Described herein are systems and methods that may be used to differentially detect viral serotype specific nucleic acid. For example, these systems may comprise multiple DNA-nanostructures, capture oligonucleotides and protector oligonucleotides, wherein each DNA-nanostructure and its associated capture oligonucleotide and protector oligonucleotide are specific for a unique viral type or serotype.

Described herein are systems and methods that may be used to differentially detect viral serotype specific nucleic acid. For example, these systems may comprise multiple DNA-nanostructures, capture oligonucleotides and protector oligonucleotides, wherein each DNA-nanostructure and its associated capture oligonucleotide and protector oligonucleotide are specific for a unique viral type or serotype.

One or more embodiments of the present invention are intended to dissolve the problem of lowering in reaction efficiency of the nucleic acid amplification reaction using a primer with a polynucleotide tag to prepare an amplified product of a target nucleic acid that can be detected on a solid-phase support. One or more other embodiments of the present invention relate to a set of primers comprising: the first primer comprising the first polynucleotide comprising, at the 3′ terminus, polynucleotide A capable of hybridizing to a complementary strand of partial polynucleotide A′ at the 5′ terminus of the target nucleic acid and the first polynucleotide tag, which is a polynucleotide independent of the nucleic acid amplification reaction; the second primer comprising the second polynucleotide comprising, at the 3′ terminus, polynucleotide B capable of hybridizing to partial polynucleotide B′ at the 3′ terminus of the target nucleic acid; and the third primer comprising the third polynucleotide hybridizing to the complementary strand of the target nucleic acid competitively with the polynucleotide A of the first primer but comprising no polynucleotide independent of the nucleic acid amplification reaction.

One or more embodiments of the present invention are intended to dissolve the problem of lowering in reaction efficiency of the nucleic acid amplification reaction using a primer with a polynucleotide tag to prepare an amplified product of a target nucleic acid that can be detected on a solid-phase support. One or more other embodiments of the present invention relate to a set of primers comprising: the first primer comprising the first polynucleotide comprising, at the 3′ terminus, polynucleotide A capable of hybridizing to a complementary strand of partial polynucleotide A′ at the 5′ terminus of the target nucleic acid and the first polynucleotide tag, which is a polynucleotide independent of the nucleic acid amplification reaction; the second primer comprising the second polynucleotide comprising, at the 3′ terminus, polynucleotide B capable of hybridizing to partial polynucleotide B′ at the 3′ terminus of the target nucleic acid; and the third primer comprising the third polynucleotide hybridizing to the complementary strand of the target nucleic acid competitively with the polynucleotide A of the first primer but comprising no polynucleotide independent of the nucleic acid amplification reaction.

In some aspects, the present disclosure relates to methods for reducing the detection of false positive ligation events. In some aspects, the method comprises use of a double split (or “split split”) probe. The methods herein have particular applicability in reducing the detection of false positive ligation events when using ligases that have high ligation efficiency but low specificity (e.g., SplintR® ligase). Also provided are kits comprising probes for use in such methods.

In some aspects, the present disclosure relates to methods for reducing the detection of false positive ligation events. In some aspects, the method comprises use of a double split (or “split split”) probe. The methods herein have particular applicability in reducing the detection of false positive ligation events when using ligases that have high ligation efficiency but low specificity (e.g., SplintR® ligase). Also provided are kits comprising probes for use in such methods.

This invention relates to methods for analyzing nucleic acids. The disclosure provides methods of a primer-dependent amplification and detection method that is capable of amplifying and detecting in a sample as few as ten copies of at least one rare intended target sequence in the presence of abundant closely related unintended target sequences. Also provided are reaction compositions and kits for performing the methods.

This invention relates to methods for analyzing nucleic acids. The disclosure provides methods of a primer-dependent amplification and detection method that is capable of amplifying and detecting in a sample as few as ten copies of at least one rare intended target sequence in the presence of abundant closely related unintended target sequences. Also provided are reaction compositions and kits for performing the methods.

In one aspect, methods of sensing are described herein. In some embodiments, such a method comprises disposing a population of luminescent species in a test sample, exposing the test sample to electromagnetic radiation having a wavelength corresponding to an excitation wavelength of the luminescent species, detecting light emitted by the luminescent species within a detection region of the test sample, and correlating the light emitted by the luminescent species within the detection region to a presence or absence of an analyte within the test sample. The luminescent species, in a non-aggregated state, exhibits luminescence blinking and, in an aggregated state, does not exhibit luminescence blinking. Additionally, correlating the light emitted by the luminescent species to the presence or absence of the analyte comprises determining whether the light emitted by the luminescent species within the detection region is blinking luminescence or non-blinking luminescence.

In one aspect, methods of sensing are described herein. In some embodiments, such a method comprises disposing a population of luminescent species in a test sample, exposing the test sample to electromagnetic radiation having a wavelength corresponding to an excitation wavelength of the luminescent species, detecting light emitted by the luminescent species within a detection region of the test sample, and correlating the light emitted by the luminescent species within the detection region to a presence or absence of an analyte within the test sample. The luminescent species, in a non-aggregated state, exhibits luminescence blinking and, in an aggregated state, does not exhibit luminescence blinking. Additionally, correlating the light emitted by the luminescent species to the presence or absence of the analyte comprises determining whether the light emitted by the luminescent species within the detection region is blinking luminescence or non-blinking luminescence.