Fluorescence resonance energy transfer (FRET)-based nucleic acid sensors and methods of their use for detecting nucleic acids are provided. The sensors are highly sensitive and detect nucleic acids at the femtomolar (fM) level, without the need for labeling and amplification.

In certain aspects, the invention disclosed herein relates to the isothermal amplification of probe linkage products to generate specific amplified signals. In some aspects, the invention provides methods, reagents, and kits for carrying out such amplification via the isothermal chain reaction (ICR).

In certain aspects, the invention disclosed herein relates to the isothermal amplification of probe linkage products to generate specific amplified signals. In some aspects, the invention provides methods, reagents, and kits for carrying out such amplification via the isothermal chain reaction (ICR).

A multiplex assay for nucleic acid detection includes a substrate, a sample, and a fluorophore-labeled oligonucleotide. The substrate has a plurality of physically separated assay locations, each of which includes a nucleotide-targeting enzyme configured to cleave nucleic acids, a guide ribonucleic acid (gRNA), and a quencher-labeled oligonucleotide. A portion of the sample is distributed to each assay location. The gRNA recognizes target nucleic acid in the sample, thereby activating the nucleotide-targeting enzyme to cleave nucleic acids, including the quencher-labeled oligonucleotide. The fluorophore-labeled oligonucleotide is subsequently added to each assay location, which facilitates identification of a presence of the target nucleic acid in the sample via detection of unquenched light emitted by the fluorophore in one or more of the plurality of assay locations.

A multiplex assay for nucleic acid detection includes a substrate, a sample, and a fluorophore-labeled oligonucleotide. The substrate has a plurality of physically separated assay locations, each of which includes a nucleotide-targeting enzyme configured to cleave nucleic acids, a guide ribonucleic acid (gRNA), and a quencher-labeled oligonucleotide. A portion of the sample is distributed to each assay location. The gRNA recognizes target nucleic acid in the sample, thereby activating the nucleotide-targeting enzyme to cleave nucleic acids, including the quencher-labeled oligonucleotide. The fluorophore-labeled oligonucleotide is subsequently added to each assay location, which facilitates identification of a presence of the target nucleic acid in the sample via detection of unquenched light emitted by the fluorophore in one or more of the plurality of assay locations.

The invention pertains to methods for measuring DNA repair capacity of a test solution, for example, a cell lysate. The method can comprise incubating the test solution with a damaged DNA molecule and measuring the damaged DNA remaining at the end of the incubation. The damaged DNA used in the method comprises a marker attached to a first strand of the damaged DNA and a quencher attached to a second strand of the damaged DNA, characterized in that the quencher inhibits the release of a detectable signal from the marker when damaged DNA is in a double stranded form and the marker emits the detectable signal when at least a portion of the damaged DNA is in a single stranded form. The invention also provides screening assays for identifying one or more compounds from a plurality of compounds as an inhibitor of DNA repair mechanism.

The invention pertains to methods for measuring DNA repair capacity of a test solution, for example, a cell lysate. The method can comprise incubating the test solution with a damaged DNA molecule and measuring the damaged DNA remaining at the end of the incubation. The damaged DNA used in the method comprises a marker attached to a first strand of the damaged DNA and a quencher attached to a second strand of the damaged DNA, characterized in that the quencher inhibits the release of a detectable signal from the marker when damaged DNA is in a double stranded form and the marker emits the detectable signal when at least a portion of the damaged DNA is in a single stranded form. The invention also provides screening assays for identifying one or more compounds from a plurality of compounds as an inhibitor of DNA repair mechanism.

Provided herein are methods and systems for sequencing a single nucleic acid molecule utilizing a polymerase enzyme, a template nucleic acid, and a polymerase reagent solution.

Provided herein are methods and systems for sequencing a single nucleic acid molecule utilizing a polymerase enzyme, a template nucleic acid, and a polymerase reagent solution.

Sandwich separation is based on forming a sandwich complex with a magnetic bead, buoyant bead, and a target. Once a sandwich formation is created, the sandwich can be separated using its dual physical properties, namely magnetism and buoyancy. Sandwich separation is highly specific, allows for removal of the beads that do not have any attached target, and reduces the number of background beads. Sandwich separation can also be used to allow for target detection in raw specimen. Also, improvement of detection capability is accomplished by performing AMBR measurements on a solid interface, where the rotational period speeds up and allows for dramatically reduced time-to-result.