Provided herein in various embodiments, is a method for detecting and/or quantifying an analyte molecule present in a sample without employing a sequencing operation. As discussed, detection supramolecular structures are used to perform the detection and/or quantification of the analyte of interest. In one embodiment the detection supramolecular structures include a supramolecular structure (e.g., a nucleic acid origami structure) that comprises a core structure composed of one or more core molecules, a single affinity binder linked to the supramolecular structure at a first location, and one or more unique identifiers also attached to the supramolecular structure and which convey information about the affinity binder present on a respective detection supramolecular structure.
Compositions and methods are provided for forming single-analyte arrays with enhanced characteristics for inhibiting orthogonal binding of molecules to the array. Arrays are modified to contain covalently incorporated passivating moieties at array addresses where orthogonal binding may occur. The compositions and methods may facilitate detection of an increased quantity of array features at single-analyte resolution.
Fluidic vessels having flow-altering properties are provided. The fluidic vessels may alter fluid flow velocity profiles downstream of ports or inlets to produce a more substantially uniform flow velocity profile. Fluidic vessels provided herein may be useful for delivering and/or discharging fluidic media containing pluralities of macromolecules during fluid transfer processes.
Fluidic vessels having flow-altering properties are provided. The fluidic vessels may alter fluid flow velocity profiles downstream of ports or inlets to produce a more substantially uniform flow velocity profile. Fluidic vessels provided herein may be useful for delivering and/or discharging fluidic media containing pluralities of macromolecules during fluid transfer processes.
Methods of formation and detection of arrays of single analytes on enhanced substrates are described. A solid support 2700 comprising a site containing a curved depression. A particle 2731 is disposed near the centerpoint. An analyte 2750 is attached to the particle 2731 by an anchoring moiety 2740. A detectable probe comprising an affinity reagent 2760 and a detectable label 2765 is attached to the analyte 2750. The detectable label 2765 transmits photons, some of which are directed toward a detection device 2770 or a component thereof (e.g., an optical lens, a sensor, etc.), and others of which reflect off the curved surface of the site and are directed toward the detection device 2770. Most photons emitted in a direction between the dashed lines denoting angle ex may be emitted directly toward the detection device 2770, while photons emitted in a direction between the two dashed lines denoted by angle β may be reflected toward the detection device 2770 after reflecting off the curved surface.
Methods of formation and detection of arrays of single analytes on enhanced substrates are described. The arrays may comprise pluralities of single analytes containing heterogeneity with respect to one or more properties. Enhanced substrates may be utilized to amplify the relative detection of optical signals form single analytes or moieties attached to single analytes with respect to sources of background, baseline, or erroneous optical signals.
Systems and methods for obtaining qualitative or quantitative measurements of proteoforms of polypeptides are described. The described methods include measurements of affinity reagent binding on single-molecule polypeptide arrays to distinguish between polypeptide isoforms. The described methods may provide high resolution quantitative comparisons of proteoforms with very low copy numbers.
Methods and systems for analysis of large numbers of analytes using large numbers of reagents and processes using multiplexed, independent systems and subsystems for efficient processing and increased throughput of biological analyses.
Provided are methods of detecting analytes. In some configurations, the methods can employ analytes attached to a solid support or particle and affinity reagents that are attached to the solid support or particle via a flexible linker. In some configurations, the methods can employ analytes attached to a solid support or particle and solution-phase affinity reagents can be attracted to the analytes via application of a stimulus.
C12Q 1/6818 - Hybridisation assays characterised by the detection means involving interaction of two or more labels, e.g. resonant energy transfer
G01N 33/542 - ImmunoassayBiospecific binding assayMaterials therefor with immune complex formed in liquid phase with steric inhibition or signal modification, e.g. fluorescent quenching
10.
COMPOSITIONS AND METHODS FOR DETECTING BINDING INTERACTIONS UNDER EQUILIBRIUM OR NON-EQUILIBRIUM CONDITIONS
Provided are methods of detecting analytes. In some configurations, the methods can employ analytes attached to a solid support or particle and affinity reagents that are attached to the solid support or particle via a flexible linker. In some configurations, the methods can employ analytes attached to a solid support or particle and solution-phase affinity reagents can be attracted to the analytes via application of a stimulus.
Methods and systems are provided for accurate and efficient identification and quantification of proteins. In an aspect, disclosed herein is a method for identifying a protein in a sample of unknown proteins, comprising receiving information of a plurality of empirical measurements performed on the unknown proteins; comparing the information of empirical measurements against a database comprising a plurality of protein sequences, each protein sequence corresponding to a candidate protein among a plurality of candidate proteins; and for each of one or more of the plurality of candidate proteins, generating a probability that the candidate protein generates the information of empirical measurements, a probability that the plurality of empirical measurements is not observed given that the candidate protein is present in the sample, or a probability that the candidate protein is present in the sample; based on the comparison of the information of empirical measurements against the database.
G01N 27/26 - Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variablesInvestigating or analysing materials by the use of electric, electrochemical, or magnetic means by using electrolysis or electrophoresis
G01N 27/60 - Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrostatic variables
G01N 27/72 - Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating magnetic variables
12.
COMPOSITIONS AND METHODS FOR IMPROVING AFFINITY REAGENT AVIDITY
The present disclosure provides a method of processing an analyte, including steps of (a) providing an analyte including an epitope and a docker; (b) providing an affinity reagent, wherein the affinity reagent includes a paratope that recognizes the epitope and a tether that recognizes the docker; and (c) contacting the analyte with the affinity reagent, whereby the affinity reagent associates with the analyte via binding of the paratope to the epitope and via binding of the tether to the docker. Optionally, the method further includes the step of (d) detecting association of the affinity reagent with the analyte, thereby identifying the analyte.
