Nucleic acid sequencing and electronic detection

Abstract

Embodiments of the present invention provide devices methods for sequencing DNA using arrays of reaction regions containing sensors to monitor changes in solutions or bound molecules contained in the reaction regions. Additional embodiments provide devices and methods for sequencing DNA using arrays of reaction regions that allow for optical monitoring of solutions in the reaction regions. Chemical amplification schemes that allow DNA to be sequenced in which multiple nucleotide addition reactions are performed to detect the incorporation of a base are disclosed. By sequencing DNA using parallel reactions contained in large arrays, DNA can be rapidly sequenced.

What is claimed is: 
     
         1 . A method for determining sequences of a sample of DNAs to be sequenced comprising,
 providing an array comprising a plurality of regions, and a sensor;   providing primer strands of DNA hybridized to the DNAs to be sequenced wherein the primer strands of DNA cannot be digested by a nuclease, and wherein statistically one DNA to be sequenced is immobilized in one region;   preventing extension of the primer strands hybridized to only those DNAs to be sequenced whose next unpaired base is adenine, or preventing extension of the primer strands hybridized to only those DNAs to be sequenced whose next unpaired base is guanine, or preventing extension of the primer strands hybridized to only those DNAs to be sequenced whose next unpaired base is thymine, or preventing extension of the primer strands hybridized to only those DNAs to be sequenced whose next unpaired base is cytosine;   extending the primer strands whose extension is not prevented;   detecting with the sensor increases in reaction products in the regions resulting from extending the primer strands whose extension is not prevented;   determining sequence information for the sample of DNAs to be sequenced based on detected increases in reaction products by the sensor.   
     
     
         2 . The method of  claim 1  wherein the array comprises about 2 to about 10,000 regions. 
     
     
         3 . The method of  claim 1  wherein the array comprises about 10,000 to about 1,000,000,000 regions. 
     
     
         4 . The method of  claim 1  wherein the sensor is a field effect transistor. 
     
     
         5 . The method of  claim 1  wherein the sensor is comprised of single walled carbon nanotubes that are capable of acting as a field effect transistor. 
     
     
         6 . The method of  claim 3  wherein detecting increases in reaction products comprises detecting a change in current flow in a field effect transistor. 
     
     
         7 . The method of  claim 1  wherein the sensor is an electrode. 
     
     
         8 . The method of  claim 1  wherein the enzyme capable of extending a DNA molecule is a polymerase enzyme. 
     
     
         9 . A method for determining sequences of a sample of DNAs to be sequenced comprising,
 providing an array comprising a plurality of regions, and a sensor;   providing primer strands of DNA hybridized to the DNAs to be sequenced wherein the primer strands of DNA cannot be digested by a nuclease, and wherein statistically one DNA to be sequenced is immobilized in one region;   preventing extension of the primer strands hybridized to only those DNAs to be sequenced whose next unpaired base is adenine, guanine or thymine, or preventing extension of the primer strands hybridized to only those DNAs to be sequenced whose next unpaired base is adenine, guanine or cytosine, or preventing extension of the primer strands hybridized to only those DNAs to be sequenced whose next unpaired base is guanine, thymine or cytosine, or preventing extension of the primer strands hybridized to only those DNAs to be sequenced whose next unpaired base is adenine, thymine or cytosine;   extending the primer strands whose extension is not prevented;   detecting with the sensor increases in reaction products in the regions resulting from extending the primer strands whose extension is not prevented;   determining sequence information for the sample of DNAs to be sequenced based on detected increases in reaction products by the sensor.   
     
     
         10 . The method of  claim 9  wherein the array comprises about 2 to about 10,000 regions. 
     
     
         11 . The method of  claim 9  wherein the array comprises about 10,000 to about 1,000,000,000 regions. 
     
     
         12 . The method of  claim 9  wherein the sensor is a field effect transistor. 
     
     
         13 . The method of  claim 9  wherein the sensor is comprised of single walled carbon nanotubes that are capable of acting as a field effect transistor. 
     
     
         14 . The method of  claim 12  wherein detecting increases in reaction products comprises detecting a change in current flow in a field effect transistor. 
     
     
         15 . The method of  claim 13  wherein detecting increases in reaction products comprises detecting a change in current flow in a field effect transistor. 
     
     
         16 . The method of  claim 9  wherein the sensor is an electrode. 
     
     
         17 . The method of  claim 9  wherein the enzyme capable of extending a DNA molecule is a polymerase enzyme. 
     
     
         18 . The method of  claim 4  wherein detecting increases in reaction products comprises detecting a change in current flow in a field effect transistor.