Systems and methods for biomolecule retention
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.
1 . A system, comprising:
a) a solid support comprising a plurality of sites, wherein a plurality of nucleic acid particles is attached to the plurality of sites, wherein each site of the plurality of sites is attached to only one nucleic acid particle of the plurality of nucleic acid particles, wherein a plurality of polypeptides is attached to the plurality of nucleic acid particle, wherein each nucleic acid particle of the plurality of nucleic acid particles is attached to only one polypeptide of the plurality of polypeptides, wherein each nucleic acid particle of the plurality of nucleic acid particles comprises a first double-stranded region that is attached to the solid support and a second double-stranded region that is oriented substantially orthogonal to the surface of the solid support, wherein only one polypeptide of the plurality of polypeptides is attached to the second double-stranded region, and wherein each site of the plurality of sites is optically resolvable from any other site of the plurality of sites;
b) a first fluidic medium comprising a first plurality of binding reagents, wherein binding reagents of the first plurality of binding reagents are configured to provide a first optical signal, and wherein the first fluidic medium is deliverable to the solid support;
c) a second fluidic medium comprising a second plurality of binding reagents, wherein binding reagents of the second plurality of binding reagents are configured to provide a second optical signal, wherein the second optical signal is distinguishable from the first optical signal, and wherein the second fluidic medium is deliverable to the solid support; and
d) an optical detector, wherein the optical detector is configured to detect at each individual site of the plurality of sites a presence or an absence of a first optical signal from a binding reagent of the first plurality of binding reagents, and wherein the optical detector is configured to detect at each individual site of the plurality of sites a presence or an absence of a second optical signal from a binding reagent of the second plurality of binding reagents.
2 . The system of claim 1 , wherein the sites of the plurality of sites are separated by at least 500 nanometers.
3 . The system of claim 1 , further comprising a processor that is configured to receive measurements of the presences or absences of the first optical signals and the second optical signals for each site of the plurality of sites from the optical detector.
4 . The system of claim 3 , wherein the processor is configured with an algorithm to characterize the polypeptide at each site of the plurality of sites based upon the measurements of the presences or absences of the first optical signals and the second optical signals for each site of the plurality of sites from the optical detector.
5 . The system of claim 4 , wherein characterizing each polypeptide at each site of the plurality of sites comprises identifying each polypeptide at each site of the plurality of sites.
6 . The system of claim 4 , wherein characterizing each polypeptide at each site of the plurality of sites further comprises quantifying the polypeptides attached to the solid support.
7 . The system of claim 6 , wherein quantifying the polypeptides attached to the solid support comprises quantifying a dynamic range of a first polypeptide species and a second polypeptide species of the plurality of polypeptides.
8 . The system of claim 4 , wherein the algorithm comprises a machine learning algorithm.
9 . The system of claim 1 , wherein the solid support comprises a material selected from the group consisting of ceramic, glass, polymer, and semiconductor.
10 . The system of claim 9 , wherein the solid support further comprises a layer disposed upon the material.
11 . The system of claim 10 , wherein the layer comprises a metal or metal oxide.
12 . The system of claim 11 , wherein the layer has a thickness of at least 10 nanometers.
13 . The system of claim 10 , wherein the layer comprises a plurality of wells, wherein each well of the plurality of wells individually comprises a site of the plurality of sites.
14 . The system of claim 1 , wherein the only one polypeptide is attached to a linking moiety of the nucleic acid particle.
15 . The system of claim 14 , wherein the linking moiety provides a separation distance of at least 10 nanometers between the only one polypeptide and the solid support.
16 . The system of claim 1 , wherein the only one nucleic acid particle comprises a surface-interacting moiety.
17 . The system of claim 16 , wherein the surface-interacting moiety comprises an inorganic nanoparticle, a carbon nanoparticle, a polymer nanoparticle, or a biopolymer.
18 . The system of claim 1 , wherein the optical detector comprises a time delay integration (TDI) device, a complementary metal oxide semiconductor (CMOS) detector, an avalanche photodiode (APD) detector, a Geiger-mode photon counter, a photomultiplier tube (PMT), a charge injection device (CID) sensor, or a JOT image sensor.
