Abstract: Provided herein are compositions and methods for functionalizing a polypeptide for single-molecule analysis. In some aspects, the disclosure provides compositions and methods for immobilizing a peptide barcode to a surface. In some aspects, the disclosure provides compositions and methods for luminescently labeling a protein of interest.

Abstract: Aspects of the application provide methods of identifying and sequencing proteins, polypeptides, and amino acids, and compositions useful for the same. In some aspects, the application provides methods of obtaining data during a degradation process of a polypeptide, and outputting a sequence representative of the polypeptide. In some aspects, the application provides amino acid recognition molecules comprising a shielding element that enhances photostability in polypeptide sequencing reactions.

Abstract: Provided herein are methods that are useful for controlled cleavage of polypeptides (e.g., modified polypeptides). In some aspects, provided herein are methods that are useful in combination with polypeptide sequencing techniques. For example, provided herein is a method comprising contacting a terminal amino acid of a polypeptide with one or more modification agents to produce a polypeptide comprising a modified terminal amino acid; and contacting the polypeptide comprising a modified terminal amino acid with an enzyme that catalyzes the removal of the modified terminal amino acid, wherein the enzyme has increased catalytic activity for removal of the modified terminal amino acid relative to a reference polypeptide comprising an unmodified terminal amino acid.

Abstract: Described herein are techniques for detecting amino acid variants in peptides using data from a sequencing device. Sequencing data is generated from traces of light pulses output by the sequencing device from detecting light emissions by fluorescently tagged N-terminal amino acid (NAA) recognizers during sequencing of at least one peptide. The sequencing data comprising light pulse durations and inter-pulse durations between successive light pulses. The techniques generate read(s) each comprising a sequence of recognition segments indicating time periods in which fluorescently tagged NAA recognizers were binding to particular NAAs of the peptide, assign fluorescently tagged NAA recognizers to recognition segments, align read(s) to reference peptide sequences to obtain peptide alignments, and detect amino acid variants using the peptide alignments.

Abstract: Methods of sequencing molecules based on luminescence lifetimes and/or intensities are provided. In some aspects, methods of sequencing nucleic acids involve determining the luminescence lifetimes, and optionally luminescence intensities, of a series of luminescently labeled nucleotides incorporated during a nucleic acid sequencing reaction.

Abstract: Aspects of the present disclosure provide improved fluorescence imaging techniques suitable for fluorescence-based analysis (e.g., sequencing) of an excited sample. Some aspects relate to directing an imaging aperture of a fluorescence imaging device towards a sample well region and capturing an image of the sample well region. Some aspects relate to selecting a sample well region and capturing an image of the selected sample well region. Some aspects relate to, during at least a portion of performing a controlled cleavage of a terminal amino acid in a first sample well, capturing a fluorescence image of a second sample well. Some aspects relate to setting a duration of imaging by and/or a location of an imaging aperture of a fluorescence imaging device. In some embodiments, aspects of the present disclosure provide for faster, less expensive, and/or greater control over fluorescence imaging and analysis of a sample.

Abstract: Compositions useful for the detection of single molecules in a sample are provided. In some aspects, the disclosure provides a nucleic acid connected to a nucleotide and two or more luminescent labels. In some embodiments, the nucleic acids described herein comprise one or more structural features that provide enhanced fluorescence intensity. In some aspects, methods of sequencing using the labeled nucleotides of the disclosure are provided.

Abstract: Aspects of the application provide methods of identifying and sequencing proteins, polypeptides, and amino acids, and compositions useful for the same. In some aspects, the application provides methods of obtaining data during a degradation process of a polypeptide, and outputting a sequence representative of the polypeptide. In some aspects, the application provides amino acid recognition molecules comprising a shielding element that enhances photostability in polypeptide sequencing reactions.

