Compositions and methods for identifying, quantifying, and/or characterizing an analyte

1. A nucleic acid probe composition comprising a first functional nucleic acid probe comprising:

a first end coupled to a quencher or a fluorophore, wherein the quencher or fluorophore is coupled directly to the first end or is coupled to the first end by a first terminal linker;

a second end coupled to a fluorophore or a quencher, wherein the quencher or fluorophore is coupled directly to the second end or is coupled to the second end by a second terminal linker; and

from the first end to the second end:

(a) a first substrate recognition sequence;

(b) a first catalytic core sequence;

(c) a second substrate recognition sequence that is also operable as a landing sequence for an enzymatic sequence;

(d) a cleavage site that can be cleaved by the enzymatic sequence;

(e) a second landing sequence for the enzymatic sequence;

(f) a linker comprising a target binding region or a spacer region comprising a target binding region; and

(g) a first inhibitory sequence that is complementary to all or some of the first substrate recognition sequence;

wherein (1) the first inhibitory sequence or (2) the first inhibitory sequence and the second terminal linker sequesters the first substrate recognition sequence when the cleavage site is uncleaved.

2. The composition of claim 1 , wherein the first substrate recognition sequence, the first catalytic core sequence, and the second substrate recognition sequence form a nucleic acid enzyme (NAE).

3. The composition of claim 2 , wherein the NAE is a 10-23 DNAzyme, an 8-17 DNAzyme, or a G-quadruplex DNAzyme.

4. The composition of claim 1 , wherein the target binding region comprises an aptamer.

5. The composition of claim 1 , further comprising a second functional nucleic acid probe comprising:

a first end coupled to a quencher or a fluorophore, wherein the quencher or fluorophore is coupled directly to the first end or is coupled to the first end by a first terminal linker; and

from the first end to a second end of the second functional nucleic acid probe:

(i) first substrate recognition sequence;

(ii) a catalytic core sequence;

(iii) a second substrate recognition sequence that is also operable as a landing sequence for an enzymatic sequence; and

(iv) a cleavage site that can be cleaved by the enzymatic sequence of (iii).

6. A method for analyzing target analytes, comprising:

(a) providing a plurality of partitions with at least one partition comprising at least one target analyte, a first functional nucleic acid probe of claim 1 , an oligonucleotide probe substrate, and constituents required for analyte binding, substrate binding, and substrate catalysis;

(b) incubating the partitions with the first functional nucleic acid probe, probe substrate, and constituents wherein at least one probe binds to the target analyte;

(c) activating a nucleic acid enzyme within the first functional nucleic acid probe that continuously catalyzes a reaction throughout the incubation, whereby the product of the reaction releases a detectable label;

(d) producing an accumulation of detectable label within the partition; and

(e) detecting the detectable label.

7. The method of claim 6 , wherein the partitions comprise droplets in an immiscible fluid.

8. The method of claim 7 , wherein the droplets are arranged in a static two-dimensional array monolayer for incubation and detection.

9. The method of claim 8 , wherein the immiscible fluid is a fluorocarbon comprising a fluorosurfactant.

10. The method of claim 8 , wherein the droplet partitions are generated using Laplace pressure gradients or shear stress.

11. The method of claim 8 , wherein detection is performed using a camera comprising a plurality of emission filters and magnifications or a plurality of light emitting diodes (LEDs) combined with a plurality of excitation filters.

12. The method of claim 6 , wherein the nucleic acid enzyme is an endonuclease.

13. The method of claim 12 , wherein the oligonucleotide probe substrate is labeled with a fluorophore and a quencher wherein the fluorophore is separated from the quencher after endonucleatic cleavage.

14. The method of claim 13 , wherein the oligonucleotide probe substrate is a stem-loop structure.

15. The method of claim 12 , wherein the first functional nucleic acid probe comprises an aptazyme, or an allosteric aptazyme.

16. The method of claim 12 , wherein the nucleic acid enzyme is a 10-23 DNAzyme or derivative thereof, or an 8-17 DNAzyme or derivative thereof, or a G-quadruplex DNAzyme or derivative thereof.

17. The method of claim 6 , wherein the partitions further comprise an environmental stressor.

18. The method of claim 17 , wherein the environmental stressor is an antimicrobial.

19. The method of claim 6 , wherein the oligonucleotide probe substrate is a cleavage-activated catalytic substrate comprising a nucleic acid enzyme encoded within an enzymatic sequence region that is partially bound to an inhibiting sequence region and when the substrate is cleaved, the inhibiting sequence region is severed from the enzymatic sequence region, liberating the nucleic acid enzyme encoded within the enzymatic sequence region.

20. The method of claim 19 , wherein an allosteric sequence region in the at least one probe binds to the target analyte, and wherein an exponential deoxyribozyme ribonuclease cleavage cascade is initiated by the liberated nucleic acid enzyme, wherein the liberated nucleic acid enzyme:

(a) binds to a loop region of the first functional nucleic acid probe; and

(b) catalyzes the cleavage of the first functional nucleic acid probe, bypassing the allosteric sequence region by severing the inhibiting sequence region from the enzymatic sequence region.