The present disclosure provides a method of processing an analyte, including steps of (a) providing an analyte including an epitope and a docker; (b) providing an affinity reagent, wherein the affinity reagent includes a paratope that recognizes the epitope and a tether that recognizes the docker; and (c) contacting the analyte with the affinity reagent, whereby the affinity reagent associates with the analyte via binding of the paratope to the epitope and via binding of the tether to the docker. Optionally, the method further includes the step of (d) detecting association of the affinity reagent with the analyte, thereby identifying the analyte.
C40B 30/04 - Methods of screening libraries by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
14.
MAKING AND USING STRUCTURED NUCLEIC ACID PARTICLES
The present disclosure provides a structured nucleic acid particle comprising a scaffold strand and a plurality of staple strands hybridized to the scaffold, forming a structured nucleic acid particle having a first planar structure coupled to a first protruding structure extending from a face of the first planar structure. Also, the present disclosure provides a structured nucleic acid particle comprising a scaffold strand and a plurality of staple strands hybridized to the scaffold, forming a structured nucleic acid particle having a plurality of planar faces. In some instances, the structured nucleic acid particle has six planar faces.
The present disclosure provides a structured nucleic acid particle comprising a scaffold strand and a plurality of staple strands hybridized to the scaffold, forming a structured nucleic acid particle having a first planar structure coupled to a first protruding structure extending from a face of the first planar structure. Also, the present disclosure provides a structured nucleic acid particle comprising a scaffold strand and a plurality of staple strands hybridized to the scaffold, forming a structured nucleic acid particle having a plurality of planar faces. In some instances, the structured nucleic acid particle has six planar faces.
Systems and methods for obtaining qualitative or quantitative measurements of proteoforms of polypeptides are described. The described methods include measurements of affinity reagent binding on single-molecule polypeptide arrays to distinguish between polypeptide isoforms. The described methods may provide high resolution quantitative comparisons of proteoforms with very low copy numbers.
Methods and systems are provided for determining a parameter of a detector model for a detection device that translates between two spatial dimensions (image coordinates) and three spatial dimensions (real coordinates). Methods for determining a parameter of a detector model utilize detected patterns of detection events to provide a basis for parametrization.
Methods and systems are provided for determining a parameter of a detector model for a detection device that translates between two spatial dimensions (image coordinates) and three spatial dimensions (real coordinates). Methods for determining a parameter of a detector model utilize detected patterns of detection events to provide a basis for parametrization.
Compositions, systems, and methods for the display of analytes such as biomolecules are described. Display of analytes is achieved by coupling of the analytes to displaying molecules that are configured to associate with surfaces or interfaces. Arrays of analytes may be formed from the described systems for utilization in assays and other methods.
Compositions, systems, and methods are disclosed for preparing and utilizing arrays, such as single-analyte arrays containing a plurality of fiducial elements with random spatial distributions. Arrays may be prepared with pluralities of fiducial elements comprising optically active or passive moieties. Arrays containing random spatial distributions of fiducial elements may be utilized for various array-based processes that require spatial information.
Provided herein is a protein including an epitope display motif, the motif having a sequence of amino acids that forms the following sequence of secondary structures: alpha1-X1-beta1-X2-beta2-X3-alpha2-X4-beta3-X5-beta4, wherein “alpha” is a sequence of amino acids that forms, or is capable of forming, an alpha helix, wherein “beta” is a sequence of amino acids that forms, or is capable of forming, a beta strand, and wherein X1, X2, X3, X4 and X5 each, independently, include a sequence of amino acids that forms an unstructured loop. Optionally, the unstructured loops can each, independently, include 2 to 10 amino acids.
11122324354123455 each, independently, include a sequence of amino acids that forms an unstructured loop. Optionally, the unstructured loops can each, independently, include 2 to 10 amino acids.
C07K 14/00 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof
C07K 16/00 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies
C12N 15/00 - Mutation or genetic engineeringDNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purificationUse of hosts therefor
Methods and systems are provided herein for selecting an affinity reagent which binds a desired peptide epitope in a plurality of sequence contexts. The method relies on obtaining a peptide library, each peptide having the sequence αXβ, wherein X is the desired peptide epitope, wherein each of α and β comprise an amino acid, using the peptide library to select an affinity reagent.
C40B 30/04 - Methods of screening libraries by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
Methods and systems are provided for forming arrays of analytes, in which the arrays are characterized by a high site occupancy and optionally a low site co-occupancy, and in which the arrays are configured for single-analyte processes. Methods for effecting transport of binding entities to array sites are also provided.
Methods and systems are provided for forming arrays of analytes, in which the arrays are characterized by a high site occupancy and optionally a low site co-occupancy, and in which the arrays are configured for single-analyte processes. Methods for effecting transport of binding entities to array sites are also provided.
Compositions and methods for detecting, characterizing and identifying proteoforms including, for example, determining presence or absence of a particular post-translational modification or a post-translational modification of a particular amino acid in a proteoform, and determining the location(s) of one or more post-translational modifications in the amino acid sequence of a proteoform.
Compositions and methods for detecting, characterizing and identifying proteoforms including, for example, determining presence or absence of a particular post-translational modification or a post-translational modification of a particular amino acid in a proteoform, and determining the location(s) of one or more post-translational modifications in the amino acid sequence of a proteoform.
An affinity reagent, including (a) an artificial polymer comprising a branched chain; (b) an affinity moiety attached to the artificial polymer; and (c) a label attached to the artificial polymer. Also provided are methods for making and using the affinity reagent.
An affinity reagent, including (a) an artificial polymer comprising a branched chain; (b) an affinity moiety attached to the artificial polymer; and (c) a label attached to the artificial polymer. Also provided are methods for making and using the affinity reagent.
