Methods and/or Systems Producing and Providing Sets of Oligonucleotide Conjugates for Assays and Detections

Abstract

The present disclosure is directed to methods and/or systems producing and providing uses sets of oligonucleotide conjugates for assays and detections and related systems and/or kits. Certain methods are directed to a method for detecting one or more biological targets of a sample in a detection assay, comprising: providing a molecular probe, comprising a binding moiety and an oligonucleotide sequence, to a sample comprising one or more biological targets; binding the one or more biological targets with the binding moiety; providing a detectable component to the sample, wherein the detectable component comprises a signal generating moiety conjugated to an oligonucleotide sequence complementary to the oligonucleotide sequence of the molecular probe; hydridizing the oligonucleotide sequence of the target-bound molecular probe to the detectable component; and detecting a signal generated from the hydridized detectable component. Various other embodiments, applications etc. are disclosed herein.

1 . A manufacturing system, comprising:
 i) a first series, comprising a plurality of molecular probes, said first series prepared by independently pairing, via conjugation, a plurality of first oligonucleotide sequences to a plurality of binding moieties; and   ii) a second series, comprising a plurality of detectable components, said second series prepared by independently pairing, via conjugation, a plurality of second oligonucleotide sequences to a plurality of signal generating moieties or to a plurality of scaffolds having one or more of the plurality of signal generating moieties, wherein the plurality of second oligonucleotide sequences are complementary to the plurality of first oligonucleotide sequences;   wherein the manufacturing system is characterized by one or more of the following:   a) the first series and the second series are made available for one or more users to combine the first series and the second series to produce one or more hybridized molecular probes;   b) at least a portion of preassembled combinations of the first series and the second series are produced and made available for one or more users;   c) the first series and the second series are made available for one or more users to combine the first series, the second series, and a sample potentially having one or more targets, to produce one or more hybridized target-bound molecular probes;   d) the time in which to produce the possible combinations of said first series and said second series is less than that of conventional preparations; and   e) the time in which to hybridize and detect of the target-bound hybrids formed from said first series and said second series is less than conventional conjugation and detection.   
     
     
         2 . The manufacturing system of  claim 1 , wherein the manufacturing system is further characterized by one or more of the following:
 i) the first series and/or second series is provided to one or more end users as a customized matrix or semi-matrix of the first series and the second series as independently selected and paired by said one or more end users, wherein the customized matrix or semi-matrix comprises an assay useful amount of said first series and said second series which are capable of producing a plurality of hybridized molecular probe-detectable components;   ii) the manufacturing system reduces to manageable proportions the number of catalog products a vendor of labeled molecular probes must manufacture, stock, market, and distribute; and   iii) at least 90% of the possible hybridized combinations of said first series and second series can be produced in 10 hours or less.   
     
     
         3 . The manufacturing system of  claim 1 , wherein the first series comprises a plurality of between 2-100 different molecular probes. 
     
     
         4 . The manufacturing system of  claim 1 , wherein the first series comprises:
 i) a plurality of different first oligonucleotide sequences; or   ii) a plurality of identical first oligonucleotide sequences.   
     
     
         5 . The manufacturing system of  claim 1 , wherein the second series comprises a plurality of between 2-30 different detectable components. 
     
     
         6 . The manufacturing system of  claim 1 , wherein the second series comprises a plurality of scaffolds independently paired, via conjugation, with the plurality of second oligonucleotide sequences, wherein said plurality of scaffolds comprise one or more signal generating moieties. 
     
     
         7 . The manufacturing system of  claim 1 , wherein the manufacturing system produces at least one or more of the following:
 i) a customized first series; and   ii) a customized second series;   wherein the manufacturing system reduces to manageable proportions the number of catalog products a vendor of labeled molecular probes and/or detectable components to manufacture, stock, market, and/or distribute.   
     
     
         8 . The manufacturing system of  claim 1 , wherein the manufacturing system enables either the manufacturer or the end user to produce the plurality of customizable molecular probes and/or the plurality of customizable detectable components in a time at least 10% less, 20%, 30%, 40%, 50%, 75%, 100%, 200%, 300%, or 500% less than as required by conventional conjugations to prepare the directly labeled binding moieties. 
     
