Regulated multiplex reactions in a single tube

1. A reaction system comprising:

a single reaction compartment comprising:

a first set of reaction components comprising Cas endonuclease proteins and guide RNAs that together form a complex that target sequences that flank a target nucleic acid, thereby protecting the target nucleic acid, if present in the compartment, from exonuclease digestion and an exonuclease,

wherein the first set of reaction components are active at a first temperature and inactive at a second higher temperature; and

a second set of reaction components comprising primers and a thermostable polymerase active at the second temperature and inactive at the first temperature, wherein the first and second set of reaction components may be independently activated and/or deactivated by a change in the temperature of the compartment.

2. The system of claim 1 , wherein the compartment comprises a sample tube.

3. The system of claim 1 , wherein the first and second set of reaction components are packaged together within a sample tube.

4. The system of claim 1 , wherein when a sample comprising target nucleic acid and non-target nucleic acid is added to the reaction compartment and heated to the first temperature, the first set of reaction components digests the non-target nucleic acid, and when the reaction compartment is heated to a second temperature, the second set of reaction components synthesizes a copy of the target nucleic acid.

5. The system of claim 1 , wherein, when a sample comprising target nucleic acid and non-target nucleic acid is added to the reaction compartment, the reaction compartment may be sealed and brought to a first temperature at which the first set of reaction components degrades the non-target nucleic acid and protects the target nucleic acid and then the reaction compartment may, without unsealing the reaction compartment, be brought to a second temperature at which the second set of reaction components synthesizes a copy of the target nucleic acid.

6. The system of claim 1 , wherein the Cas endonuclease proteins are complexed with the guide RNAs as ribonucleoproteins and the primers include phosphorothioate linkages rendering the primers resistant to digestion by the exonuclease.

7. The system of claim 1 , wherein the first set of reaction components and the second set of reaction components are pre-packaged into the reaction compartment, and the reaction compartment is a sample tube or a well of a multi-well plate.

8. The system of claim 1 , wherein the reaction compartment is provided as a sample tube or a well of a multi-well plate containing therein the first and second set of reaction components, each present in the form of one or more beads or particles, wherein the first set of reaction components includes: at least one active or catalytically-inactive Cas endonuclease complexed with a guide RNA that targets the Cas endonuclease to sequences that flank a target nucleic acid, and exonuclease; and the second set of reaction components includes:

at least one exonuclease resistant primer that hybridizes to the target nucleic acid and polymerase.

9. The system of claim 8 , wherein the first set of reaction components is active between about 30 and 45 degrees C. and the second set of reaction components is active between about 80 and 105 degrees C.

10. The system of claim 8 , wherein the first and second set of reaction components are present as lyophilized particles or provided by hydrogel beads.