The present disclosure provides systems and methods for detecting components of an array of biological, chemical, or physical entities. In an aspect, the present disclosure provides a method for detecting an array of biological, chemical, or physical entities, comprising: (a) using one or more light sensing devices, acquiring pixel information from sites in an array, wherein the sites comprise biological, chemical, or physical entities that produce light; (b) processing the pixel information to identify a set of regions of interest (ROIs) corresponding to the sites in the array that produce the light; (c) classifying the pixel information for the ROIs into a categorical classification from among a plurality of distinct categorical classifications, thereby producing a plurality of pixel classifications; and (d) identifying one or more components of the array of biological, chemical, or physical entities based at least in part on the plurality of pixel classifications.
A method, including (a) providing an array of extant glycans or glycoconjugates, wherein the array comprises a plurality of addresses, wherein different extant glycans or glycoconjugates are attached to different addresses of the array; (b) contacting the array with a plurality of different probes, the different probes recognizing different carbohydrate moieties; (c) detecting positive recognition outcomes of the plurality of different probes at individual addresses of the array, thereby producing outcome profiles for the addresses; (d) providing a database comprising a set of candidate glycans or glycoconjugates, the database comprising, for each candidate glycan or glycoconjugate, the probability of a positive recognition outcome for the plurality of different probes; and (e) determining with a computer, using the database and the outcome profiles, candidate glycans or glycoconjugates in the database corresponding to different extant glycans or glycoconjugates in the array.
A method, including (a) providing an array of extant glycans or glycoconjugates, wherein the array comprises a plurality of addresses, wherein different extant glycans or glycoconjugates are attached to different addresses of the array; (b) contacting the array with a plurality of different probes, the different probes recognizing different carbohydrate moieties; (c) detecting positive recognition outcomes of the plurality of different probes at individual addresses of the array, thereby producing outcome profiles for the addresses; (d) providing a database comprising a set of candidate glycans or glycoconjugates, the database comprising, for each candidate glycan or glycoconjugate, the probability of a positive recognition outcome for the plurality of different probes; and (e) determining with a computer, using the database and the outcome profiles, candidate glycans or glycoconjugates in the database corresponding to different extant glycans or glycoconjugates in the array.
Compositions, systems, and methods for the display of analytes such as biomolecules are described. Display of analytes is achieved by coupling of the analytes to displaying molecules that are configured to associate with surfaces or interfaces. Arrays of analytes may be formed from the described systems for utilization in assays and other methods.
Methods of providing photodamage inhibitors to single-analyte arrays are described. Photodamage inhibitors may be incorporated into various reagents that are subsequently coupled to single-analyte arrays. Photodamage inhibitors may be replenished during a single-analyte assay through provision of more reagents containing photodamage inhibitors. Useful reagent compositions containing photodamage inhibitors are described.
Methods of providing photodamage inhibitors to single-analyte arrays are described. Photodamage inhibitors may be incorporated into various reagents that are subsequently coupled to single-analyte arrays. Photodamage inhibitors may be replenished during a single-analyte assay through provision of more reagents containing photodamage inhibitors. Useful reagent compositions containing photodamage inhibitors are described.
Methods of minimizing detection of unintended signals during array-based processes are provided. Methods include the use of sets of fluidic media that inhibit sources of unintended signals during array-based processes. Also provided are systems containing the sets of fluidic media that are configured to perform the array-based processes provided herein.
Methods of minimizing detection of unintended signals during array-based processes are provided. Methods include the use of sets of fluidic media that inhibit sources of unintended signals during array-based processes. Also provided are systems containing the sets of fluidic media that are configured to perform the array-based processes provided herein.
G01N 33/543 - ImmunoassayBiospecific binding assayMaterials therefor with an insoluble carrier for immobilising immunochemicals
C12Q 1/00 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions
A set of polypeptides including a plurality of different polypeptides, each of the different polypeptides including a non-naturally occurring amino acid sequence, wherein a set of different epitopes occurs in the set of polypeptides, each of the different epitopes occurring in the non-naturally occurring amino acid sequence of a subset of the different polypeptides, and the non-naturally occurring amino acid sequence of each of the different polypeptides including a plurality of different epitopes of the set of epitopes.
A set of polypeptides including a plurality of different polypeptides, each of the different polypeptides including a non-naturally occurring amino acid sequence, wherein a set of different epitopes occurs in the set of polypeptides, each of the different epitopes occurring in the non-naturally occurring amino acid sequence of a subset of the different polypeptides, and the non-naturally occurring amino acid sequence of each of the different polypeptides including a plurality of different epitopes of the set of epitopes.
G01N 33/96 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving blood or serum control standard
C07K 14/00 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof
Methods and systems are provided herein for selecting an affinity reagent which binds a desired peptide epitope in a plurality of sequence contexts. The method relies on obtaining a peptide library, each peptide having the sequence αXβ, wherein X is the desired peptide epitope, wherein each of α and β comprise an amino acid, using the peptide library to select an affinity reagent.
Compositions, systems, and methods for the display of analytes such as biomolecules are described. Display of analytes is achieved by coupling of the analytes to displaying molecules that are configured to associate with surfaces or interfaces. Arrays of analytes may be formed from the described systems for utilization in assays and other methods.
The present disclosure provides a method of identifying a polypeptide. The method can include steps of (a) attaching a polypeptide to a particle or solid support, thereby producing an immobilized polypeptide having a plurality of amino acids linked to the particle or solid support; (b) fragmenting the immobilized polypeptide, whereby the particle is attached to a set of fragments of the polypeptide; (c) performing a binding assay including contacting the set of fragments with a plurality of affinity reagents and detecting binding of affinity reagents of the plurality of affinity reagents to the set of fragments; and (d) identifying the polypeptide from results of the binding assay.
