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 method of preparing a proteomic array, comprising:
(a) coupling a plurality of sample polypeptides from a proteome to a plurality of nucleic acid nanostructures, wherein each nucleic acid nanostructure is coupled to one and only one sample polypeptide by a separating group, wherein the separating group provides an average separation distance of at least 10 nanometers between the one and only one sample polypeptide and a nucleic acid nanostructure to which the one and only sample polypeptide is coupled, and wherein the plurality of nucleic acid nanostructures is coupled to at least 25% of all polypeptide species in the proteome;
(b) after coupling the plurality of sample polypeptides to the plurality of nucleic acid nanostructures, coupling the plurality of nucleic acid nanostructures to an array comprising a plurality of sites; and
(c) after coupling the plurality of nucleic acid nanostructures to the array, detecting presence or absence of a nucleic acid nanostructure at each site of the plurality of sites.
2. The method of claim 1 , wherein detecting the presence or absence of a nucleic acid nanostructure at each site of the plurality of sites comprises detecting the presence of a nucleic acid nanostructure for at least 65% of sites of the plurality of sites.
3. The method of claim 1 , wherein detecting the presence or absence of a nucleic acid nanostructure at each site of the plurality of sites comprises detecting the absence of a nucleic acid nanostructure for no more than 35% of sites of the plurality of sites.
4. The method of claim 1 , wherein, after coupling the plurality of nucleic acid nanostructures to the array, at least 40% of sites of the plurality of sites comprise one and only one sample polypeptide.
5. The method of claim 1 , wherein detecting presence or absence of a nucleic acid nanostructure at each site of the plurality of sites comprises detecting the presence or absence of a first signal from a first detectable label coupled to a nucleic acid nanostructure.
6. The method of claim 1 , further comprising: i) coupling affinity agents to sites of the plurality of sites, and ii) detecting presence or absence of an affinity agent at each site of the plurality of sites.
7. The method of claim 6 , wherein detecting the presence or absence of the affinity agent at each site of the plurality of sites comprises detecting the presence or absence of a signal from a detectable label coupled to the affinity agent.
8. The method of claim 6 , further comprising detecting coupling of affinity agents to at least 50% of the sample polypeptides on the proteomic array.
9. The method of claim 8 , further comprising identifying at least 50% of sample polypeptides of the plurality of sample polypeptides based upon detected coupling of affinity agents to the at least 50% of the sample polypeptides.
10. The method of claim 1 , wherein coupling the plurality of sample polypeptides to the plurality of nucleic acid nanostructures comprises covalently coupling the plurality of sample polypeptides to the plurality of nucleic acid nanostructures.
11. The method of claim 10 , wherein nucleic acid nanostructures of the plurality of nucleic acid nanostructures comprises linking moieties, and wherein covalently coupling the plurality of sample polypeptides to the plurality of nucleic acid nanostructures comprises covalently coupling sample polypeptides to the linking moieties.
12. The method of claim 1 , further comprising obtaining the plurality of sample polypeptides from an organism.
13. The method of claim 12 , comprising obtaining the plurality of sample polypeptides from a tissue or a biological fluid of the organism.
14. The method of claim 12 , wherein the organism comprises a mammal or a plant.
15. The method of claim 1 , further comprising detecting a terminal amino acid residue of a sample polypeptide on the array.
16. The method of claim 1 , wherein coupling a nucleic acid nanostructure of the plurality of nucleic acid nanostructures to a site of the plurality of sites comprises hybridizing a nucleic acid strand of the nucleic acid nanostructure to a complementary nucleic acid strand, wherein the complementary nucleic acid strand is coupled to the site.
17. The method of claim 1 , wherein a nucleic acid nanostructure of the plurality of nucleic acid nanostructures comprises a nucleic acid origami.
18. The method of claim 17 , wherein the nucleic acid nanostructure of the plurality of nucleic acid nanostructures further comprises a pervious structure, wherein the pervious structure comprises a plurality of pendant moieties.
19. The method of claim 18 , wherein coupling a nucleic acid nanostructure of the plurality of nucleic acid nanostructures to a site of the plurality of sites comprises coupling a pendant moiety of the plurality of pendant moieties to a site of the plurality of sites.
20. The method of claim 18 , wherein coupling a nucleic acid nanostructure of the plurality of nucleic acid nanostructures to a site of the plurality of sites comprises coupling a subset of pendant moieties of the plurality of pendant moieties to a site of the plurality of sites.
21. The method of claim 18 , wherein a pendant moiety of the plurality of pendant moieties comprises a single-stranded nucleic acid.
22. The method of claim 18 , wherein a pendant moiety of the plurality of pendant moieties comprises a polymer chain.
23. The method of claim 1 , further comprising: i) fragmenting a sample polypeptide into at least one peptide fragment, and ii) coupling a peptide fragment of the at least one peptide fragment to a nucleic acid nanostructure.
24. The method of claim 1 , wherein the at least 25% of species of the proteome comprise a complexity of at least about 1×10 3 native-length primary protein sequences.
25. The method of claim 1 , wherein the separating group comprises a polymer linker, a nucleic acid linker, or a nanoparticle linker.
26. The method of claim 25 , wherein the polymer linker comprises a polyethylene glycol (PEG) moiety.
27. The method of claim 25 , wherein the nucleic acid linker comprises a double-stranded nucleic acid.
28. The method of claim 1 , wherein the separating group provides an average separation distance of at least 15 nanometers between the one and only one sample polypeptide and a surface of a solid support.
29. A method of preparing a proteomic array, comprising:
a) coupling a plurality of sample polypeptides from a proteome to a plurality of nucleic acid nanostructures, wherein each nucleic acid nanostructure is coupled to one and only one sample polypeptide, wherein the coupling occurs in the presence of a denaturing species, and wherein the plurality of nucleic acid nanostructures is coupled to at least 25% of all polypeptide species in the proteome;
b) after coupling the plurality of sample polypeptides from the proteome to the plurality of nucleic acid nanostructures, coupling the plurality of nucleic acid nanostructures to an array comprising a plurality of sites; and
c) after coupling the plurality of nucleic acid nanostructures to the array, detecting presence or absence of a nucleic acid nanostructure at each site of the plurality of sites.
30. A method of preparing a proteomic array, comprising:
a) coupling a plurality of sample polypeptides from a proteome to a plurality of nucleic acid nanostructures, wherein each nucleic acid nanostructure is coupled to one and only one sample, and wherein the plurality of nucleic acid nanostructures is coupled to at least 25% of all polypeptide species in the proteome;
b) after coupling the plurality of sample polypeptides from the proteome to the plurality of nucleic acid nanostructures, coupling the plurality of nucleic acid nanostructures to an array comprising a plurality of sites, wherein coupling a nucleic acid nanostructure of the plurality of nucleic acid nanostructures comprises hybridizing a nucleic acid strand of the nucleic acid nanostructure to two or more complementary nucleic acid strands of a site of the plurality of sites, wherein the two or more complementary nucleic acid strands are coupled to the site; and
c) after coupling the plurality of nucleic acid nanostructures to the array, detecting presence or absence of a nucleic acid nanostructure at each site of the plurality of sites.