Quantification and spatio-temporal tracking of a target using a spherical nucleic acid (SNA)
The present invention relates to methods of detecting and tracking a target molecule using a nanoparticle wherein the nanoparticle comprises a polynucleotide that can specifically associate with the target molecule, and wherein the association results in a change in a detectable marker that can be measured after association with the target molecule.
1. A method comprising:
contacting a target polynucleotide with a composition comprising a nanoparticle under conditions that allow association of the target polynucleotide with the nanoparticle;
the nanoparticle comprising a first polynucleotide attached thereto, wherein a portion of the first polynucleotide comprises a sequence that is identical to a portion of the target polynucleotide;
the nanoparticle further comprising a second polynucleotide, wherein the second polynucleotide:
(i) comprises a marker;
(ii) is hybridized to the first polynucleotide; and
(iii) wherein hybridization of the second polynucleotide to the first polynucleotide results in an overhang of the second polynucleotide, wherein the overhang is from about 2 to about 30 nucleotides in length;
wherein association of the target polynucleotide and the nanoparticle results in:
(i) release of the second polynucleotide from the nanoparticle; and
(ii) association of the second polynucleotide and the target polynucleotide;
the association causing a detectable signal.
2. The method of claim 1 , wherein the position of the signal is determined.
3. The method of claim 1 , wherein the detectable signal is measured at time X and at time Y, wherein time Y is subsequent to time X.
4. The method of claim 3 , wherein the position of the signal is determined at time X and at time Y.
5. The method of claim 4 , wherein the change in position between time X and time Y is determined.
6. The method of claim 1 , wherein the detectable signal is measured in vitro.
7. The method of claim 1 , wherein the detectable signal is measured in a cell.
8. The method of claim 7 , wherein the cell is fixed and permeabilized.
9. The method of claim 1 , wherein the first polynucleotide and/or the second polynucleotide is DNA.
10. The method of claim 1 , wherein the first polynucleotide and/or the second polynucleotide is RNA.
11. The method of claim 1 , wherein the marker is quenched when the second polynucleotide comprising the marker is hybridized to the first polynucleotide.
12. The method of claim 1 , wherein the second polynucleotide comprises a marker which is a detectable label, wherein the marker is detectable only when the second polynucleotide is associated with the target polynucleotide.
13. The method of claim 1 , wherein the nanoparticle comprises a multiplicity of first polynucleotides and a multiplicity of second polynucleotides.
14. The method of claim 13 wherein at least one polynucleotide in the multiplicity of second polynucleotides associates with a different target polynucleotide than at least one other polynucleotide in the multiplicity of second polynucleotides.
15. The method of claim 1 , wherein the target polynucleotide is a non-coding RNA.
16. The method of claim 15 , wherein the non-coding RNA is a piwi-interacting RNA (piRNA).
17. The method of claim 1 , wherein the composition further comprises a therapeutic agent.
18. The method of claim 1 wherein the second polynucleotide hybridizes over the entire length of the first polynucleotide.
19. The method of claim 1 wherein the nanoparticle comprises about 10 second polynucleotides.
20. The method of claim 1 wherein the difference in melting temperature (T m ) between the first polynucleotide and the second polynucleotide is about 20-25° C.
21. The method of claim 1 wherein the nanoparticle comprises gold, silver copper, or platinum.
22. The method of claim 21 wherein the nanoparticle comprises gold.