Provided herein are structures and methods for detecting one or more analyte molecules present in a sample. In some embodiments, the one or more analyte molecules are detected using one or more supramolecular structures. In some embodiments, the supramolecular structures are configured to form a linkage with a particular capture barcode, which is configured to form a linkage with a particular capture molecule. In some embodiments the capture molecule is configured to interact with a particular analyte molecule. In some embodiments, the locations of supramolecular structures are mapped on a substrate having a plurality of binding locations, according to the capture barcode and/or another barcode linked with the supramolecular structures. In some embodiments, the linkage between the analyte molecules and supramolecular structures enable a signal to be generated. In some embodiments, the signal generated enables the identification and quantification of the analyte molecules in the sample based on the mapped location of the supramolecular structures on the substrate.
The present disclosure provides a method of identifying a polypeptide. The method can include steps of (a) attaching a polypeptide to a particle or solid support, thereby producing an immobilized polypeptide having a plurality of amino acids linked to the particle or solid support; (b) fragmenting the immobilized polypeptide, whereby the particle is attached to a set of fragments of the polypeptide; (c) performing a binding assay including contacting the set of fragments with a plurality of affinity reagents and detecting binding of affinity reagents of the plurality of affinity reagents to the set of fragments; and (d) identifying the polypeptide from results of the binding assay.
C12Q 1/37 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving hydrolase involving peptidase or proteinase
G01N 33/543 - ImmunoassayBiospecific binding assayMaterials therefor with an insoluble carrier for immobilising immunochemicals
G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids
45.
PREPARATION OF ARRAY SURFACES FOR SINGLE-ANALYTE PROCESSES
Compositions and methods are provided for forming single-analyte arrays with enhanced characteristics for inhibiting orthogonal binding of molecules to the array. Arrays are modified to contain covalently incorporated passivating moieties at array addresses where orthogonal binding may occur. The compositions and methods may facilitate detection of an increased quantity of array features at single-analyte resolution.
A method including contacting an array of macromolecules with a plurality of different assay reagents, wherein individual addresses of the array are attached to single macromolecules, and the macromolecule comprising a plurality of different reactive sites; detecting reaction of the array of macromolecules with the different assay reagents at single-molecule resolution; determining a first reaction extent comprising the fraction of the individual addresses observed to react with a first assay reagent; determining a second reaction extent comprising the fraction of the individual addresses observed to react with a second assay reagent; determining an observed double reaction extent comprising the fraction of the individual addresses observed to react with both the first and second assay reagents; determining an expected double reaction extent from the first and second reaction extents; and determining accessibility of a reactive site of the macromolecules based on a comparison of the observed and expected double reaction extents.
Disclosed are systems and methods for identifying the binding characteristics of a partially characterized or completely unknown affinity reagent, such as an antibody or aptamer, by binding that affinity reagent against an array of known proteins. The proteins on the array which bind to the partially characterized or completely unknown affinity reagent are then determined and an analysis performed to determine the binding characteristics of the affinity reagent.
The present disclosure provides methods, compositions and apparatus for generating probes having affinity for analytes of interest, such as polypeptides. Also provided are methods, compositions and apparatus for evaluating and characterizing probes.
A method including contacting an array of macromolecules with a plurality of different assay reagents, wherein individual addresses of the array are attached to single macromolecules, and the macromolecule comprising a plurality of different reactive sites; detecting reaction of the array of macromolecules with the different assay reagents at single-molecule resolution; determining a first reaction extent comprising the fraction of the individual addresses observed to react with a first assay reagent; determining a second reaction extent comprising the fraction of the individual addresses observed to react with a second assay reagent; determining an observed double reaction extent comprising the fraction of the individual addresses observed to react with both the first and second assay reagents; determining an expected double reaction extent from the first and second reaction extents; and determining accessibility of a reactive site of the macromolecules based on a comparison of the observed and expected double reaction extents.
C40B 30/04 - Methods of screening libraries by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
G16B 15/00 - ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids
50.
SYSTEMS AND METHODS OF VALIDATING NEW AFFINITY REAGENTS
Disclosed are systems and methods for identifying the binding characteristics of a partially characterized or completely unknown affinity reagent, such as an antibody or aptamer, by binding that affinity reagent against an array of known proteins. The proteins on the array which bind to the partially characterized or completely unknown affinity reagent are then determined and an analysis performed to determine the binding characteristics of the affinity reagent.
Provided are antibody conjugates, including a pair of cysteines crosslinked via a two-carbon bridge covalently connecting the sulfur atoms of the cysteines. Methods for making and using antibody conjugates are also provided. The compositions and methods of the present disclosure although particularly well suited to antibodies can be extended to other analytes having sulfur moieties such as proteins obtained from biological or artificial sources.
The present disclosure provides methods, compositions and apparatus for generating probes having affinity for analytes of interest, such as polypeptides. Also provided are methods, compositions and apparatus for evaluating and characterizing probes.
Provided are antibody conjugates, including a pair of cysteines crosslinked via a two-carbon bridge covalently connecting the sulfur atoms of the cysteines. Methods for making and using antibody conjugates are also provided. The compositions and methods of the present disclosure although particularly well suited to antibodies can be extended to other analytes having sulfur moieties such as proteins obtained from biological or artificial sources.
A61K 47/54 - Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additivesTargeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound
A61K 47/68 - Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additivesTargeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
Provided herein are structures and methods for detecting one or more analyte molecules present in a sample. In some embodiments, the one or more analyte molecules are detected using one or more supramolecular structures. In some embodiments, the one or more supramolecular structures are specifically designed to minimize cross-reactivity with each other. In some embodiments, the supramolecular structures are bi-stable, wherein the supramolecular structures shift from an unstable state to a stable state through interaction with one or more analyte molecules from the sample. In some embodiments, the stable state supramolecular structures are configured to provide a signal for analyte molecule detection and quantification. In some embodiments, the signal correlates to a DNA signal, such that detection and quantification of an analyte molecule comprises converting the presence of the analyte molecule into a DNA signal.
