Method of analysis for alleles of a target. In the method, a plurality of fluid volumes may be formed. Each fluid volume may contain a first primer pair to amplify a first allele of a target, a second primer pair to amplify a second allele of the target, a first reporter including a first photoluminophore and providing a primer of the first primer pair, and a second reporter including a second photoluminophore and providing a primer of the second primer pair. Each of the first and second reporters may include an oligomer having a quencher, and the oligomer may be configured to base-pair with the primer of the first primer pair and the primer of the second primer pair. The first and second alleles may be amplified using the first and second primer pairs. Photoluminescence may be detected. A level of each allele may be determined.

Method of analysis for alleles of a target. In the method, a plurality of fluid volumes may be formed. Each fluid volume may contain a first primer pair to amplify a first allele of a target, a second primer pair to amplify a second allele of the target, a first reporter including a first photoluminophore and providing a primer of the first primer pair, and a second reporter including a second photoluminophore and providing a primer of the second primer pair. Each of the first and second reporters may include an oligomer having a quencher, and the oligomer may be configured to base-pair with the primer of the first primer pair and the primer of the second primer pair. The first and second alleles may be amplified using the first and second primer pairs. Photoluminescence may be detected. A level of each allele may be determined.

Methods, compositions, reaction mixtures, kits, and/or systems for producing a complementary sequence to a region in a target polynucleotide in a sample are provided. In some aspects, the methods, compositions, reaction mixtures, kits, and/or systems comprise subjecting the sample to a nucleic acid amplification reaction in a reaction mixture under conditions to yield the complete sequence to the region of the target polynucleotide. In some aspects, the complementary sequence produced is amplified.

Methods, compositions, reaction mixtures, kits, and/or systems for producing a complementary sequence to a region in a target polynucleotide in a sample are provided. In some aspects, the methods, compositions, reaction mixtures, kits, and/or systems comprise subjecting the sample to a nucleic acid amplification reaction in a reaction mixture under conditions to yield the complete sequence to the region of the target polynucleotide. In some aspects, the complementary sequence produced is amplified.

A method for generating labelled amplification fragments of a nucleic acid template including the steps of providing a template nucleic acid, annealing at least one oligonucleotide primer to the template nucleic acid, elongating the at least one oligonucleotide primer in a template specific manner thereby creating an elongation product, wherein said elongating reaction stops when the elongation product reaches the 5′ end of the template nucleic acid or a nucleic acid elongation stopper that is annealed to the template nucleic acid downstream of the elongation product, providing an adaptor nucleic acid that has an identification sequence on its 5′ end, wherein the identification sequence does not hybridize to the elongation stopper when in contact thereto, and ligating the adaptor nucleic acid at its 5′ end to the 3′ end of the elongation product, thereby generating a labelled amplification fragment.

A method for generating labelled amplification fragments of a nucleic acid template including the steps of providing a template nucleic acid, annealing at least one oligonucleotide primer to the template nucleic acid, elongating the at least one oligonucleotide primer in a template specific manner thereby creating an elongation product, wherein said elongating reaction stops when the elongation product reaches the 5′ end of the template nucleic acid or a nucleic acid elongation stopper that is annealed to the template nucleic acid downstream of the elongation product, providing an adaptor nucleic acid that has an identification sequence on its 5′ end, wherein the identification sequence does not hybridize to the elongation stopper when in contact thereto, and ligating the adaptor nucleic acid at its 5′ end to the 3′ end of the elongation product, thereby generating a labelled amplification fragment.

In a case where the target (30) is not supplied, binding through a nucleic acid sequence from the base end on a side of the solid phase surface of the complementary sequence complementary to a part of the nucleic acid sequence of the detection sequence to the other base end is maintained, which causes fluorescence of the fluorescent molecule (11) to be quenched by the quenching molecule (21) close to the fluorescent molecule (11). In a case where the target (30) is supplied, the target is bound to the detection sequence and the binding through the complementary sequence is released, which causes the fluorescent molecule (11) to separate from the quenching molecule (21) and emit fluorescence.

In a case where the target (30) is not supplied, binding through a nucleic acid sequence from the base end on a side of the solid phase surface of the complementary sequence complementary to a part of the nucleic acid sequence of the detection sequence to the other base end is maintained, which causes fluorescence of the fluorescent molecule (11) to be quenched by the quenching molecule (21) close to the fluorescent molecule (11). In a case where the target (30) is supplied, the target is bound to the detection sequence and the binding through the complementary sequence is released, which causes the fluorescent molecule (11) to separate from the quenching molecule (21) and emit fluorescence.

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.