Sensor and sensing system

Abstract

A sensor includes: a substrate; a polymerase attached to the substrate; two electrodes having a space therebetween and being supported by the substrate; and a modulatable electrically conductive channel attached to the two electrodes, the modulatable electrically conductive channel including a modified, partially double stranded nucleic acid polymer electrically connected to the two electrodes and bridging the space between the two electrodes. The modified, partially double stranded nucleic acid polymer includes: a first polynucleotide chain and a second polynucleotide chain partially bonded together; a gap in the first polynucleotide chain wherein nucleotides are missing, the gap configured to at least partially receive the switch strand; and a plurality of nucleotide bases of the second polynucleotide chain exposed at the gap in the first polynucleotide chain.

What is claimed is: 
     
         1 . A sensor, comprising:
 a substrate;   a polymerase attached to the substrate;   two electrodes having a space therebetween and being supported by the substrate; and   a modulatable electrically conductive channel attached to the two electrodes, the modulatable electrically conductive channel including a modified, partially double stranded nucleic acid polymer electrically connected to the two electrodes and bridging the space between the two electrodes, the modified, partially double stranded nucleic acid polymer including:
 a first polynucleotide chain and a second polynucleotide chain partially bonded together; 
 a gap in the first polynucleotide chain wherein nucleotides are missing, the gap configured to at least partially receive the switch strand; and 
 a plurality of nucleotide bases of the second polynucleotide chain exposed at the gap in the first polynucleotide chain. 
   
     
     
         2 . The sensor as defined in  claim 1 , wherein the gap has a length ranging from about 10 nm to about 50 nm. 
     
     
         3 . The sensor as defined in  claim 1 , wherein:
 i) linkers respectively attach each end of the first polynucleotide chain to a respective one of the two electrodes; or   ii) linkers respectively attach each end of the second polynucleotide chain to a respective one of the two electrodes; or   iii) both i and ii.   
     
     
         4 . The sensor as defined in  claim 1 , wherein at least one of the plurality of nucleotide bases exposed at the gap is a guanine base. 
     
     
         5 . The sensor as defined in  claim 1 , wherein each of the plurality of nucleotide bases exposed at the gap is a guanine base. 
     
     
         6 . The sensor as defined in  claim 1 , further comprising a detector to detect a response from the modified, partially double stranded nucleic acid polymer when a switch strand, including a strand of nucleotides including bases complementary to at least some of the plurality of nucleotide bases exposed at the gap, associates with the at least some of the plurality of nucleotide bases at the gap. 
     
     
         7 . The sensor as defined in  claim 1 , further comprising a fluidic system including a fluid inlet to introduce a reagent to the modified, partially double stranded nucleic acid polymer. 
     
     
         8 . The sensor as defined in  claim 7 , wherein the fluid inlet of the fluidic system is attached to a reagent delivery system to introduce the reagent to the fluid inlet, wherein the reagent delivery system includes a sample container and the reagent stored in the sample container, and wherein the reagent includes labeled nucleotides, at least one of the labeled nucleotides including:
 a nucleotide;   a linking molecule attached to a phosphate group of the nucleotide; and   a switch strand attached to the linking molecule, the switch strand including a strand of nucleotides including bases complementary to at least some of the plurality of nucleotide bases exposed at the gap.   
     
     
         9 . The sensor as defined in  claim 1 , further comprising a plurality of other modulatable electrically conductive channels attached to the two electrodes, each of the other modulatable electrically conductive channels including a respective modified, partially double stranded nucleic acid polymer electrically connected to the two electrodes and bridging the space between the two electrodes. 
     
     
         10 . The sensor as defined in  claim 1 , wherein the modulatable electrically conductive channel exhibits:
 a first conductance when the plurality of nucleotide bases are exposed at the gap; and   a second conductance that is different than the first conductance when at least some of the plurality of nucleotide bases at the gap are associated with complementary nucleotide bases.   
     