An affinity reagent, having: (a) a retaining component such as a structured nucleic acid particle; and (b) one or both of (i) one or more label components attached to the retaining component, and (ii) one or more binding components attached to the retaining component.
Methods of formation and detection of arrays of single analytes on enhanced substrates are described. The arrays may comprise pluralities of single analytes containing heterogeneity with respect to one or more properties. Enhanced substrates may be utilized to amplify the relative detection of optical signals form single analytes or moieties attached to single analytes with respect to sources of background, baseline, or erroneous optical signals.
Compositions, systems, and methods for the display of analytes such as biomolecules are described. Display of analytes is achieved by coupling of the analytes to displaying molecules that are configured to associate with surfaces or interfaces. Arrays of analytes may be formed from the described systems for utilization in assays and other methods.
A method of identifying extant proteins, including (a) inputting to a computer processor: (i) a plurality of empirical binding profiles, individual empirical binding profiles including empirical binding outcomes for binding of an extant protein to a plurality of different affinity reagents, (ii) a plurality of candidate outcome profiles, individual candidate outcome profiles including binding outcomes for binding of a candidate protein to the plurality of different affinity reagents, and (iii) a plurality of pseudo outcome profiles, individual pseudo outcome profiles including a rearrangement of a candidate outcome profile; (b) performing a process in the computer processor to identify extant proteins based on the empirical binding profiles of the extant proteins and the plurality of candidate outcome profiles; and (c) performing a process in the computer processor to determine a false discovery statistic for the extant proteins based on the plurality of pseudo outcome profiles.
G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
G16B 50/30 - Data warehousingComputing architectures
59.
SYSTEMS AND METHODS FOR ASSESSING AND IMPROVING THE QUALITY OF MULTIPLEX MOLECULAR ASSAYS
A method of identifying extant proteins, including (a) inputting to a computer processor: (i) a plurality of empirical binding profiles, individual empirical binding profiles including empirical binding outcomes for binding of an extant protein to a plurality of different affinity reagents, (ii) a plurality of candidate outcome profiles, individual candidate outcome profiles including binding outcomes for binding of a candidate protein to the plurality of different affinity reagents, and (iii) a plurality of pseudo outcome profiles, individual pseudo outcome profiles including a rearrangement of a candidate outcome profile; (b) performing a process in the computer processor to identify extant proteins based on the empirical binding profiles of the extant proteins and the plurality of candidate outcome profiles; and (c) performing a process in the computer processor to determine a false discovery statistic for the extant proteins based on the plurality of pseudo outcome profiles.
C40B 30/04 - Methods of screening libraries by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
C12Q 1/6837 - Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
C40B 20/00 - Methods specially adapted for identifying library members
G01N 33/543 - ImmunoassayBiospecific binding assayMaterials therefor with an insoluble carrier for immobilising immunochemicals
G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids
The methods described herein provide a means of producing an array of spatially separated proteins. The method relies on covalently attaching each protein of the plurality of proteins to a structured nucleic acid particle (SNAP), and attaching the SNAPs to a solid support.
Compositions, systems, and methods are disclosed for preparing and utilizing arrays, such as single-analyte arrays containing a plurality of fiducial elements with random spatial distributions. Arrays may be prepared with pluralities of fiducial elements comprising optically active or passive moieties. Arrays containing random spatial distributions of fiducial elements may be utilized for various array-based processes that require spatial information.
Compositions, systems, and methods are disclosed for preparing and utilizing arrays, such as single-analyte arrays containing a plurality of fiducial elements with random spatial distributions. Arrays may be prepared with pluralities of fiducial elements comprising optically active or passive moieties. Arrays containing random spatial distributions of fiducial elements may be utilized for various array-based processes that require spatial information.
Compositions, systems, and methods are disclosed for preparing and utilizing arrays, such as single-analyte arrays containing a plurality of fiducial elements with random spatial distributions. Arrays may be prepared with pluralities of fiducial elements comprising optically active or passive moieties. Arrays containing random spatial distributions of fiducial elements may be utilized for various array-based processes that require spatial information.
Methods and systems for identifying a protein within a sample are provided herein. A panel of antibodies are acquired, none of which are specific for a single protein or family of proteins. Additionally, the binding properties of the antibodies in the panel are determined. Further, the protein is iteratively exposed to a panel of antibodies. Additionally, a set of antibodies which bind the protein are determined. The identity of the protein is determined using one or more deconvolution methods based on the known binding properties of the antibodies to match the set of antibodies to a sequence of a protein.
Systems for optically detecting single-analytes, such as cells, nucleic acids, and polypeptides, are described. The described optical detection systems are suitable for multiplexed detection of single-analytes, including single-analytes provided in an array-based format. Methods for identifying single-analyte properties and interactions utilizing optical detection systems are provided.
An affinity reagent, having: (a) a retaining component such as a structured nucleic acid particle; and (b) one or both of (i) one or more label components attached to the retaining component, and (ii) one or more binding components attached to the retaining component.
The present disclosure provides methods and systems for performing single-molecule detection using fabricated integrated on-chip devices. In an aspect, the present disclosure provides a method for on-chip detection of an array of biological, chemical, or physical entities, comprising: (a) providing an array of light sensing devices; (b) immobilizing the array of biological, chemical, or physical entities on a substrate of the array of light sensing devices; (c) exposing the array of biological, chemical, or physical entities to electromagnetic radiation sufficient to excite the array of biological, chemical, or physical entities, thereby producing an emission signal of the array of biological, chemical, or physical entities; (d) using the array of light sensing devices, acquiring pixel information of the emission signal of the array of biological, chemical, or physical entities without scanning the array of light sensing devices across the array of biological, chemical, or physical entities; and (d) detecting the array of biological, chemical, or physical entities based at least in part on the acquired pixel information.
