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 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 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 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: 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 (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 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.