     
         9 . The manufacturing system of  claim 1 , wherein the manufacturing system enables the end user to choose the mode of addition of the first series and the second series to the sample comprising one or more targets. 
     
     
         10 . The manufacturing system of  claim 1 , wherein manufacturing system enables the end user to prepare and utilize an assay comprising:
 i) a singleplex or multiplex assay; and   ii) the assay detects, measures, or quantifies the level of binding and/or amount of the target present in the sample with one or more of the following:   flow cytometry, immunomagnetic cellular depletion, immunomagnetic cell capture, array, bead array, multiplex bead array, microarray, antibody array, cellular array, chemiluminescence, infrared, microscopy, imaging, high content screening (HCS), mass cytometry, lateral flow immunoassay, immunodetection, immunoturbidity, latex agglutination, gold particle agglutination, visual inspection, a change in light transmittance through said sample, increased light transmittance through said sample, immunohistochemistry (IHC), immunocytochemistry (ICC), in situ hybridization (ISH), enzyme immuno-assay (EIA), enzyme linked immuno-assay (ELISA), ELISpot, a blotting method, a Western blot, a Southern blot, a Southwestern blot, labeling inside an electrophoresis system, labeling on a surface, labeling on an array, PCR amplification, elongation followed by PCR amplification, immunoprecipitation, co-immunoprecipitation, chromatin immunoprecipitation, pretargeting imaging, therapeutic agent, or combinations thereof.   
     
     
         11 . The manufacturing system of  claim 1 , wherein the manufacturing system wherein the prepared molecular probes and prepared detectable components have at least 90% purity. 
     
     
         12 . The manufacturing system of  claim 1 , wherein the preparation further comprises an isolation step utilizing an immobilized binder, chromatography, affinity chromatography, size exclusion chromatography, HPLC, reverse-phase chromatography, electrophoresis, capillary electrophoresis, polyacrylamide gel electrophoresis, agarose gel electrophoresis, free flow electrophoresis, differential centrifugation, thin layer chromatography, immunoprecipitation, hybridization, solvent extraction, dialysis, filtration, diafiltration, tangential flow filtration, ion exchange chromatography, hydrophobic interaction chromatography, or combinations thereof. 
     
     
         13 . The manufacturing system of  claim 1 , wherein the binding moiety comprises an antibody, a monoclonal antibody, a polycolonal antibody, an enzyme, a protein, a peptide, a carbohydrate, a nuclear receptor, a small molecule, an aptamer, a chelator, or combinations or derivatives thereof. 
     
     
         14 . The manufacturing system of  claim 1 , wherein the scaffold comprises a dendrimer, a polysaccharide, a dextran, a protein, a peptide, a further oligonucleotide sequence, a portion of the second oligonucleotide sequence that is not complementary to the first oligonucleotide sequence of the molecular probe, a polymer, a hydrophilic polymer, a bead, a nanoparticle, or combinations or derivatives thereof. 
     
     
         15 . The manufacturing system of  claim 1 , wherein the signal generating moiety or the one or more signal generating moieties of the detectable component or the hybridized detectable component, comprises one or more of the following:
 a directly detectable signal generating moiety, an indirectly detectable signal generating moiety, a fluorescent dye, a fluorophore, a fluorochrome, a chromophore, a biofluorescent protein, a luminescent species, a chemiluminescent compound, a electrochemiluminescent label, a bioluminescent label, a phosphorescent species, a fluorophore labeled DNA dendrimer, Quantum Dot, a tandem dye, a FRET dye, a heavy atom, a spin label, a radioactive isotope, a nanoparticle, a light scattering nanoparticle or microsphere, a diffracting particle, a polymer, a polymer particle, a bead, a solid surface, a Raman particle, a metal particle, a stable isotope, a heavy metal chelate, a magnetic particle, an RFID tag, a microbarcode particle, an enzyme, an enzyme substrate, a molecule specifically recognized by another substance carrying a label or reacts with a substance carrying a label, an antibody, an antibody fragment, an antigen, a nucleic acid, a nucleic acid analog, oligonucleotide, oligonucleotide analog, complementary oligonucleotide, complementary oligonucleotide analog, a ligand, a protein, a peptide ligand, a protein substrate, a receptor; a substrate, a secondary reporter, a hapten, or combinations or derivatives thereof.   
     