Methods for the preparation of sample polypeptide fractions are described. Sample polypeptides may be isolated from any of a variety of sources, including biological and non-biological systems. Sample polypeptides may be coupled or conjugated to other molecules to permit characterization of the sample polypeptide fractions. Sample polypeptide fractions may be prepared for analysis by a polypeptide assay.
The present disclosure provides methods and systems for performing single-molecule detection using fabricated integrated on-chip devices. In an aspect, the present disclosure provides a method for on-chip detection of an array of biological, chemical, or physical entities, comprising: (a) providing an array of light sensing devices; (b) immobilizing the array of biological, chemical, or physical entities on a substrate of the array of light sensing devices; (c) exposing the array of biological, chemical, or physical entities to electromagnetic radiation sufficient to excite the array of biological, chemical, or physical entities, thereby producing an emission signal of the array of biological, chemical, or physical entities; (d) using the array of light sensing devices, acquiring pixel information of the emission signal of the array of biological, chemical, or physical entities without scanning the array of light sensing devices across the array of biological, chemical, or physical entities; and (d) detecting the array of biological, chemical, or physical entities based at least in part on the acquired pixel information.
Methods and systems for analysis of large numbers of analytes using large numbers of reagents and processes using multiplexed, independent systems and subsystems for efficient processing and increased throughput of biological analyses.
G01N 35/08 - Automatic analysis not limited to methods or materials provided for in any single one of groups Handling materials therefor using a stream of discrete samples flowing along a tube system, e.g. flow injection analysis
G01N 35/10 - Devices for transferring samples to, in, or from, the analysis apparatus, e.g. suction devices, injection devices
B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
71.
PARTICLE-BASED ISOLATION OF PROTEINS AND OTHER ANALYTES
Methods, compositions and apparatus useful for individually manipulating and individually detecting analytes such as proteins. Analytes can be attached to particles to facilitate individual manipulation or detection of the particle-attached analytes. The particle-attached analytes can be composed of a single analyte attached to a single particle, such that no more than one analyte is attached per particle and no more than one particle is attached per analyte.
Methods, compositions and apparatus useful for individually manipulating and individually detecting analytes such as proteins. Analytes can be attached to particles to facilitate individual manipulation or detection of the particle-attached analytes. The particle-attached analytes can be composed of a single analyte attached to a single particle, such that no more than one analyte is attached per particle and no more than one particle is attached per analyte.
Methods, compositions and apparatus useful for individually manipulating and individually detecting analytes such as proteins. Analytes can be attached to particles to facilitate individual manipulation or detection of the particle-attached analytes. The particle-attached analytes can be composed of a single analyte attached to a single particle, such that no more than one analyte is attached per particle and no more than one particle is attached per analyte.
Systems and methods for the formation of single-analyte arrays are described. Array sites are formed via the patterning of surface-linked organic layers by electromagnetic radiation. Each array site may be modified after patterning to produce a chemistry at the array site that facilitates the controlled deposition of a single analyte at the array site.
Methods and systems are provided for accurate and efficient identification and quantification of proteins. In an aspect, disclosed herein is a method for identifying a protein in a sample of unknown proteins, comprising receiving information of a plurality of empirical measurements performed on the unknown proteins; comparing the information of empirical measurements against a database comprising a plurality of protein sequences, each protein sequence corresponding to a candidate protein among a plurality of candidate proteins; and for each of one or more of the plurality of candidate proteins, generating a probability that the candidate protein generates the information of empirical measurements, a probability that the plurality of empirical measurements is not observed given that the candidate protein is present in the sample, or a probability that the candidate protein is present in the sample; based on the comparison of the information of empirical measurements against the database.
G01N 27/26 - Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variablesInvestigating or analysing materials by the use of electric, electrochemical, or magnetic means by using electrolysis or electrophoresis
G01N 27/60 - Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrostatic variables
G01N 27/72 - Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating magnetic variables
76.
HIGHLY MULTIPLEXABLE ANALYSIS OF PROTEINS AND PROTEOMES
A method of identifying an extant protein, including (a) providing inputs including: (i) a binding profile, wherein the binding profile includes a plurality of binding outcomes for binding of the extant protein to a plurality of different affinity reagents, wherein individual binding outcomes of the plurality of binding outcomes include a measure of binding between the extant protein and a different affinity reagent of the plurality of different affinity reagents, (ii) a database including information characterizing or identifying a plurality of candidate proteins, and (iii) a binding model; (b) determining a probability for each of the affinity reagents binding to each of the candidate proteins in the database according to the binding model; and (c) identifying the extant protein as a selected candidate protein having a probability for binding each of the affinity reagents that is most compatible with the binding profile for the extant protein.
A method of identifying an extant protein, including (a) providing inputs including: (i) a binding profile, wherein the binding profile includes a plurality of binding outcomes for binding of the extant protein to a plurality of different affinity reagents, wherein individual binding outcomes of the plurality of binding outcomes include a measure of binding between the extant protein and a different affinity reagent of the plurality of different affinity reagents, (ii) a database including information characterizing or identifying a plurality of candidate proteins, and (iii) a binding model; (b) determining a probability for each of the affinity reagents binding to each of the candidate proteins in the database according to the binding model; and (c) identifying the extant protein as a selected candidate protein having a probability for binding each of the affinity reagents that is most compatible with the binding profile for the extant protein.
G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids
C40B 30/04 - Methods of screening libraries by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
Compositions, systems, and methods for the display of analytes such as biomolecules are described. Display of analytes is achieved by coupling of the analytes to displaying molecules that are configured to associate with surfaces or interfaces. Arrays of analytes may be formed from the described systems for utilization in assays and other methods.
