Abstract: Methods and compositions for detecting the presence of a pathogen are described. In particular, this document provides a method of detecting a pathogen-associated nucleic acid in a biological sample of a subject, where the method comprises using one or more unimolecular aptamer-based sensors comprising an aptamer-fluorophore complex and an amplification step to detect the pathogen-associated nucleic acid. Methods specific for detecting the presence of malaria and other mosquito-borne virus infections are also provided.

Abstract: Provided herein are methods and compositions for rapid, highly sensitive detection of SARS-CoV-2, the causative agent of the COVID-19 pandemic or other target nucleic acids. The methods are low-cost and can be implemented in a portable format that does not require elaborate biosafety precautions or sophisticated laboratory equipment.

Abstract: Methods and compositions for detecting the presence of a pathogen are described. In particular, this document provides a method of detecting a pathogen-associated nucleic acid in a biological sample of a subject, where the method comprises using one or more unimolecular aptamer-based sensors comprising an aptamer-fluorophore complex and an amplification step to detect the pathogen-associated nucleic acid. Methods specific for detecting the presence of malaria and other mosquito-borne virus infections are also provided.

Abstract: Ultraspecific, programmable nucleic acid sensors capable of detecting and preferentially amplifying target DNA molecules comprising a particular SNP or mutation are provided. In some cases, the ultraspecific programmable nucleic acid sensors are useful for detecting SNP-containing DNA molecules indicative of cancer such as cell-free DNA circulating in the blood or indicative of organ transplant rejection Also provided are methods for construction of such ultraspecific nucleic acid sensors and methods for preferential amplification of target DNA molecules containing a mutation of interest, as well as testing systems for early cancer screening and routine monitoring of circulating cancer DNA using liquid biological samples such as serum, plasma, or saliva.

Abstract: Ultraspecific, programmable nucleic acid sensors capable of detecting and preferentially amplifying target DNA molecules comprising a particular SNP or mutation are provided. In some cases, the ultraspecific programmable nucleic acid sensors are useful for detecting SNP-containing DNA molecules indicative of cancer such as cell-free DNA circulating in the blood or indicative of organ transplant rejection Also provided are methods for construction of such ultraspecific nucleic acid sensors and methods for preferential amplification of target DNA molecules containing a mutation of interest, as well as testing systems for early cancer screening and routine monitoring of circulating cancer DNA using liquid biological samples such as serum, plasma, or saliva.

Abstract: Ultraspecific, programmable nucleic acid sensors capable of detecting and preferentially amplifying target DNA molecules comprising a particular SNP or mutation are provided. In some cases, the ultraspecific programmable nucleic acid sensors are useful for detecting SNP-containing DNA molecules indicative of cancer such as cell-free DNA circulating in the blood or indicative of organ transplant rejection Also provided are methods for construction of such ultraspecific nucleic acid sensors and methods for preferential amplification of target DNA molecules containing a mutation of interest, as well as testing systems for early cancer screening and routine monitoring of circulating cancer DNA using liquid biological samples such as serum, plasma, or saliva.

Abstract: Provided herein is a RNA-based riboregulator that detects protein translation and uses this stimulus to regulate expression of an unrelated protein. In one embodiment, provided herein is a synthetic nucleic acid molecule configured as a translation-sensing riboregulator, where the synthetic nucleic acid molecule comprises a first nucleotide sequence encoding a polypeptide, a translation-sensing riboswitch (TSR), and a second nucleotide sequence encoding a polypeptide, wherein the translation-sensing riboswitch comprises a stop codon of the first nucleotide sequence, a fully or partially double-stranded stem-forming domain, and translation initiation elements of the second nucleotide sequence.

Abstract: Methods and compositions for detecting the presence of a pathogen are described. In particular, this document provides a method of detecting a pathogen-associated nucleic acid in a biological sample of a subject, where the method comprises using one or more unimolecular aptamer-based sensors comprising an aptamer-fluorophore complex and an amplification step to detect the pathogen-associated nucleic acid. Methods specific for detecting the presence of malaria and other mosquito-borne virus infections are also provided.

Abstract: Provided herein is a RNA-based riboregulator that detects protein translation and uses this stimulus to regulate expression of an unrelated protein. In one embodiment, provided herein is a synthetic nucleic acid molecule configured as a translation-sensing riboregulator, where the synthetic nucleic acid molecule comprises a first nucleotide sequence encoding a polypeptide, a translation-sensing riboswitch (TSR), and a second nucleotide sequence encoding a polypeptide, wherein the translation-sensing riboswitch comprises a stop codon of the first nucleotide sequence, a fully or partially double-stranded stem-forming domain, and translation initiation elements of the second nucleotide sequence.