Systems and methods for nucleic acid detection

A method for asymmetric CRISPR amplification to detect a target nucleic acid in a sample, the method comprising:

• (a) reacting an effective amount of a CRISPR-Cas protein, at least one crRNA, and at least one split crRNA in a sample comprising or suspected of comprising at least a first target nucleic acid for a period of time sufficient for the Cas protein to initiate a first trans-cleavage reaction involving a Cas protein/crRNA complex and a second trans-cleavage reaction involving a Cas protein/scrRNA complex;
• and
• (b) measuring the first and second signal produced in the sample in step (a);
• and
• (c) detecting the target nucleic acid in the sample based on the first and second signal measured in step (b).

An asymmetric CRISPR amplification system, comprising:

• (a) a CRISPR-Cas protein;
• (b) at least one single stranded DNA (ssDNA) probe comprising a 5′ region with a first detectable label and a 3′ region with a second detectable label;
• (c) at least one crisprRNA (crRNA) configured to simultaneously and specifically bind to the 5′ region of the ssDNA probe and a target nucleic acid;
• and
• (d) at least one split crRNA (scrRNA) configured to specifically bind to the 3′ region of the ssDNA probe.

A method for asymmetric CRISPR amplification to detect a target nucleic acid in a sample, the method comprising:

• (a) reacting an effective amount of a CRISPR-Cas protein, at least one crRNA, at least one split crRNA, and at least one ssDNA probe in a sample comprising or suspected of comprising at least a first target nucleic acid for a period of time sufficient for the Cas protein to initiate a first trans-cleavage reaction involving a Cas protein/crRNA complex and a second trans-cleavage reaction involving a Cas protein/scrRNA complex;
• (b) measuring the first and second signal produced in the sample in step (a);
• and
• (c) detecting the target nucleic acid in the sample based on the first and second signal measured in step (b).