Super resolution imaging

Abstract

A detection apparatus that includes (a) an array of responsive pads on a substrate surface; (b) an array of pixels, wherein each pixel in the array has a detection zone on the surface that includes a subset of at least two of the pads; and (c) an activation circuit to apply a force at a first and second pad in the subset, wherein the activation circuit is configured to apply a different force at the first pad compared to the second pad, and wherein the activation circuit has a switch to selectively alter the force at the first pad and the second pad.

What is claimed is: 
     
         1 . A detection apparatus, comprising
 (a) an array of responsive pads on a substrate surface,
 wherein each responsive pad comprises a nucleic acid feature of a plurality of nucleic acid features in the array, 
 wherein a first subset of nucleic acid features in the plurality of nucleic acid features have a first universal sequence and different target sequences, 
 wherein a second subset of nucleic acid features in the plurality of nucleic acid features have a second universal sequence and different target sequences, 
 wherein the first universal sequence is different from the second universal sequence; 
   (b) an array of pixels, wherein each pixel in the array has a detection zone on the surface that comprises at least two nucleic acid features of the plurality of nucleic acid features, the at least two nucleic acid features comprising a nucleic acid from the first subset of nucleic acid features and a nucleic acid from the second subset of nucleic acid features; and   (c) an activation module to alter a characteristic of a pad in the first subset and of a pad in the second subset, wherein the activation module is configured to apply a different characteristic at the pad in the first subset compared to the pad in the second subset, and wherein the activation module has a switch to selectively alter the characteristic at the pads in the first and second subsets.   
     
     
         2 . The apparatus of  claim 1 , wherein the plurality of the nucleic acid features comprises features that are separated by less than 15 μm. 
     
     
         3 . The apparatus of  claim 1 , wherein the first subset of nucleic acid features comprises at least 1000 features and the second subset of nucleic acid features comprises at least 1000 features. 
     
     
         4 . A nucleic acid sequencing system, comprising
 (I) the apparatus of  claim 1     (II) a readout circuit to acquire signals from the array of pixels;   (III) a control module that directs the readout circuit to acquire signals from each of the pixels during a sensing period and that directs the activation circuit to sequentially actuate different responsive pads in each of the detection zones during the sensing period; and   (IV) a processing module that correlates (i) the signals acquired from the pixels during the sensing period and (ii) the sequential actuation of the different responsive pads during the sensing period, in order to distinguish a sequence of signals for each of the pads.   
     
     
         5 . A method of detecting target nucleic acids, comprising
 (a) providing a substrate comprising an array of pads, the array of pads comprising a first subset of the pads and a second subset of the pads;   (b) delivering a first solution to the substrate, wherein the first solution comprises a first plurality of different target nucleic acids that selectively attach to the first subset of pads compared to the second subset of pads;   (c) delivering a second solution to the substrate, wherein the second solution comprises a second plurality of different target nucleic acids that selectively attach to the second subset of pads compared to the first subset of pads; and   (d) detecting the substrate using an apparatus comprising an array of pixels, wherein each pixel in the array has a detection zone that comprises   (i) at least one of the target nucleic acids that is attached to a pad of the first subset of pads, and   (ii) at least one of the target nucleic acids that is attached to a pad of the second subset of pads.   
     
     
         6 . The method of  claim 5 , wherein the first solution and second solution are combined, whereby the first plurality of target nucleic acids is contacted with the substrate simultaneously with the second plurality of target nucleic acids. 
     
     
         7 . The method of  claim 5 , wherein the first solution and second solution are delivered to the substrate sequentially. 
     
     
         8 . The method of  claim 7 , further comprising washing the substrate to remove the first solution between steps (b) and (c). 
     
     
         9 . The method of  claim 5 , wherein the target nucleic acids in the first plurality comprise a first universal sequence and different target sequences. 
     
     
         10 . The method of  claim 9 , wherein the target nucleic acids in the second plurality comprise a second universal sequence and different target sequences. 
     
     
         11 . The method of  claim 10 , wherein the selective attachment of the first target nucleic acids to the first subset of pads comprises the first universal sequences hybridizing to first capture probes attached to the first subset of pads. 
     