Methods and systems are provided herein for selecting an affinity reagent which binds a desired peptide epitope in a plurality of sequence contexts. The method relies on obtaining a peptide library, each peptide having the sequence αXβ, wherein X is the desired peptide epitope, wherein each of α and β comprise an amino acid, using the peptide library to select an affinity reagent.
C40B 30/04 - Methods of screening libraries by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
80.
METHODS AND SYSTEMS FOR DETERMINING POLYPEPTIDE INTERACTIONS
Methods and systems for identifying and/or quantifying polypeptide binding interactions of ligand-binding polypeptides are disclosed. Detailed methods include methods for identifying binding ligands of ligand-binding polypeptides and methods for assessing changes in binding behavior due to alterations of ligand-binding polypeptides. Detailed systems include array-based systems that permit detection of ligand binding interactions at single-analyte resolution.
C40B 30/04 - Methods of screening libraries by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
C40B 40/10 - Libraries containing peptides or polypeptides, or derivatives thereof
G01N 33/58 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving labelled substances
G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids
81.
METHODS AND SYSTEMS FOR DETERMINING POLYPEPTIDE INTERACTIONS
Methods and systems for identifying and/or quantifying polypeptide binding interactions of ligand-binding polypeptides are disclosed. Detailed methods include methods for identifying binding ligands of ligand-binding polypeptides and methods for assessing changes in binding behavior due to alterations of ligand-binding polypeptides. Detailed systems include array-based systems that permit detection of ligand binding interactions at single-analyte resolution.
G01N 33/543 - ImmunoassayBiospecific binding assayMaterials therefor with an insoluble carrier for immobilising immunochemicals
C40B 60/06 - Integrated apparatus specially adapted for both creating libraries and identifying library members
G01N 21/77 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator
B01J 19/00 - Chemical, physical or physico-chemical processes in generalTheir relevant apparatus
A method for characterizing proteins, including steps of (a) detecting a plurality of proteins, wherein individual proteins of the plurality are associated with unique identifiers, wherein the detecting distinguishes the identities of the individual proteins and the unique identifiers associated with the individual proteins; (b) digesting the proteins to form peptides, wherein the peptides from each protein are associated with the unique identifiers for the respective individual protein; (c) detecting the peptides and associated unique identifiers, wherein the detecting distinguishes characteristics of individual peptides, and wherein the detecting distinguishes unique identifiers associated with the individual peptides; and (d) correlating characteristics detected in step (c) with individual proteins detected in step (a) based on the unique identifiers associated with the individual proteins and the peptides.
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
C40B 20/02 - Identifying library members by their fixed physical location on a support or substrate
C40B 20/04 - Identifying library members by means of a tag, label, or other readable or detectable entity associated with the library members, e.g. decoding processes
C40B 70/00 - Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or barcodes
G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids
Methods and systems for identifying a protein within a sample are provided herein. A panel of antibodies are acquired, none of which are specific for a single protein or family of proteins. Additionally, the binding properties of the antibodies in the panel are determined. Further, the protein is iteratively exposed to a panel of antibodies. Additionally, a set of antibodies which bind the protein are determined. The identity of the protein is determined using one or more deconvolution methods based on the known binding properties of the antibodies to match the set of antibodies to a sequence of a protein.
Methods for performing procedures on single analytes at single-analyte resolution are disclosed. The methods utilize an iterative approach to performing a sequence of steps during a single-analyte process. Control of the single-analyte process is achieved by implementing actions during each iteration based upon one or more determined process metrics. Systems are also detailed for implementing the disclosed methods at single-analyte resolution.
Methods for performing procedures on single analytes at single-analyte resolution are disclosed. The methods utilize an iterative approach to performing a sequence of steps during a single-analyte process. Control of the single-analyte process is achieved by implementing actions during each iteration based upon one or more determined process metrics. Systems are also detailed for implementing the disclosed methods at single-analyte resolution.
Provided herein are structures and methods for detecting one or more analyte molecules present in a sample. In some embodiments, the one or more analyte molecules form a complex in solution with a supramolecular structure. The supramolecular structures of the complex may be detectable such that binding of the analyte molecule to a binding site of an array is detectable via one or more features of the supramolecular structure. A binding site of an array includes capture molecules to capture bound complexes to facilitate detection.
Systems and methods for flow cells are provided. Flow cells may encompass a range of fluidic devices for various applications ranging from microfluidic systems to bulk phase flow systems. Flow cells may comprise one or more components for passive or active fluid transfer. Descriptions are provided for advantageous methods of fabricating flow cells for particular applications such as biological assays. Provided is a composition, comprising a first substrate comprising a first covalently-bound ligand; and a second substrate comprising a second covalently-bound ligand; wherein the first covalently-bound ligand and the second covalently-bound ligand are covalently bonded to form a heterocyclic compound. Also provided is a flow cell device, comprising: a first substrate comprising a microfabricated surface; and a second substrate comprising a non-patterned surface; wherein the first substrate is joined to the second substrate to form an enclosure; and wherein the microfabricated surface comprises at least one chamber, wherein the chamber comprises a microarray of active sites with specific functionalization separated by an optically resolvable distance and a functionalized surface comprising a passivating group or a blocking group; and wherein each active site of the microarray of active sites comprises a capture agent.
B32B 7/10 - Interconnection of layers at least one layer having inter-reactive properties
B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
B32B 9/04 - Layered products essentially comprising a particular substance not covered by groups comprising such substance as the main or only constituent of a layer, next to another layer of a specific substance
B32B 17/06 - Layered products essentially comprising sheet glass, or fibres of glass, slag or the like comprising glass as the main or only constituent of a layer, next to another layer of a specific substance
B32B 37/10 - Methods or apparatus for laminating, e.g. by curing or by ultrasonic bonding characterised by the pressing technique, e.g. using direct action of vacuum or fluid pressure
B32B 37/18 - Methods or apparatus for laminating, e.g. by curing or by ultrasonic bonding characterised by the properties of the layers with all layers existing as coherent layers before laminating involving the assembly of discrete sheets or panels only
C03C 27/06 - Joining glass to glass by processes other than fusing
88.
