PKR activation via hybridization chain reaction
The present application relates to the use of hybridization chain reaction (HCR) to form double stranded RNA polymers in the presence of a target, such as a nucleic acid associated with a disease or disorder. The RNA polymers are preferably able to activate the RNA-dependent kinase PKR. Activation of PKR via RNA-HCR can be used to treat a wide variety of diseases and disorders by specifically targeting diseased cells.
1. A method of activating the RNA-dependent protein kinase PKR by hybridization chain reaction (HCR), the method comprising:
contacting a sample comprising PKR with a first metastable RNA hairpin monomer comprising an initiator complement region; and
contacting the sample with a second metastable RNA hairpin monomer, wherein the second monomer comprises a propagation region that is complementary to a portion of the first monomer,
wherein a double-stranded RNA polymer comprising the first and second monomers is formed upon binding of a nucleic acid initiator to the initiator complement region and the polymer activates PKR.
2. The method of claim 1 , wherein the polymer comprises at least 35 base pairs.
3. The method of claim 1 , wherein the nucleic acid initiator is a portion of a target nucleic acid.
4. The method of claim 3 , further comprising: contacting the sample with at least one accessory molecule comprising a DNA sequence that binds to a region flanking the nucleic acid initiator.
5. The method of claim 1 , wherein the nucleic acid initiator is able to bind to the initiator complement region when a target is present in the sample.
6. The method of claim 5 , wherein the target is associated with a disease or disorder.
7. The method of claim 6 , wherein the target is an mRNA associated with a cancer.
8. The method of claim 6 , wherein the target is a viral nucleic acid.
9. The method of claim 1 , wherein the nucleic acid initiator is part of a nucleic acid probe.
10. The method of claim 9 , wherein upon binding of the nucleic acid probe to a target nucleic acid sequence the nucleic acid initiator is made available to bind to the initiator complement region of the first monomer.
11. The method of claim 10 , wherein the target is an mRNA molecule associated with a disease or disorder.
12. The method of claim 5 , wherein the nucleic acid initiator comprises a nucleic acid recognition molecule such that upon binding of the nucleic acid recognition molecule to the target the nucleic acid initiator is made available to bind to the initiator complement region of the first monomer.
13. The method of claim 12 , wherein the nucleic acid recognition molecule is an aptamer.
14. The method of claim 12 , wherein the target is a nucleic acid.
15. The method of claim 12 , wherein the target is selected from the group consisting of polypeptides, carbohydrates, lipids and small molecules.
16. A method of treating a disease or disorder, comprising:
providing a first RNA hairpin monomer to a cell comprising a target nucleic acid associated with the disease or disorder, wherein the first RNA hairpin monomer comprises an initiator complement region that is substantially complementary to a portion of the target nucleic acid; and
providing a second RNA hairpin monomer to the cell, wherein the second monomer comprises a propagation region that is substantially complementary to a portion of the first monomer;
wherein in the presence of the target nucleic acid, the portion of the target nucleic acid hybridizes to the initiator complement region and the portion of the first monomer hybridizes to the propagation region to form an RNA polymer that activates the RNA-dependent kinase PKR.
17. The method of claim 16 , wherein the disease or disorder is selected from the group consisting of cancer and HIV infection.
18. The method of claim 16 , wherein the RNA polymer comprises at least 35 base pairs.
19. A kit for activating the RNA-dependent protein kinase PKR within a sample comprising a target nucleic acid and PKR, the kit comprising:
a first RNA hairpin monomer comprising an initiator complement region; and
a second RNA hairpin monomer comprising a propagation region that is substantially complementary to a portion of the first monomer,
wherein the first RNA hairpin monomer and the second RNA hairpin monomer are configured so that, upon contact with a sample comprising a target nucleic acid and PKR, a portion of the target nucleic acid hybridizes to the initiator complement region, and the portion of the first monomer hybridizes to the propagation region to form an RNA polymer that activates PKR.
20. A method of activating a double-stranded-RNA-dependent immune response, the method comprising:
contacting a cell comprising a nucleic acid initiator with a first metastable RNA hairpin monomer that comprises a propagation region that is complementary to a portion of the nucleic acid initiator;
contacting the cell with a second metastable RNA hairpin monomer, wherein the second metastable RNA hairpin monomer comprises a propagation region that is complementary to a portion of the first metastable RNA hairpin monomer, thereby forming a double stranded RNA polymer comprising the first and second metastable RNA hairpin monomers; and
allowing the double stranded RNA polymer to activate an immune response, wherein the nucleic acid initiator will not activate the immune response without the first and second metastable RNA hairpin monomers.