Methods and systems for detecting and/or sorting targets

Abstract

Provided herein are methods and systems for detecting and/or sorting targets in a sample based on the combined use of polynucleotide-encoded-protein and substrate polynucleotides. The polynucleotide-encoded protein is comprised of a protein that specifically binds to a predetermined target and of an encoding polynucleotide that specifically binds to a substrate polynucleotide, wherein the substrate polynucleotide is attached to a substrate.

1 . A method to detect a target in a sample, the method comprising
 combining a substrate polynucleotide attached to a substrate with a polynucleotide-encoded protein, the polynucleotide-encoded protein comprising a protein and an encoding polynucleotide attached to the protein, wherein the protein specifically binds to the target and the encoding polynucleotide specifically binds to the substrate polynucleotide; and   detecting a polynucleotide-encoded protein-target complex bound to the substrate polynucleotide attached to the substrate.   
     
     
         2 . The method of  claim 1 , wherein combining a substrate polynucleotide attached to a substrate with a polynucleotide-encoded protein is performed by
 providing a substrate polynucleotide attached to a substrate;   providing a polynucleotide-encoded protein comprising a protein and an encoding polynucleotide attached to the protein, wherein the protein specifically binds to the target and the encoding-polynucleotide specifically binds to the substrate polynucleotide; and   contacting the polynucleotide-encoded protein with the sample and with the substrate for a time and under conditions to allow binding of the polynucleotide-encoded protein with the target in a polynucleotide-encoded protein-target complex; and binding of the encoding polynucleotide with the substrate polynucleotide.   
     
     
         3 . The method of  claim 2 , wherein contacting the polynucleotide-encoded protein with the sample and with the substrate is performed by
 contacting the polynucleotide-encoded protein with the sample for a time and under conditions to allow binding of the polynucleotide-encoded protein with the target in a polynucleotide-encoded-protein-target complex; and   contacting the polynucleotide-encoded protein-target complex with the substrate for a time and under conditions to allow binding the encoding-polynucleotide with the substrate polynucleotide.   
     
     
         4 . The method of  claim 2 , wherein contacting the polynucleotide-encoded protein with the sample and with the substrate is performed by
 contacting the polynucleotide-encoded protein with the substrate for a time and under conditions to allow binding the encoding polynucleotide with the substrate polynucleotide; and   contacting the polynucleotide-encoded protein with the sample for a time and under conditions to allow binding of the polynucleotide-encoded protein in a polynucleotide-encoded protein-target complex.   
     
     
         5 . The method of  claim 1 , wherein detecting the polynucleotide-encoded protein-target complex on the substrate is performed by
 providing a labeled molecule comprising a molecule that specifically binds to the target and a label compound attached to the molecule, the label compound providing a labeling signal;   contacting the labeled molecule with the polynucleotide-encoded protein-target complex for a time and under condition to allow binding of the labeled molecule with the polynucleotide-encoded protein-target complex; and   detecting the labeling signal from the labeled molecule bound to the polynucleotide-encoded protein-target complex on the substrate.   
     
     
         6 . The method of  claim 5 , wherein the label compound is a metal nanoparticle. 
     
     
         7 . The method of  claim 1 , wherein the polynucleotide-encoded-protein is an antibody. 
     
     
         8 . The method of  claim 1 , wherein the target is a plurality of targets, and wherein combining a substrate polynucleotide attached to a substrate with a polynucleotide-encoded protein is performed by
 providing a plurality of substrate polynucleotides attached to a substrate, each substrate polynucleotide being sequence specific and positionally distinguishable from another;   providing a plurality of polynucleotide-encoded proteins, each polynucleotide-encoded protein comprising a protein and an encoding-polynucleotide attached to the protein, wherein the protein specifically binds to a target of the plurality of targets and the encoding-polynucleotide specifically binds to a sequence specific and positionally distinguishable substrate polynucleotide of the plurality of substrate polynucleotides, each protein and encoding polynucleotide being bindingly distinguishable from another; and   contacting the plurality of polynucleotide-encoded proteins with the sample and the plurality of substrate polynucleotides for a time and under conditions to allow binding of the proteins with the target molecules in a plurality of polynucleotide-encoded protein-target complexes and binding of the encoding polynucleotides to the substrate polynucleotides.   
     