     
         12 . The method of  claim 11 , wherein the selective attachment of the second target nucleic acids to the second subset of pads comprises the second universal sequences hybridizing to second capture probes attached to the second subset of pads, wherein the first capture probes have a different sequence from the second capture probe. 
     
     
         13 . The method of  claim 12 , wherein the detecting comprises sequentially:
 hybridizing first primers to the first universal sequence of the target nucleic acids that are attached to the first subset of pads;   extending the first primers by addition of at least one nucleotide;   hybridizing second primers to the second universal sequence of the target nucleic acids that are attached to the second subset of pads; and   extending the second primers by addition of at least one nucleotide,   whereby signals are detected from the target nucleic acids that are attached to the first subset of responsive pads at a different time than when signals are detected from the target nucleic acids that are attached to the second subset of responsive pads.   
     
     
         14 . The method of  claim 10 , further comprising amplifying target nucleic acids that are attached to pads of the first subset of pads using primers that are complementary to the first universal sequence, and amplifying target nucleic acids that are attached to pads of the second subset of pads using primers that are complementary to the second universal sequence. 
     
     
         15 . The method of  claim 5 , wherein step (b) comprises contacting the first solution with the substrate while selectively actuating the first subset of responsive pads in the array, wherein the first plurality of different target nucleic acids attach to responsive pads of the first subset that are selectively actuated. 
     
     
         16 . The method of  claim 15 , wherein step (c) comprises contacting the second solution with the substrate while selectively actuating the second subset of responsive pads in the array, wherein the second plurality of different target nucleic acids attach to responsive pads of the second subset that are selectively actuated. 
     
     
         17 . The method of  claim 16 , wherein the target nucleic acids comprise a universal sequence that is the same for nucleic acids of the first and second plurality. 
     
     
         18 . The method of  claim 16 , wherein the universal sequence of the target nucleic acids hybridize to capture probes attached to the first and second subset of pads. 
     
     
         19 . The method of  claim 5 , further comprising contacting a solution of first amplification primers with the substrate while selectively actuating the first subset of responsive pads in the array, wherein the first amplification primers selectively hybridize to the first plurality of different target nucleic acids compared to the second plurality of different target nucleic acids. 
     
     
         20 . The method of  claim 19 , further comprising contacting a solution of second amplification primers with the substrate while selectively actuating the second subset of responsive pads in the array, wherein the second amplification primers selectively hybridize to the second plurality of different target nucleic acids compared to the first plurality of different target nucleic acids. 
     
     
         21 . The method of  claim 20 , wherein the first amplification primers have the same sequence as the second amplification primers. 
     
     
         22 . The method of  claim 20 , wherein the first amplification primers have a different sequence compared to the second amplification primers. 
     
     
         23 . The method of  claim 5 , further comprising amplifying target nucleic acids that are attached to pads of the first subset of pads, thereby forming target nucleic acid clusters on the pads. 
     
     
         24 . The method of  claim 5 , wherein the selective attachment of the first target nucleic acids to the first subset of pads comprises hybridizing the first target nucleic acids to capture probes that are attached to the first subset of pads. 
     
     
         25 . The method of  claim 24 , wherein the selective attachment of the second target nucleic acids to the second subset of pads comprises hybridizing the second target nucleic acids to capture probes that are attached to the second subset of pads. 
     
     
         26 . The method of  claim 25 , wherein the capture probes attached to the first subset of pads have a different sequence from the capture probes at the second subset of pads, thereby providing the selective attachment. 
     
     
         27 . The method of  claim 25 , wherein the selective attachment comprises differential activation of the first and second subset of pads. 
     
     
         28 . The method of  claim 27 , wherein the capture probes attached to the first subset of pads and the capture probes attached to the second subset of pads have the same nucleic acid sequence. 
     
     
         29 . The method of  claim 25 , wherein the selective attachment comprises selectively hybridizing a first adapter nucleic acid to the capture probes that are attached to the first subset of pads and selectively hybridizing a second adapter nucleic acid to the capture probes that are attached to the second subset of pads, wherein the first adapter nucleic acid has a sequence that is complementary to a sequence of the first target nucleic acids and the second adapter nucleic acid has a sequence that is complementary to a sequence of the second target nucleic acids.