     
         16 . The manufacturing system of  claim 1 , wherein the molecular probe and/or the detectable component further comprises a spacer group, comprising a polymerized ethylene oxide, a PEG, a PEO, a protein, a peptide, a DNA, an RNA, an oligonucleotide sequence, or a dextran. 
     
     
         17 . The manufacturing system of  claim 1 , wherein the manufacturing system further enables the end user to remove the hybridized detectable component or plurality of detectable components from the bound target or plurality of targets, respectively, wherein said removal is by a washing or stripping process. 
     
     
         18 . A manufacturing method, comprising:
 i) a first series, comprising a plurality of molecular probes, said first series prepared by independently pairing, via conjugation, a plurality of first oligonucleotide sequences to a plurality of binding moieties; and   ii) a second series, comprising a plurality of detectable components, said second series prepared by independently pairing, via conjugation, a plurality of second oligonucleotide sequences to a plurality of signal generating moieties or to a plurality of scaffolds having one or more of the plurality of signal generating moieties, wherein the plurality of second oligonucleotide sequences are complementary to the plurality of first oligonucleotide sequences;   wherein the manufacturing system is characterized by one or more of the following:   a) the first series and the second series are made available for one or more users to combine the first series and the second series to produce one or more hybridized molecular probes;   b) at least a portion of preassembled combinations of the first series and the second series are produced and made available for one or more users;   c) the first series and the second series are made available for one or more users to combine the first series, the second series, and a sample potentially having one or more targets, to produce one or more hybridized target-bound molecular probes;   d) the time in which to produce the possible combinations of said first series and said second series is less than that of conventional preparations; and   e) the time in which to hybridize and detect of the target-bound hybrids formed from said first series and said second series is less than conventional conjugation and detection.   
     
     
         19 . A method of offering detectable molecular probes, comprising:
 i) offering to one or more users a first series, comprising a plurality of molecular probes, said first series prepared by independently pairing, via conjugation, a plurality of first oligonucleotide sequences to a plurality of binding moieties;   ii) offering to one or more users a second series, comprising a plurality of detectable components, said second series prepared by independently pairing, via conjugation, a plurality of second oligonucleotide sequences to a plurality of signal generating moieties or to a plurality of scaffolds having one or more of the plurality of signal generating moieties, wherein the plurality of second oligonucleotide sequences are complementary to the plurality of first oligonucleotide sequences; and   iii) providing the first series and the second series to the one or more users, to combine the first series, the second series, and a sample having one or more targets, at an appropriate time, and in an appropriate amount, to produce one or more hybridized target-bound molecular probes;   wherein the method is characterized by one or more of the following:   a) the first series and the second series are made available for one or more users to combine the first series and the second series to produce one or more hybridized molecular probes;   b) at least a portion of preassembled combinations of the first series and the second series are produced and made available for one or more users;   c) the first series and the second series are made available for one or more users to combine the first series, the second series, and a sample potentially having one or more targets, to produce one or more hybridized target-bound molecular probes;   d) the time in which to produce the possible combinations of said first series and said second series is less than that of conventional preparations; and   e) the time in which to hybridize and detect of the target-bound hybrids formed from said first series and said second series is less than conventional conjugation and detection.   
     
     
         20 . The method of  claim 19 , wherein:
 i) the first series and/or second series is provided to the one or more end users as a customized matrix or semi-matrix of the first series and the second series, independently selected and paired by said one or more end users, wherein the customized matrix or semi-matrix comprises an assay useful amount of said first series and said second series which are capable of producing a plurality of hybridized molecular probe-detectable components;   ii) the method reduces to manageable proportions the number of catalog products a vendor of labeled molecular probes must manufacture, stock, market, and distribute; and   iii) at least 90% of the possible hybridized combinations of said first series and second series can be produced in 10 hours or less.