Spatial sequestration of dynamic nucleic acid circuits

1. A synthetic system comprising

(a) a first three-dimensional nucleic acid nanostructure shaped in the form of a container comprising walls, an interior surface and an exterior surface,

(b) a first tethered nucleic acid attached to the interior surface of the first three-dimensional nucleic acid nanostructure and partially hybridized to a first output signal nucleic acid, wherein the first tethered nucleic acid contains a toehold domain that is not complementary to the first output signal nucleic acid,

(c) a second three-dimensional nucleic acid nanostructure shaped in the form of a container comprising walls, an interior surface and an exterior surface, and

(d) a second tethered nucleic acid attached to the interior surface of the second three-dimensional nucleic acid nanostructure and partially hybridized to a second output signal nucleic acid, wherein the second tethered nucleic acid contains a toehold domain that is not complementary to the second output signal nucleic acid, and

wherein the toehold domain of the second tethered nucleic acid is complementary to a domain of the first output signal nucleic acid.

2. The system of claim 1 , wherein the first and second tethered nucleic acids are not integral to the first and second nucleic acid nanostructures.

3. The system of claim 1 , wherein the first and second nucleic acid nanostructures are independently selected from the group consisting of closed nucleic acid nanostructures and open nucleic acid nanostructures.

4. The system of claim 3 , wherein the open nucleic acid nanostructures comprise two open ends.

5. The system of claim 3 , wherein the closed nucleic acid nanostructures comprise a nucleic acid lock.

6. The system of claim 1 , further comprising one or more upstream and/or downstream nucleic acid nanostructures.

7. The system of claim 6 , wherein the one or more of the upstream and/or downstream nucleic acid nanostructures comprise tethered nucleic acid.

8. A method comprising

contacting a first input signal nucleic acid with the system of claim 1 in an amount effective to release the second output signal nucleic acid from the second nucleic acid nanostructure.

9. The system of claim 6 , wherein the one or more of the upstream and/or downstream nucleic acid nanostructures comprise free flowing nucleic acids.

10. The system of claim 9 , wherein the free flowing nucleic acids are output signal nucleic acids.

11. The system of claim 1 , wherein the first nucleic acid nanostructures and/or the second nucleic acid nanostructure comprises an agent.

12. The system of claim 11 , wherein the agent is or comprises a therapeutic agent.

13. The system of claim 11 , wherein the agent is or comprises a detectable marker.

14. The system of claim 1 , wherein the first nucleic acid nanostructures and/or the second nucleic acid nanostructure comprises a plurality of tethered nucleic acids.

15. The system of claim 1 , wherein the first nucleic acid nanostructures and/or the second nucleic acid nanostructure comprises a plurality of free flowing nucleic acids.

16. The system of claim 1 , wherein the length of the toehold domain of the first tethered nucleic acid is 4-12 nucleotides.

17. The system of claim 1 , wherein the length of the toehold domain of the second tethered nucleic acid is 4-12 nucleotides.

18. The system of claim 1 , wherein the first nucleic acid nanostructure is a deoxyribonucleic acid (DNA) nanostructure.

19. The system of claim 1 , wherein the second nucleic acid nanostructure is a DNA nanostructure.