     
         9 . The method of  claim 8 , wherein detecting the plurality of polynucleotide-encoded protein-target complexes on the substrate is performed by
 providing a plurality of labeled molecules, each labeled molecule comprising a molecule that specifically binds one target of the plurality of targets and a label compound providing a labeling signal, the label compound attached to a labeled molecule, each labeled molecule detectably distinguishable from another;   contacting the plurality of labeled molecules with the plurality of polynucleotide-encoded protein-target complexes for a time and under condition to allow binding of the plurality of polynucleotide encoded-target complexes with the plurality of labeled molecules; and   detecting the labeling signal from the plurality of labeled molecules bound to the plurality of polynucleotide encoded-target complexes on the substrate.   
     
     
         10 . The method of  claim 9 , wherein the label compound is a metal nanoparticle. 
     
     
         11 . The method of  claim 8 , wherein the protein component of the polynucleotide —encoded protein is an antibody. 
     
     
         12 . The method of  claim 1 , wherein the target is a plurality of targets, the targets comprising at least one target polynucleotide, and wherein combining a substrate polynucleotide attached to a substrate with a polynucleotide-encoded protein is performed by
 providing a plurality of substrate polynucleotides attached to a substrate, each substrate polynucleotide being sequence-specific and positionally distinguishable from another;   providing at least one labeled polynucleotide that specifically binds to the at least one target polynucleotide, each labeled polynucleotide being bindingly distinguishable from another;   contacting the at least one labeled polynucleotide with the sample for a time and under conditions to allow binding of the labeled polynucleotide with the target polynucleotide to provide at least one labeled target polynucleotide, wherein the at least one labeled target polynucleotide is comprised of a sequence that specifically binds to a sequence-specific and positionally distinguishable substrate polynucleotide;   providing at least one polynucleotide-encoded protein comprising a protein and an encoding polynucleotide attached to the protein, wherein the protein specifically binds to a target of the plurality of the targets and the encoding polynucleotide specifically binds to a sequence-specific and positionally distinguishable substrate polynucleotide, each protein and encoding polynucleotide being bindingly distinguishable from another, each protein being bindingly distinguishable from each labeled polynucleotide, each polynucleotide-encoded protein being bindingly distinguishable from each labeled target polynucleotide;   contacting the at least one polynucleotide-encoded protein with the sample for a time and under conditions to allow binding of the protein with the target, in at least one polynucleotide-encoded protein-target complex; and   contacting the at least one labeled target polynucleotide with the at least one polynucleotide-encoded protein-target complex with the plurality of substrate polynucleotides for a time and under conditions to allow binding of the at least one labeled target polynucleotide with a corresponding substrate polynucleotide and binding of the at least one encoding polynucleotide with a corresponding substrate polynucleotide;   the method further comprising   detecting the labeled target polynucleotides bound to the plurality of spatially located substrate polynucleotides on the substrate.   
     
     
         13 . The method of  claim 12 , wherein detecting the polynucleotide-encoded protein-target complexes on the substrate is performed by
 providing a plurality of labeled proteins, each labeled molecule comprising a molecule component that specifically binds one target of the plurality of targets and a label compound providing a labeling signal; the label compound attached to a labeled molecule.   contacting the plurality of labeled molecules with the plurality of polynucleotide-encoded protein-target complexes for a time and under condition to allow binding of the plurality of polynucleotide encoded-target complexes with the plurality of labeled molecules; and   detecting the labeling signal from the plurality of labeled proteins bound to the plurality of polynucleotide encoded-target complexes on the substrate.   
     
     
         14 . The method of  claim 13 , wherein the label compound is a metal nanoparticle attached to the protein. 
     
     
         15 . The method of  claim 12 , wherein the protein component of the polynucleotide —encoded protein is an antibody. 
     
     
         16 . A system for the detection of a target molecule in a sample, the system comprising
 a substrate with a substrate polynucleotide attached to the substrate; and   a polynucleotide-encoded protein comprising a protein and an encoding polynucleotide attached to the protein, wherein the protein specifically binds a target and the encoding-polynucleotide specifically binds to the substrate polynucleotide.   
     
     
         17 . The system of  claim 16 , the system further comprising
 a labeled molecule comprising a molecule that specifically binds to the target and a label compound attached to the protein, the label compound providing a labeling signal.   
     
     
         18 . The system of  claim 16 , wherein the target is a plurality of targets, the system comprising,
 a substrate with a plurality of substrate polynucleotides attached to the substrate, each polynucleotide of the plurality of substrate polynucleotides attached to the substrate being sequence specific and positionally distinguishable from another; and   a plurality of polynucleotide-encoded proteins, each polynucleotide-encoded protein comprising a protein and an encoding polynucleotide attached to the protein, wherein the protein specifically binds to a predetermined target of the plurality of targets and the encoding polynucleotide specifically binds to a sequence-specific and positionally distinguishable polynucleotide of the plurality of polynucleotides attached to the substrate, each protein and encoding polynucleotide being bindingly distinguishable from another.   
     
