Abstract: The present disclosure describes various improvements for programmable nuclease-based detection assays. Also provided are compositions, methods, kits, systems, and devices for practicing the same. Such improvements include improved reporter designs to facilitate the cleavage of a reporter immobilized on a substrate by an activated programmable nuclease. Improved reporter designs may comprise various lengths and structures of the reporter. The substrate can also comprise immobilized guide nucleic acids and/or programmable nucleases.

Abstract: The present disclosure provides various systems, diagnostic devices, and methods for nucleic acid analysis. The systems, devices, and methods allow for the analysis of nucleic acids, in a sample, via programmable nuclease-based assays. Provided are systems comprising an instrument and a cartridge allowing for point of care use. The systems, devices, and methods described herein can be configured for multiplexed detection of nucleic acids in a single sample.

Abstract: Disclosed herein are systems and methods for providing a high-throughput DETECTR assay in a single chamber. The single chamber may be one well of a microplate, and multiple assays may be conducted in a staggered fashion in separate chambers. The methods described herein implement a process including lysing a sample, isolating nucleic acid molecules, eluting the nucleic acid molecules, amplifying the nucleic acid molecules, and detecting a presence of a target nucleic acid.