Abstract: Disclosed are compositions, systems, kits, and methods for detecting an analyte or target molecule in a sample by regulated in vitro transcription. The compositions, systems, kits, and methods typically comprise and/or utilize one or more components selected from: (a) an RNA polymerase; (b) an allosteric transcription factor (aTF), wherein the aTF binds an analyte or target molecule as a ligand; (c) an engineered transcription template; (d) a dsDNA signal gate molecule; and/or any combination thereof.

Abstract: The disclosed subject matter relates to compositions, systems, kits, and methods that typically comprise and/or utilize a lyophilized composition comprising components for performing in vitro transcription prepared by lyophilizing an aqueous composition that includes: (i) the one or more components for performing in vitro transcription; and (ii) a non-reducing polysaccharide at a concentration of at least about 40 mM and/or a sugar alcohol at a concentration of at least about 40 mM. In some embodiments, the lyophilized composition is prepared by lyophilizing an aqueous composition that comprises no more than 5% (v/v) glycerol.

Abstract: Disclosed are methods and systems for detecting fluoride as a target molecule in a test sample which utilize a cell-protein synthesis (CFPS) reaction and an engineered fluoride-sensing riboswitch. The components used in the disclosed methods and systems may be dried or lyophilized and may be present or immobilized on a paper substrate.

Abstract: Disclosed are compositions, systems, kits, and methods for detecting an analyte or target molecule in a sample by regulated in vitro transcription. The compositions, systems, kits, and methods typically comprise and/or utilize one or more components selected from: (a) an RNA polymerase; (b) an allosteric transcription factor (ATT), wherein the ATT binds an analyte or target molecule as a ligand; (c) an engineered transcription template; and/or any combination thereof. The engineered transcription template typically comprises a promoter sequence for the RNA polymerase and an operator sequence for the ATT. The promoter sequence and operator sequence are operably linked to a sequence encoding an RNA, wherein the ATT modulates transcription of the encoded RNA when the ATT binds the analyte or target molecule as a ligand, wherein the transcribed RNA generates a detectable signal in conjunction with a reporter molecule.

Abstract: Disclosed are systems and methods that include and utilize engineered riboregulated switchable feedback promoters (rSFPs). The disclosed systems and methods include and utilize as a component one or more expression cassettes. At least one expression cassette of the disclosed systems and methods comprises a promoter operably linked to DNA encoding an RNA switch located 3? of the promoter and a target gene or operon located 3? of the DNA encoding the RNA switch, where the RNA switch regulates expression of the target gene. Suitable promoters may include stress responsive promoters. The disclosed systems and methods may include and utilize a second expression cassette that includes an inducible promoter for expressing an RNA effector of the RNA switch in the first expression cassette.

Abstract: Disclosed are methods, devices, kits, components, and compositions for detecting a target molecule in a test sample using a cell-free protein synthesis (CFPS) reaction. The methods, devices, kits, components, and compositions may be utilized for detecting target molecules which may include small molecules and/or metabolites of small molecules. The components and compositions used in the disclosed methods, devices, and kits may be dried or lyophilized and may be present or immobilized on a paper substrate, for example, as a paper test article.

Abstract: Disclosed are methods, devices, kits, components, and compositions for detecting a target molecule in a test sample using a cell-free protein synthesis (CFPS) reaction. The methods, devices, kits, components, and compositions may be utilized for detecting target molecules which may include small molecules and/or metabolites of small molecules. The methods, devices, kits, components, and compositions employ one or more transcription templates that encode and conditionally express one or more exogenous RNA polymerases in the presence of the target molecule. The expressed RNA polymerases in turn induce expression of one or more reporter molecules from transcription templates comprising promoters for the RNA polymerases, thereby amplifying an output signal that is generated in the presence of a detected target molecule.

Abstract: Disclosed herein are compositions for transcriptional regulation of a target gene, and methods of using the compositions. The compositions utilize a novel antisense RNA design that activates transcription of a target gene and involve a sense genetic construct that represses transcription of the target gene, and an antisense construct selected from an antisense activating RNA, or an antisense genetic construct encoding an antisense activating RNA, that binds to the sense genetic construct RNA to relieve repression of the target gene, thus activating expression of the gene.