 identify the base of the DNA molecule to be sequenced immediately upstream from the base of the DNA molecule complementary to the first nuclease-resistant nucleotide by monitoring increases in reaction; and 
 attach a second nuclease-resistant blocking nucleotide or a second nuclease-resistant blocking nucleotide analog to the 3′-end of the DNA oligo, the second nuclease-resistant blocking nucleotide or the second nuclease-resistant blocking nucleotide analog being complementary to the identified base, 
 
     
     
         2 . The sensor of  claim 1 , wherein the sensor comprises a single walled carbon nanotube that is capable of acting as field effect transistor. 
     
     
         3 . The sensor of  claim 1 , wherein the reactants comprise a polymerase. 
     
     
         4 . The sensor of  claim 1 , wherein the reactants comprises an exonuclease. 
     
     
         5 . The sensor of  claim 1 , wherein the first nuclease-resistant blocking nucleoside comprises alpha-thiophosphate. 
     
     
         6 . The sensor of  claim 1 , wherein the nucleotide is a naturally occurring nucleotide or an analog thereof, 
     
     
         7 . The sensor of  claim 1 , wherein the nucleotide is labeled, 
     
     
         8 . The sensor of  claim 1 , further wherein the sensor is configured to deblock the second nuclease-resistant blocking nucleotide or the second nuclease-resistant blocking nucleotide analog. 
     
     
         9 . The sensor of  claim 1 , wherein the reactants comprises only one type of nucleobase selected from the group consisting of adenine, cytosine, guanine, thymine and uracil. 
     
     
         10 . The sensor of  claim 3 , wherein the polymerase is Klenow (exo-). 
     
     
         11 . The sensor of  claim 4 , wherein the exonuclease is exonuclease III. 
     
     
         12 . A sensor comprising a plurality of reaction cavities for holding reactants, the cavities having DNA molecules to be sequenced with each of the cavities having statistically one DNA molecule to be sequenced, each of the cavities having a surface for attachment of the one DNA molecule to be sequenced and a coupled electronic sensor for detecting changes resulting from a chemical reaction in each of the cavities, furthermore each of the cavities comprises a DNA oligo, the DNA oligo comprising a first nuclease-resistant nucleotide or a first nuclease-resistant nucleotide analog at the 3′-end of the DNA oligo,
 wherein the sensor is configured to perform: 
 repeated nucleotide addition and excision reactions without cleavage of the first nuclease-resistant nucleotide or the first nuclease-resistant nucleotide analog; 
 identify the base of the DNA molecule to be sequenced immediately upstream from the base of the DNA molecule complementary to the first nuclease-resistant nucleotide by monitoring increases in reaction; and 
 attach a second nuclease-resistant blocking nucleotide or a second nuclease-resistant blocking nucleotide analog to the 3′-end of the DNA oligo, the second nuclease-resistant blocking nucleotide or the second nuclease-resistant blocking nucleotide analog being complementary to the identified base, 
 
     
     
         13 . The sensor of  claim 12 , wherein the sensor comprises a single walled carbon nanotube that is capable of acting as field effect transistor. 
     
     
         14 . The sensor of  claim 12 , wherein the reactants comprise a polymerase. 
     
     
         15 . The sensor of  claim 12 , wherein the reactants comprises an exonuclease. 
     
     
         16 . The sensor of  claim 12 , wherein the first nuclease-resistant blocking nucleoside comprises alpha-thiophosphate. 
     
     
         17 . The sensor of  claim 12 , wherein the nucleotide is a naturally occurring nucleotide or an analog thereof. 
     
     
         18 . The sensor of  claim 12 , wherein the nucleotide is labeled. 
     
     
         19 . The sensor of  claim 12 , further wherein the sensor is configured to deblock the second nuclease-resistant blocking nucleotide or the second nuclease-resistant blocking nucleotide analog. 
     
     
         20 . The sensor of  claim 12 , wherein the reactants comprises only one type of nucleobase selected from the group consisting of adenine, cytosine, guanine, thymine and uracil.