Systems Containing Microfluidic Devices, Structures And Methods For Detection And Quantification Of Sample Analytes
Provided herein are structures and methods for detecting one or more analyte molecules present in a sample. In some embodiments, the one or more analyte molecules are detected using one or more supramolecular structures. In some embodiments, the supramolecular structures are bi-stable, wherein the supramolecular structures shift from an unstable state to a stable state through interaction with one or more analyte molecules from the sample. In some embodiments, the stable state supramolecular structures are configured to provide a signal for analyte molecule detection and quantification.
Provided herein are structures and methods for detecting one or more analyte molecules present in a sample. In some embodiments, the one or more analyte molecules are detected using one or more supramolecular structures. In some embodiments, the supramolecular structures are bi-stable, wherein the supramolecular structures shift from an unstable state to a stable state through interaction with one or more analyte molecules from the sample. In some embodiments, the stable state supramolecular structures are configured to provide a signal for analyte molecule detection and quantification.
Compositions, systems, and methods for the display of analytes such as biomolecules are described. Display of analytes is achieved by coupling of the analytes to displaying molecules that are configured to associate with surfaces or interfaces. Arrays of analytes may be formed from the described systems for utilization in assays and other methods.
Compositions, systems, and methods for the display of analytes such as biomolecules are described. Display of analytes is achieved by coupling of the analytes to displaying molecules that are configured to associate with surfaces or interfaces. Arrays of analytes may be formed from the described systems for utilization in assays and other methods.
Compositions, systems, and methods for the display of analytes such as biomolecules are described. Display of analytes is achieved by coupling of the analytes to displaying molecules that are configured to associate with surfaces or interfaces. Arrays of analytes may be formed from the described systems for utilization in assays and other methods.
Provided herein are structures and methods for detecting one or more analyte molecules present in a sample. In some embodiments, the one or more analyte molecules are detected using one or more supramolecular structures. In some embodiments, the supramolecular structures are configured to form a linkage with a particular capture barcode, which is configured to form a linkage with a particular captur molecule. In some embodiments the capture molecule is configured to interact with a particular analyte molecule. In some embodiments, the locations of supramolecular structures are mapped on a substrate having a plurality of binding locations, according to the capture barcode and/or another barcode linked with the supramolecular structures. In some embodiments, the linkage between the analyte molecules and supramolecular structures enable a signal to be generated. In some embodiments, the signal generated enables the identification and quantification of the analyte molecules in the sample based on the mapped location of the supramolecular structures on the substrate.
Provided herein are structures and methods for detecting one or more analyte molecules present in a sample. In some embodiments, the one or more analyte molecules are detected using one or more supramolecular structures. In some embodiments, the supramolecular structures facilitate binding of a single detector molecule. In some embodiments, the stable state supramolecular structures are configured to provide a signal for analyte molecule detection and quantification. In some embodiments, the signal correlates to a DNA signal, such that detection and quantification of an analyte molecule comprises converting the presence of the analyte molecule into a DNA signal.
Provided herein are structures and methods for detecting one or more analyte molecules present in a sample. In some embodiments, the one or more analyte molecules are detected using one or more supramolecular structures. In some embodiments, the supramolecular structures facilitate binding of a single detector molecule. In some embodiments, the stable state supramolecular structures are configured to provide a signal for analyte molecule detection and quantification. In some embodiments, the signal correlates to a DNA signal, such that detection and quantification of an analyte molecule comprises converting the presence of the analyte molecule into a DNA signal.
Methods for the preparation of sample polypeptide fractions are described. Sample polypeptides may be isolated from any of a variety of sources, including biological and non-biological systems. Sample polypeptides may be coupled or conjugated to other molecules to permit characterization of the sample polypeptide fractions. Sample polypeptide fractions may be prepared for analysis by a polypeptide assay.
Systems and methods for obtaining qualitative or quantitative measurements of proteoforms of polypeptides are described. The described methods include measurements of affinity reagent binding on single-molecule polypeptide arrays to distinguish between polypeptide isoforms. The described methods may provide high resolution quantitative comparisons of proteoforms with very low copy numbers.
Systems and methods for obtaining qualitative or quantitative measurements of proteoforms of polypeptides are described. The described methods include measurements of affinity reagent binding on single-molecule polypeptide arrays to distinguish between polypeptide isoforms. The described methods may provide high resolution quantitative comparisons of proteoforms with very low copy numbers.
Provided herein are structures and methods for detecting one or more analyte molecules 44 present in a sample. In some embodiments, the one or more analyte molecules 44 are detected using one or more supramolecular structures 40 that are coupled to a substrate, e.g., a solid support. In some embodiments, the supramolecular structures 40 are bi-stable, wherein the supramolecular structures 40 transition from an unstable state to a stable state through interaction with one or more analyte molecules 44 from the sample. In some embodiments, the stable state supramolecular structures 40 are configured to provide a signal for analyte molecule detection and quantification.
Provided herein are structures and methods for detecting one or more analyte molecules present in a sample. In some embodiments, the one or more analyte molecules are detected using one or more supramolecular structures that are coupled to a substrate, e.g., a solid support. In some embodiments, the supramolecular structures are bi-stable, wherein the supramolecular structures transition from an unstable state to a stable state through interaction with one or more analyte molecules from the sample. In some embodiments, the stable state supramolecular structures are configured to provide a signal for analyte molecule detection and quantification.
patents