     
         11 . The sensor as defined in  claim 1 , wherein the polymerase is attached to the substrate with a tether. 
     
     
         12 . The sensor as defined in  claim 11 , wherein the tether is selected from the group consisting of a polyethylene glycol with a cleavable link, Nickel NTA/His tag chemistry, streptavidin/biotin chemistry, DNA-DNA hybridization, DNA-PNA hybridization, and carboxyl silane 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide. 
     
     
         13 . The sensor as defined in  claim 1 , wherein the tether holds the polymerase at least 10 nm away from the substrate. 
     
     
         14 . A sensing system, comprising:
 a flow cell; and   an electronic sensor integrated into the flow cell, the electronic sensor including:
 a substrate; 
 a polymerase attached to the substrate; 
 two electrodes having a space therebetween and being supported by the substrate; and 
 a modulatable electrically conductive channel attached to the two electrodes, the modulatable electrically conductive channel including a modified, partially double stranded nucleic acid polymer electrically connected to the two electrodes and bridging the space between the two electrodes, the modified, partially double stranded nucleic acid polymer including:
 a first polynucleotide chain and a second polynucleotide chain partially bonded together; 
 a gap in the first polynucleotide chain wherein nucleotides are missing, the gap configured to at least partially receive the switch strand; and 
 a plurality of nucleotide bases of the second polynucleotide chain exposed at the gap in the first polynucleotide chain. 
 
   
     
     
         15 . The sensing system as defined in  claim 14 , further comprising:
 a fluidic system including a fluid inlet to introduce a reagent to the modified, partially double stranded nucleic acid polymer; and   the fluid inlet of the fluidic system is attached to a reagent delivery system to introduce the reagent to the fluid inlet, wherein the reagent delivery system includes a sample container and the reagent stored in the sample container, and wherein the reagent includes labeled nucleotides, at least one of the labeled nucleotides including:   a nucleotide;   a linking molecule attached to a phosphate group of the nucleotide; and   a switch strand attached to the linking molecule, the switch strand including a strand of nucleotides including bases complementary to at least some of the plurality of nucleotide bases exposed at the gap.   
     
     
         16 . The sensing system as defined in  claim 14 , further comprising a detector to detect a response from the electronic sensor. 
     
     
         17 . A method, comprising:
 introducing a template polynucleotide chain to an electronic sensor having a polymerase tethered to a substrate supporting two electrodes, the modulatable electrically conductive channel including a modified, partially double stranded nucleic acid polymer, which includes:
 a first polynucleotide chain and a second polynucleotide chain partially bonded together; 
 a gap in the first polynucleotide chain wherein nucleotides are missing, the gap configured to at least partially receive the switch strand; and 
 a plurality of nucleotide bases of the second polynucleotide chain exposed at the gap in the first polynucleotide chain. 
   introducing reagents including labeled nucleotides to the electronic sensor, whereby a nucleotide of one of the labeled nucleotides associates with the polymerase and a nucleotide-specific switch strand of the one of the labeled nucleotides associates with at least some of the plurality of nucleotide bases exposed at the gap; and   in response to the association at the gap, detecting a response of the electronic sensor.   
     
     
         18 . The method as defined in  claim 17 , further comprising:
 associating the response of the electronic sensor with the associated nucleotide-specific switch strand; and   based on the associated nucleotide-specific switch strand, identifying the nucleotide of the one of the labeled nucleotides.   
     
     
         19 . The method as defined in  claim 17 , further comprising heating to disassociate the nucleotide-specific switch strand from the gap. 
     
     
         20 . The method as defined in  claim 17 , wherein:
 the electronic sensor includes a plurality of other modulatable electrically conductive channels attached to the two electrodes, each of the other modulatable electrically conductive channels including a respective modified, partially double stranded nucleic acid polymer electrically connected to the two electrodes and bridging the space between the two electrodes;   the gap of each of the modulatable electrically conductive channel and the plurality of other modulatable electrically conductive channels is configured to at least partially receive a different nucleotide-specific switch strand; and   introducing the reagents involves introducing four different labeled nucleotides, each including a different nucleotide and the different nucleotide-specific switch strand.   
     
