The invention relates to a method of performing in situ hybridization such as fluorescence in situ hybridization (FISH) using liposomal spherical nucleic acids (L-SNAs) nanoparticles labeled with dye molecules. The nanoparticles contain one or more nucleic acids that recognize a target of interest in a sample.

The invention relates to a method of performing in situ hybridization such as fluorescence in situ hybridization (FISH) using liposomal spherical nucleic acids (L-SNAs) nanoparticles labeled with dye molecules. The nanoparticles contain one or more nucleic acids that recognize a target of interest in a sample.

The present invention provides methods for immobilizing target nucleic acids on a solid support utilizing combinatorial capture probe pairs. These pairs contain first and second capture oligonucleotides that each comprise a target binding region, a capture region and a stem region positioned between the target binding and capture regions. The target binding regions comprise nucleic acid sequences that allow them to hybridize to adjacent regions on the target nucleic acid. The stem regions have nucleic acid sequences that are complementary to each other and the capture regions each comprise a sequence that when positioned adjacent to one another produce a combined nucleic acid sequence that is complementary to a portion of an oligonucleotide bound to a solid support. When the first and second capture oligonucleotides are annealed to the target nucleic acid, the stem regions are brought together allowing them to hybridize, which in turn brings the capture regions together to produce a combined nucleic acid sequence. This combined nucleic acid sequence is then able to hybridize to the oligonucleotide bound to the solid support thereby immobilizing the target nucleic acid.

The present invention provides methods for immobilizing target nucleic acids on a solid support utilizing combinatorial capture probe pairs. These pairs contain first and second capture oligonucleotides that each comprise a target binding region, a capture region and a stem region positioned between the target binding and capture regions. The target binding regions comprise nucleic acid sequences that allow them to hybridize to adjacent regions on the target nucleic acid. The stem regions have nucleic acid sequences that are complementary to each other and the capture regions each comprise a sequence that when positioned adjacent to one another produce a combined nucleic acid sequence that is complementary to a portion of an oligonucleotide bound to a solid support. When the first and second capture oligonucleotides are annealed to the target nucleic acid, the stem regions are brought together allowing them to hybridize, which in turn brings the capture regions together to produce a combined nucleic acid sequence. This combined nucleic acid sequence is then able to hybridize to the oligonucleotide bound to the solid support thereby immobilizing the target nucleic acid.

Methods and systems including a set of interacting nucleic acid structures for use in detecting and/or identifying a target comprising: a nucleic acid sequence capable of being conjugated to a moiety directed to the target; and a nucleic acid nanostructure comprising a segment sequence complementary to a portion of the nucleic acid sequence capable of being conjugated to a moiety directed to the target. The moiety directed to the target may be an antibody, and the nucleic acid nanostructure may be a tetrahedron.

Methods and systems including a set of interacting nucleic acid structures for use in detecting and/or identifying a target comprising: a nucleic acid sequence capable of being conjugated to a moiety directed to the target; and a nucleic acid nanostructure comprising a segment sequence complementary to a portion of the nucleic acid sequence capable of being conjugated to a moiety directed to the target. The moiety directed to the target may be an antibody, and the nucleic acid nanostructure may be a tetrahedron.

Described herein are compositions that may be used to detect viral nucleic acid. For example, these compositions may comprise a DNA-nanostructure, a capture oligonucleotide and a protector oligonucleotide, wherein the components are designed based on a duo-toehold-mediated displacement reaction (duo-TMDR) strategy. In this strategy, a first TMDR can switch off a Faster resonance energy transfer (FRET) process and a second TMDR can release the target viral nucleic acid and amplify the signal. Methods of using such compositions are also provided herein.

Described herein are compositions that may be used to detect viral nucleic acid. For example, these compositions may comprise a DNA-nanostructure, a capture oligonucleotide and a protector oligonucleotide, wherein the components are designed based on a duo-toehold-mediated displacement reaction (duo-TMDR) strategy. In this strategy, a first TMDR can switch off a Faster resonance energy transfer (FRET) process and a second TMDR can release the target viral nucleic acid and amplify the signal. Methods of using such compositions are also provided herein.

Bistable devices are constructed using a polynucleotide platform for the sensing of molecular events such as binding or conformational changes of target molecules. Uses include measurement of target concentration, measuring the effect of environmental condition (such as heat, light, or pH) on the target, or screening a library for molecules that bind the target or modulate its biological function. Devices comprise three regions: a top lid, bottom lid, and flexible linker or hinge between them. A device has an open configuration in which the top and bottom lid are separated, and a closed configuration they are bound close together. Binding domains or variations of the target molecule are fixed to a device so that when the molecular event occurs, the device switches from open to closed, or vice versa, which generates a signal. Devices carry DNA tags to enable separation of open and closed devices, as well as barcoding for multiplexed detection.

The present invention discloses a method for detecting the mutation and methylation of tumor-specific genes in ctDNA, and this method can simultaneously detect the mutation (including point mutation, insertion-deletion mutation, HBV integration and other mutation forms) and/or methylation of tumor-specific genes in ctDNA in one sample. Not only the sample size requirement is low, but the MC library prepared by this method can support 10-20 subsequent detections. The results of each test can represent the mutation status of all the original ctDNA specimens and the methylation modification status of the region covered by the restriction sites, without reducing the sensitivity and specificity. The present invention has important clinical significance for early tumor screening, disease tracking, efficacy evaluation, prognosis prediction and the like, and has great application value.