Abstract: Methods are provided for determining a primer set for amplifying a target nucleic acid, as well as apparatuses and computer-readable storage media configured to perform aspects of the methods. In some cases, the methods include obtaining a first primer set; generating multiple child primer sets by performing modifications to the first primer set; and, for each of the child primer sets, determining a fitness score of the child primer set and, if the fitness score is at or above a predetermined threshold, determining the child primer set to be an acceptable primer set and adding the child primer set to a collection of acceptable primer sets stored in a memory device. The generating may generate at least some of the child primer sets in parallel. Multiple collections of acceptable primer sets may be generated in parallel. Various aspects of the methods may be controlled by a genetic algorithm.

Abstract: The disclosure relates, in part, to a method for detecting an analyte in a sample, comprising: contacting a substrate construct with a sample that may comprise the analyte, and using evanescent wave imaging to detect the analyte.

Abstract: The disclosure is directed to a compound of formula III: wherein: X is a heteroatom; Base is a nucleobase; R1 and R2 are each independently selected from the group consisting of H, CF3, CN, a C1-C12 straight chain or branched alkyl, a C2-C12 straight chain or branched alkenyl or polyenyl, a C2-C12 straight chain or branched alkynyl or polyalkynyl, a C1-C12 ether, and an aromatic group (e.g., a phenyl, a naphthyl, a pyridine), with the proviso that at least one of R1 and R2 is CF3, CN, a C1-C12 straight chain or branched alkyl, a C2-C12 straight chain or branched alkenyl or polyenyl, a C2-C12 straight chain or branched alkynyl or polyalkynyl, a C1-C12 ether, or an aromatic group (e.g., a phenyl, a naphthyl, a pyridine); R3 is NO2; R4 is H; R5 comprises a C1-C12 alkyne, an amide, and/or an amine; R6 is OMe or S—C6H6; and R7 is H or NO2.

Abstract: The disclosure is directed to a method for preparing a sample for evanescent wave imaging, comprising: isothermally amplifying a target nucleic acid present in the sample in a reservoir to produce one or more amplicons, wherein the one or more amplicons are immobilized to a bottom surface of the reservoir; and contacting the one or more amplicons with an aqueous solution comprising sequencing reagents comprising a pool of 3?-unblocked protected nucleotides.

Abstract: The disclosure is directed to (i) controlling a first light source to emit a first light into a substrate on which substrate polynucleotides are immobilized, wherein a plurality of substrate polynucleotides are each annealed to a sequencing primer and bound with a polymerase, wherein the substrate polynucleotides are in a presence of a pool of protected nucleotides, and wherein each protected nucleotide comprises a detectable moiety and a photocleavable terminating moiety; (ii) processing a fluorescence signal to identify protected nucleotides incorporated in the sequencing primers; (iii) controlling a second light source to emit a second light into the substrate to cleave the detectable moieties from the incorporated protected nucleotides; (iv) determining one of both of: a percentage of the sequencing primers that incorporated a protected nucleotide and a percentage of the detectable moieties cleaved from the incorporated protected nucleotides; and (v) modifying one or more parameters of a sequencing primer

Abstract: The disclosure is directed to a method for nucleic acid sequencing, comprising: contacting a substrate polynucleotide immobilized to a substrate with a protected nucleotide and a sequencing primer in a presence of a polymerase such that the polymerase incorporates the protected nucleotide into the sequencing primer, wherein the protected nucleotide comprises a detectable moiety and a photocleavable terminating moiety; using evanescent wave imaging to identify the protected nucleotide incorporated into the sequencing primer; and using evanescent wave imaging to cleave the photocleavable terminating moiety of the protected nucleotide.

Abstract: The disclosure is directed to a method for nucleic acid sequencing, comprising: using evanescent wave imaging to identify a 3?-unblocked protected nucleotide incorporated into a sequencing primer.

Abstract: The disclosure is directed to an imaging device comprising: a reservoir having an interior lower surface; a substrate arranged below the reservoir, wherein at least a portion of an upper surface of the substrate forms the interior lower surface of the reservoir; a first light source arranged proximate to the substrate and configured to direct light into the substrate; an image sensor arranged below the substrate and configured to receive emission light produced within the reservoir.

Abstract: Aspects of the disclosure relate to compositions and methods for amplifying and/or detecting one or more target nucleic acid sequences (e.g., a nucleic acid sequence of one or more pathogens) in a biological sample obtained from a subject. In some embodiments, the pathogens are viral, bacterial, fungal, parasitic, or protozoan pathogens, such as SARS-CoV-2 or an influenza virus. In some embodiments, the methods comprise isothermal amplification of a target nucleic acid and subsequent detection of the amplification products.

Abstract: Aspects of the disclosure relate to compositions and methods for amplifying and/or detecting one or more target nucleic acid sequences (e.g., a nucleic acid sequence of one or more pathogens) in a biological sample obtained from a subject. In some embodiments, the pathogens are viral, bacterial, fungal, parasitic, or protozoan pathogens, such as SARS-CoV-2 or an influenza virus. In some embodiments, the methods comprise isothermal amplification of a target nucleic acid and subsequent detection of the amplification products.

Abstract: Aspects of the disclosure relate to devices and methods for amplifying and/or detecting one or more target nucleic acid sequences (e.g., a nucleic acid sequence of one or more pathogens) in a biological sample obtained from a subject, wherein the biological sample is combined with a diluent and/or matrix resolving agent.

Abstract: The present disclosure provides methods, compositions, kits, and systems for identifying recombinases and cognate site-specific recombinase recognition sites as well as method for using the identified recombinase/recognition site pairs.

Abstract: Aspects of the disclosure relate to compositions and methods for amplifying and/or detecting one or more target nucleic acid sequences (e.g., a nucleic acid sequence of one or more pathogens), and use of a trap region or reagent to reduce the level of one or more target nucleic acid analytes in an amplified sample prior to or in conjunction with detection. In some embodiments, the pathogens are viral, bacterial, fungal, parasitic, or protozoan pathogens, such as SARS-CoV-2 or an influenza virus. In some embodiments, the methods comprise isothermal amplification of a target nucleic acid and subsequent reduction in the level of one or more target nucleic acid analytes and detection of the amplification products.

Abstract: Aspects of the disclosure relate to compositions and methods for amplifying and/or detecting one or more target nucleic acid sequences (e.g., a nucleic acid sequence of one or more pathogens) in a biological sample obtained from a subject. In some embodiments, the pathogens are viral, bacterial, fungal, parasitic, or protozoan pathogens, such as SARS-CoV-2 or an influenza virus. In some embodiments, the methods comprise isothermal amplification of a target nucleic acid and subsequent detection of the amplification products.