     
         21 . The method as defined in  claim 20  wherein the four different labeled nucleotides include:
 a first labeled nucleotide, which includes deoxyadenosine polyphosphate as the nucleotide and a first nucleotide-specific switch strand; 
 a second labeled nucleotide, which includes deoxyguanosine polyphosphate as the nucleotide and a second nucleotide-specific switch strand having a different sequence than the first switch strand; 
 a third labeled nucleotide, which includes deoxycytidine polyphosphate as the nucleotide and a third nucleotide-specific switch strand having a different sequence than each of the first and second switch strands; and 
 a fourth labeled nucleotide, which includes deoxythymidine polyphosphate as the nucleotide and a fourth nucleotide-specific switch strand having a different sequence than each of the first, second, and third switch strands. 
 
     
     
         22 . The method as defined in  claim 21 , wherein the first, second, third, and fourth switch strands generate different conductivity changes when associated at a complementary gap of the modulatable electrically conductive channel and the plurality of other modulatable electrically conductive channels. 
     
     
         23 . A kit, comprising:
 an electronic component, including:
 a support; and 
 two electrodes operatively disposed on the support and separated by a space; and 
   a polymeric solution, including:
 a liquid carrier; and 
 a modified, partially double stranded nucleic acid polymer in the liquid carrier, the modified, partially double stranded nucleic acid polymer including:
 two polynucleotide chains partially bonded together and having opposed ends; 
 a linker attached to each of the opposed ends, each linker to attach to a respective one of the two electrodes; 
 a gap in a first of the polynucleotide chains wherein nucleotides are missing; and 
 a plurality of nucleotide bases of a second of the polynucleotide chains exposed at the gap in the first of the polynucleotide chains; 
 
   the modified, partially double stranded nucleic acid polymer to form a modulatable electrically conductive channel in the space between the two electrodes when each linker attaches to the respective one of the two electrodes.   
     
     
         24 . The kit as defined in  claim 23 , further comprising a reagent solution including labeled nucleotides, at least one of the labeled nucleotides including:
 a nucleotide;   a linking molecule attached to a phosphate group of the nucleotide; and   a switch strand attached to the linking molecule, the switch strand including a strand of nucleotides including bases complementary to at least some of the plurality of nucleotide bases exposed at the gap.   
     
     
         25 . The kit as defined in  claim 23 , wherein the bases in the switch strand are completely complementary to the plurality of nucleotide bases exposed at the gap. 
     
     
         26 . The kit as defined in  claim 23 , wherein the switch strand further includes at least one nucleotide having a mismatched base that is non-complementary to a corresponding one of the plurality of nucleotide bases exposed at the gap. 
     
     
         27 . The kit as defined in  claim 23 , wherein the strand of nucleotides in the switch strand has at least one nucleotide fewer than the plurality of nucleotide bases exposed at the gap. 
     
     
         28 . The kit as defined in  claim 23 , wherein the strand of nucleotides in the switch strand has a higher number of nucleotides than the plurality of nucleotide bases exposed at the gap, and wherein a portion of the switch strand forms a stem loop when associated at the gap. 
     
     
         29 . The kit as defined in  claim 23 , wherein:
 the strand of nucleotides in the switch strand has a higher number of nucleotides than the plurality of nucleotide bases exposed at the gap;   a portion of the switch strand forms a stem loop when associated at the gap; and   an other portion of the switch strand is completely complementary to the plurality of nucleotide bases exposed at the gap or includes at least one nucleotide having a mismatched base that is non-complementary to a corresponding one of the plurality of nucleotide bases exposed at the gap.