DNA-cage erasable labels for fluorescence-based pathology

1. A labeling system, comprising

a nanocage assembly comprising a nanoparticle loaded with one or a plurality of imaging agents that is encapsulated by a DNA or RNA nanocage,

a single stranded oligonucleotide erasing molecule, and

optionally a plurality of single stranded oligonucleotide targeting molecules,

wherein the nanocage comprises a plurality of single stranded DNA (ssDNA) or single stranded RNA (ssRNA) targeting arms,

wherein the targeting arms are complementary to both the erasing molecule and either a DNA or RNA target or the targeting oligonucleotide, but has a higher complementarity and affinity for the oligonucleotide erasing molecule, or

wherein either the DNA or RNA target or the targeting molecule comprises a nucleic acid sequence that is complementary to both the targeting arm and the erasing molecule but has a higher complementarity and affinity for the oligonucleotide erasing molecule.

2. The system of claim 1 , wherein the targeting molecule is conjugated to a targeting agent.

3. The system of claim 2 , wherein the targeting agent is an antibody or aptamer.

4. The system of claim 1 , wherein the nanocage comprises a plurality of DNA or RNA oligomers, wherein each oligomer comprises at least three ssDNA oligonucleotides self-assembled to form at least three arms, wherein at least two of the arms terminate as ssDNA sticky ends that are complementary to each other, wherein the nanocage comprises a plurality of the oligomers linked by the sticky ends, and wherein a portion of the oligomers comprise at least one arm that terminates as the targeting arm.

5. The system of claim 4 , wherein the portion of oligomers that comprise at least one are that terminates as the targeting arm comprises about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50% or more of the total oligomers.

6. The system of claim 1 , wherein the imaging agent comprises a chromophore, fluorophore, or quantum dot.

7. A method for labeling of a sample, comprising

(a) providing a first nanocage assembly comprising a nanoparticle loaded with, bound to, or adsorbed with an imaging agent and encapsulated in a DNA or RNA nanocage, wherein the nanocage comprises a first targeting arm that selectively binds a first DNA or RNA target;

(b) providing a second nanocage assembly comprising a nanoparticle loaded with, bound to, or adsorbed with an imaging agent and encapsulated in a DNA or RNA nanocage, wherein the nanocage comprises a second targeting arm that selectively binds a second DNA or RNA target;

(c) providing a first oligonucleotide erasing molecule comprising a nucleic acid sequence that is complementary to either the first DNA or RNA target or the first targeting arm;

(d) optionally providing a second oligonucleotide erasing molecule comprising a nucleic acid sequence that is complementary to either the second DNA or RNA target or the second targeting arm;

(e) contacting the sample with the first nanocage assembly under conditions suitable for binding of the targeting arm of the first nanocage assembly to the first DNA or RNA target;

(f) imaging the sample for the imaging agents;

(g) contacting the sample with the first erasing molecule under conditions suitable for binding of the erasing molecule to either the first DNA or RNA target or the first targeting arm;

(h) washing away the first nanocage assembly;

(i) contacting the sample with the second nanocage assembly under conditions suitable for binding of the targeting arm of the second nanocage assembly to the second DNA or RNA target;

(j) imaging the sample for the imaging agents;

(k) optionally contacting the sample with the second erasing molecule under conditions suitable for binding of the erasing molecule to either the second DNA or RNA target or the second targeting arm; and

(l) optionally washing away the second nanocage assembly.

8. A method for labeling of a sample, comprising

(a) providing a first targeting agent that selectively binds a first target in the sample, wherein the first targeting agent is conjugated to a first single stranded oligonucleotide targeting molecule;

(b) providing a second targeting agent that selectively binds a second target in the sample, wherein the second targeting agent is conjugated to a second single stranded oligonucleotide targeting molecule;

(c) providing a first nanocage assembly comprising a nanoparticle loaded with, bound to, or adsorbed with an imaging agent and encapsulated in a DNA or RNA nanocage, wherein the nanocage comprises a first targeting arm that selectively binds the first targeting molecule;

(d) providing a second nanocage assembly comprising a nanoparticle loaded with, bound to, or adsorbed with an imaging agent and encapsulated in a DNA or RNA nanocage, wherein the nanocage comprises a second targeting arm that selectively binds the second targeting molecule;

(e) providing a first oligonucleotide erasing molecule comprising a nucleic acid sequence that is complementary to either the first targeting molecule or the first targeting arm;

(f) optionally providing a second oligonucleotide erasing molecule comprising a nucleic acid sequence that is complementary to either the second targeting molecule or the second targeting arm;

(g) contacting the sample with the first targeting agent under conditions suitable for the first targeting agent to selectively bind the first target in the sample;

(h) contacting the sample with a second targeting agent under conditions suitable for the second targeting agent to selectively bind the second target in the sample;

(i) contacting the sample with the first nanocage assembly under conditions suitable for binding of the targeting arm of the first nanocage assembly to the targeting molecule of the first targeting agent;

(j) imaging the sample for the imaging agents;

(k) contacting the sample with the first erasing molecule under conditions suitable for binding of the erasing molecule to either the first targeting molecule or the first targeting arm;

(l) washing away the first nanocage assembly;

(m) contacting the sample with the second nanocage assembly under conditions suitable for binding of the targeting arm of the second nanocage assembly to the targeting molecule of the second targeting agent;

(n) imaging the sample for the imaging agents;

(o) optionally contacting the sample with the second erasing molecule under conditions suitable for binding of the erasing molecule to either the second targeting molecule or the second targeting arm; and

(p) optionally washing away the second nanocage assembly.

9. The method of claim 6 , further comprising

(a) providing a third targeting agent that selectively binds a third target in the sample, wherein the third targeting agent is conjugated to a third single stranded oligonucleotide targeting molecule;

(b) providing a third nanocage assembly comprising a nanoparticle loaded with, bound to, or adsorbed with one or a plurality of imaging agents and encapsulated in a DNA or RNA nanocage, wherein the nanocage comprises a third targeting arm that selectively binds the third targeting molecule;

(c) optionally providing a third erasing molecule comprising a nucleic acid sequence that is complementary to either the third targeting molecule or the third targeting arm;

(d) contacting the sample with a third targeting agent under conditions suitable for the third targeting agent to selectively bind the third target in the sample;

(e) contacting the sample with the third nanocage assembly under conditions suitable for binding of the targeting arm of the third nanocage assembly to the targeting molecule of the third targeting agent;

(f) imaging the sample for the imaging agents;

(g) optionally contacting the sample with the third erasing molecule under conditions suitable for binding of the erasing molecule to either the third targeting molecule or the third targeting arm; and

(h) optionally washing away the third nanocage assembly.