Affinity reagents having enhanced binding and detection characteristics
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.
1. A detectable probe, comprising:
(a) a retaining component comprising nucleic acid origami, wherein the nucleic acid origami comprises a scaffold nucleic acid and a staple nucleic acid hybridized to two regions of the scaffold nucleic acid, wherein the two regions of the scaffold nucleic acid are separated by an intervening region that does not hybridize to the staple nucleic acid;
(b) a label component attached to the retaining component; and
(c) two or more binding components attached to the retaining component, wherein the two or more binding components have the same binding specificity for an epitope of a binding partner, and wherein at least one of the two or more binding components is bound to the epitope of the binding partner via non-covalent binding,
wherein the binding partner is attached to an array of different binding partners at a site that is physically isolated from all other binding partners in the array, and wherein the detectable probe is smaller than the site.
2. The detectable probe of claim 1 , wherein the label component comprises a luminophore.
3. The detectable probe of claim 1 , wherein the nucleic acid origami comprises a circular nucleic acid.
4. The detectable probe of claim 3 , wherein the nucleic acid origami further comprises a plurality of oligonucleotides hybridized to the circular nucleic acid.
5. The detectable probe of claim 1 , wherein the label component comprises a fluorescent nanoparticle.
6. The detectable probe of claim 1 , comprising two or more label components coupled to the retaining component.
7. The detectable probe of claim 1 , wherein the binding partner is attached to the site via a structured nucleic acid particle.
8. The detectable probe of claim 1 , wherein the retaining component constrains a first binding component of the two or more binding components from contacting a second binding component of the two or more binding components.
9. The detectable probe of claim 1 , wherein the retaining component comprises a three-dimensional structure having a first side that is offset from a second side and wherein the two or more binding components are constrained to residing on the first side and constrained from contacting the second side.
10. The detectable probe of claim 9 , wherein the label component is constrained to residing on the second side and constrained from contacting the first side.
11. The detectable probe of claim 1 , wherein the detectable probe comprises at least three label components.
12. The detectable probe of claim 6 , wherein the retaining component comprises a three-dimensional structure having a first side that is offset from a second side and wherein the two or more label components are constrained to residing on the first side and constrained from contacting the second side.
13. The detectable probe of claim 6 , wherein the two or more binding components are constrained to residing on the second side and constrained from contacting the first side.
14. A method of detecting the binding partner of claim 1 , comprising acquiring a signal from the label component of the detectable probe, thereby detecting the binding partner.
15. The detectable probe of claim 1 , wherein the binding partner comprises a polypeptide and wherein the array of binding partners comprises an array of polypeptides.
16. The detectable probe of claim 15 , wherein a plurality of individual polypeptides in the array of polypeptides are non-covalently bound to a binding component of a respective detectable probe, the respective detectable probe comprising
(i) a respective retaining component;
(ii) a label component; and
(iii) two or more binding components attached to the respective retaining component.
17. The detectable probe of claim 1 , wherein the two or more binding components comprises at least three binding components, wherein the at least three binding components have essentially the same binding specificity for the epitope of the binding partner.
18. The detectable probe of claim 1 , wherein the retaining component comprises a rigid structure that constrains the two or more binding components to occupy effective volumes that do not overlap.
19. The detectable probe of claim 18 , wherein the rigid structure comprises the nucleic acid origami.
20. The detectable probe of claim 1 , wherein the detectable probe has an equilibrium dissociation constant for the binding partner that is less than the equilibrium dissociation constant of any of the two or more binding components for the binding partner.
21. The detectable probe of claim 1 , wherein the detectable probe has a dissociation rate constant for the binding partner that is less than the dissociation rate constant of any of the two or more binding components for the binding partner.
22. The detectable probe of claim 1 , wherein the two or more binding components comprise antibodies or functional fragments thereof.
23. The detectable probe of claim 1 , wherein the two or more binding components comprise aptamers.
24. The detectable probe of claim 1 , wherein the binding partner comprises a polypeptide.
25. The detectable probe of claim 1 , wherein the site is separated from any site comprising a binding partner by at least 100 nm.
26. The detectable probe of claim 25 , wherein the detectable probe has a maximum length of no more than 95 nm.
27. The detectable probe of claim 1 , wherein the detectable probe is bound to the binding partner via non-covalent binding of only one of the two or more binding components to the epitope.
28. The detectable probe of claim 1 , wherein the size of the detectable probe is at most an equal size of the site in the array.