The present disclosure provides a method for sequencing target polynucleotide molecules. In some embodiments, the present disclosure provides a method of sequencing by synthesis where different subsets of nucleotide-conjugate complexes are sequentially formed and detected during each iterative extension of a plurality of nascent nucleic acid copy strands, where each nascent nucleic acid copy strand is complementary to one of a plurality of target polynucleotide molecules. In some embodiments, the plurality of target polynucleotide molecules are arrayed on a solid support.

Under one aspect, a composition includes a substrate; a first polynucleotide coupled to the substrate; a second polynucleotide hybridized to the first polynucleotide; and a catalyst coupled to a first nucleotide of the second polynucleotide, the catalyst being operable to cause a chemiluminogenic molecule to emit a photon. Under another aspect, a method includes providing a catalyst operable to cause a first chemiluminogenic molecule to emit a photon; providing a substrate; providing a first polynucleotide coupled to the substrate; hybridizing a second polynucleotide to the first polynucleotide; coupling a first quencher to a first nucleotide of the second polynucleotide; and inhibiting, by the first quencher, photon emission by the first chemiluminogenic molecule.

Described herein is a portable virometer for detecting viral targets. An exemplary virometer has a molecular electronics sensor with a first electrode, a second electrode spaced-apart from the first electrode by a nanogap, a bridge molecule having a first end and a second end, the first end coupled to the first electrode and the second end coupled to the second electrode, a hybridization probe having an oligonucleotide sequence from or related to a viral target is conjugated to the bridge molecule, a sample applicator for acquiring a sample and transferring it to the chip, and data processing software and hardware for providing a report of detection of viral targets. Methods of using the virometer for testing in the home, in schools, in workplaces, in hotels, in restaurants, or in public places are also described.

Described herein is a portable virometer for detecting viral targets. An exemplary virometer has a molecular electronics sensor with a first electrode, a second electrode spaced-apart from the first electrode by a nanogap, a bridge molecule having a first end and a second end, the first end coupled to the first electrode and the second end coupled to the second electrode, a hybridization probe having an oligonucleotide sequence from or related to a viral target is conjugated to the bridge molecule, a sample applicator for acquiring a sample and transferring it to the chip, and data processing software and hardware for providing a report of detection of viral targets. Methods of using the virometer for testing in the home, in schools, in workplaces, in hotels, in restaurants, or in public places are also described.

The present invention provides a method of detecting multiple analytes in a sample, wherein said analytes have varying levels of abundance in the sample, said method comprising: (i) providing multiple aliquots from the sample; and (ii) in each aliquot, detecting a different subset of the analytes by performing a separate multiplex assay for each aliquot, wherein the analytes in each subset are selected based on their predicted abundance in the sample.

The present invention provides a method of detecting multiple analytes in a sample, wherein said analytes have varying levels of abundance in the sample, said method comprising: (i) providing multiple aliquots from the sample; and (ii) in each aliquot, detecting a different subset of the analytes by performing a separate multiplex assay for each aliquot, wherein the analytes in each subset are selected based on their predicted abundance in the sample.

This disclosure provides, among other things, a reagent system for nucleic acid analysis. In some embodiments, the system may comprise a plurality of oligonucleotide sets each set comprising at least (a) a competitor oligonucleotide that hybridizes to a target sequence and varies in concentration from mixture to mixture and (b) a detector oligonucleotide that also hybridizes to the target sequence and contains a barcode that indicates the concentration of the competitor oligonucleotide in the oligonucleotide set. The reagent system may be used to analyze a nucleic acid sample.

This disclosure provides, among other things, a reagent system for nucleic acid analysis. In some embodiments, the system may comprise a plurality of oligonucleotide sets each set comprising at least (a) a competitor oligonucleotide that hybridizes to a target sequence and varies in concentration from mixture to mixture and (b) a detector oligonucleotide that also hybridizes to the target sequence and contains a barcode that indicates the concentration of the competitor oligonucleotide in the oligonucleotide set. The reagent system may be used to analyze a nucleic acid sample.

A method for seeding and amplifying target nucleic acids derived from a sample in a cluster at a site on a surface of a substrate includes retaining at least a portion of the target nucleic acids in an inactive form that cannot seed to provide a relatively low concentration of active form target nucleic acids available for seeding. As the active form target nucleic acids seed on the surface of the substrate, they may be amplified. Because the concentration of active form target nucleic acids is low, the likelihood is low that a second active form target nucleic acid will seed at the same site within the same cluster before the first active form target nucleic acid is sufficiently amplified to dominate. Accordingly, the likelihood that the cluster will pass filters is increased relative to traditional seeding and amplification methods employing a higher concentration of active form target nucleic acids.

A method for seeding and amplifying target nucleic acids derived from a sample in a cluster at a site on a surface of a substrate includes retaining at least a portion of the target nucleic acids in an inactive form that cannot seed to provide a relatively low concentration of active form target nucleic acids available for seeding. As the active form target nucleic acids seed on the surface of the substrate, they may be amplified. Because the concentration of active form target nucleic acids is low, the likelihood is low that a second active form target nucleic acid will seed at the same site within the same cluster before the first active form target nucleic acid is sufficiently amplified to dominate. Accordingly, the likelihood that the cluster will pass filters is increased relative to traditional seeding and amplification methods employing a higher concentration of active form target nucleic acids.