     
         19 . The system of  claim 18 , the system further comprising
 a plurality of labeled molecules, each labeled molecule comprising a molecule that specifically binds one target of the plurality of targets and a label compound attached to the protein component, the label compound providing a labeling signal, each labeled molecule being detectably distinguishable from another.   
     
     
         20 . The system of  claim 16 , wherein the target is a plurality of targets, the plurality of targets comprising at least one target polynucleotide, the system comprising
 a substrate with a plurality of substrate polynucleotides attached to the substrate, each substrate polynucleotide being sequence-specific and positionally distinguishable from another;   at least one labeled polynucleotide that specifically binds to the at least one target polynucleotide, each labeled polynucleotide bindingly distinguishable from another, each labeled polynucleotide being for the production of a labeled target polynucleotide that specifically binds to a sequence-specific and positionally distinguishable substrate polynucleotide of the plurality of spatially located substrate polynucleotides;   at least one polynucleotide-encoded protein comprising a protein and an encoding polynucleotide attached to the protein, wherein the protein specifically binds to a target of the plurality of targets and the encoding polynucleotide-specifically binds to a sequence-specific and positionally distinguishable substrate polynucleotide, each protein and encoding polynucleotide being bindingly distinguishable from another,   each protein being bindingly distinguishable from each labeled polynucleotide,   each polynucleotide-encoded protein being bindingly distinguishable from each labeled target polynucleotide.   
     
     
         21 . The system of  claim 20 , the system further comprising
 at least one labeled molecule comprising a molecule that specifically binds to the at least one target and a label compound attached to the molecule, the label compound providing a labeling signal.   
     
     
         22 . A method for sorting targets of a plurality of targets, the method comprising
 providing a plurality of substrate polynucleotides attached to a substrate, each substrate polynucleotide being sequence-specific and positionally distinguishable from another;   providing a plurality of polynucleotide-encoded proteins, each polynucleotide-encoded protein comprising a protein and an encoding polynucleotide attached to the protein, wherein the protein specifically binds to a predetermined target of the plurality of targets and the encoding polynucleotide specifically binds to a sequence-specific and positionally distinguishable substrate polynucleotide of the plurality of substrate polynucleotides, each protein and encoding polynucleotide being bindingly distinguishable from another;   contacting the plurality of polynucleotide-encoded antibodies with the sample for a time and under conditions to allow binding of the antibodies with the targets, thus providing a plurality of polynucleotide-encoded protein-target complexes; and   contacting the plurality of polynucleotide-encoded protein-target complexes with the plurality of substrate polynucleotides for a time and under conditions to allow binding of the encoding-polynucleotides to the substrate polynucleotides attached to the substrate,   thus sorting the plurality of targets in a plurality of polynucleotide-encoded protein-target-complexes bound to the substrate.   
     
     
         23 . The method of  claim 22 , wherein the targets are cells. 
     
     
         24 . A system for sorting a plurality of targets, the system comprising,
 a substrate with a plurality of substrate polynucleotides attached to the substrate, each polynucleotide of the plurality of substrate polynucleotides attached to the substrate being sequence-specific and positionally distinguishable from another; and   a plurality of polynucleotide-encoded proteins, each polynucleotide-encoded protein comprising a protein and a encoding-polynucleotide attached to the protein, wherein the protein specifically binds to a predetermined target of the plurality of targets and the encoding-polynucleotide specifically binds to a sequence-specific and positionally distinguishable polynucleotide of the plurality of polynucleotides attached to the substrate, each protein being bindingly distinguishable from the other, each encoding polynucleotide being bindingly distinguishable from the other.   
     
     
         25 . A microfluidic array for the detection of one or more targets in a sample fluid, comprising
 a microfluidic component having a microfluidic feature for carrying the sample fluid, and   a substrate component with a plurality of substrate polynucleotides attached to said substrate component, the substrate polynucleotides being sequence-specific and positionally distinguishable, the substrate component in operable association with the microfluidic feature of the microfluidic component for the analysis of the sample fluid;   wherein each of the substrate polynucleotides is comprised of a sequence that is orthogonal to the sequence of another substrate polynucleotide.   
     
     
         26 . A method to detect one or more targets in a sample fluid, comprising performing the method of  claim 1  with the microfluidic array of  claim 25 . 
     
     
         27 . A method to detect one or more targets in a sample fluid, comprising performing the method of  claim 8  with the microfluidic array of  claim 25 . 
     
     
         28 . A method to detect one or more targets in a sample fluid, comprising performing the method of  claim 12  with the microfluidic array of  claim 25 .