19 . The system of claim 1 , wherein the system further comprises a light-emitting source.
20 . The system of claim 19 , wherein the light-emitting source comprises a laser, a light-emitting diode (LED), or a lamp.
21 . The system of claim 1 , wherein the binding reagents of the first plurality of binding reagents have a binding specificity for a first polypeptide species of the plurality of polypeptides.
22 . The system of claim 21 , wherein the binding reagents of the second plurality of binding reagents have a binding specificity for a second polypeptide species of the plurality of polypeptides.
23 . The system of claim 1 , wherein a binding reagent of the first plurality of binding reagents or the second plurality of binding reagents comprises an antibody or an antibody fragment.
24 . The system of claim 1 , wherein a binding reagent of the first plurality of binding reagents or the second plurality of binding reagents comprises an aptamer or a peptamer.
25 . A system, comprising:
a) a solid support comprising a plurality of immobilized nucleic acid particles, wherein the plurality of immobilized nucleic acid particles is attached to a plurality of polypeptides, wherein the plurality of polypeptides comprises a first polypeptide species and a second polypeptide species, wherein the first polypeptide species and the second polypeptide species have a dynamic range of at least 10 4 with respect to each other, wherein each immobilized nucleic acid particle of the plurality of nucleic acid particles comprises a first double-stranded region that is attached to the solid support and a second double-stranded region that is oriented substantially orthogonal to the surface of the solid support, and wherein only one polypeptide of the plurality of polypeptides is attached to the second double-stranded region;
b) a first fluidic medium comprising a first plurality of binding reagents, wherein binding reagents of the first plurality of binding reagents are configured to provide a first optical signal, and wherein the first fluidic medium is deliverable to the solid support;
c) a second fluidic medium comprising a second plurality of binding reagents, wherein binding reagents of the second plurality of binding reagents are configured to provide a second optical signal, wherein the second optical signal is distinguishable from the first optical signal, and wherein the second fluidic medium is deliverable to the solid support; and
d) an optical detector, wherein the optical detector is configured to detect at each individual site of the plurality of sites a presence or an absence of a first optical signal from a binding reagent of the first plurality of binding reagents, and wherein the optical detector is configured to detect at each individual site of the plurality of sites a presence or an absence of a second optical signal from a binding reagent of the second plurality of binding reagents.
26 . A system, comprising:
a) a solid support comprising a plurality of sites, wherein a plurality of nucleic acid particles is attached to the plurality of sites, wherein each site of the plurality of sites is attached to only one nucleic acid particle of the plurality of nucleic acid particles, wherein a plurality of polypeptides is attached to the plurality of nucleic acid particles, wherein each nucleic acid particle is attached to only one polypeptide of the plurality of polypeptides, wherein the plurality of polypeptides comprises a first proteoform of a protein and a second proteoform of the protein, wherein each nucleic acid particle of the plurality of nucleic acid particles comprises a first double-stranded region that is attached to the solid support and a second double-stranded region that is oriented substantially orthogonal to the surface of the solid support, wherein only one polypeptide of the plurality of polypeptides is attached to the second double-stranded region;
b) a first fluidic medium comprising a first plurality of binding reagents, wherein binding reagents of the first plurality of binding reagents have a binding specificity for the first proteoform of the protein, wherein binding reagents of the first plurality of binding reagents are configured to provide a first optical signal, and wherein the first fluidic medium is deliverable to the solid support;
c) a second fluidic medium comprising a second plurality of binding reagents, wherein binding reagents of the second plurality of binding reagents have a binding specificity for the second proteoform of the protein, wherein binding reagents of the second plurality of binding reagents are configured to provide a second optical signal, wherein the second optical signal is distinguishable from the first optical signal, and wherein the second fluidic medium is deliverable to the solid support; and
d) an optical detector, wherein the optical detector is configured to detect at each individual site of the plurality of sites a presence or an absence of a first optical signal from a binding reagent of the first plurality of binding reagents, and wherein the optical detector is configured to detect at each individual site of the plurality of sites a presence or an absence of a second optical signal from a binding reagent of the second plurality of binding reagents.