Abstract: Compositions useful for the detection of single molecules in a sample are provided. In some aspects, the disclosure provides a nucleotide connected to a nucleic acid comprising a FRET label comprising at least three luminescent molecules. In some embodiments, the nucleic acids described herein comprise one or more structural features that provide enhanced fluorescence intensity. In some aspects, methods of sequencing using the labeled nucleotides of the disclosure are provided.

Abstract: Aspects of the technology described herein relate to improved semiconductor-based image sensor designs. In some embodiments, an integrated circuit may comprise a photodetection region and a drain region electrically coupled to the photodetection region, and the photodetection region may be configured to induce an intrinsic electric field in a direction from the photodetection region to the drain region(s). In some embodiments, a charge storage region and the drain region may be positioned on a same side of the photodetection region. In some embodiments, at least one drain layer may be configured to receive incident photons and/or charge carriers via the photodetection region. In some embodiments, an integrated circuit may comprise a plurality of pixels and a control circuit configured to control a transfer of charge carriers in the plurality of pixels.

Abstract: Compositions comprising modified recombinant polymerizing enzymes are provided, along with nucleic acid molecules encoding the modified polymerizing enzymes. In some aspects, methods of using such polymerizing enzymes to synthesize a nucleic acid molecule or to sequence a nucleic acid template are provided.

Abstract: The present disclosure relates to methods and compositions for protein identification via peptide barcodes.

Abstract: Provided herein are compounds of Formulae (I), (II), (III), and (III-d). Also provided herein are methods of preparation of Formulae (I), (II), and (III-d). Further provided herein are methods of functionalizing or sequencing a peptide by reaction of compounds of Formula (III-d) with peptidases.

Abstract: Integrated devices including substrates with sample wells having modified surfaces are provided. An integrated device includes a substrate with a sample well having a metal oxide surface and a silica surface, a coating layer on the metal oxide surface formed by an amphipathic reagent attached to a polymeric compound, an antifouling overlay on the coating layer formed by a block copolymer, and a functionalizing agent bound to the silica surface.

Abstract: Provided herein are novel amino acid binding proteins that recognize aspartate and/or glutamate in protein sequencing reactions; novel amino acid binding proteins that recognize arginine in protein sequencing reactions; and novel amino acid binding proteins that recognize glycine, alanine, and/or serine in protein sequencing reactions.

Abstract: Methods of forming an integrated device, and in particular forming one or more sample wells in an integrated device, are described. The methods may involve forming a metal stack over a cladding layer, forming an aperture in the metal stack, forming first spacer material within the aperture, and forming a sample well by removing some of the cladding layer to extend a depth of the aperture into the cladding layer. In the resulting sample well, at least one portion of the first spacer material is in contact with at least one layer of the metal stack.

Abstract: Aspects of the technology described herein relate to improved semiconductor-based image sensor designs. In some embodiments, an integrated circuit may comprise a photodetection region and a drain region electrically coupled to the photodetection region, and the photodetection region may be configured to induce an intrinsic electric field in a direction from the photodetection region to the drain region(s). In some embodiments, an integrated circuit may comprise a plurality of pixels and a control circuit configured to control a transfer of charge carriers in a plurality of time-binning pixels. In some embodiments, an optical component for optical rejection is provided in between a waveguide and the time-binning pixel and configured to block at least some excitation photons in a pulsed light stream from arriving at the photodetection region.

Abstract: Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.

Abstract: There is provided amino acid cleaving reagents with improved cleavage activity, allowing for more structural information to be obtained from polypeptides in sequencing reactions.

Abstract: Described herein are techniques to reduce or remove the impact of secondary path photons and/or charge carriers on storage bins of an integrated device to improve noise performance, and thus, sample analysis. Some embodiments relate to optical rejection techniques such as including an optical barrier positioned to block at least some photons from reaching the storage bins. Some embodiments relate to electrical rejection techniques such as including an electrical barrier configured to block at least some charge carriers from reaching the storage bins along at least one secondary path. Some embodiments relate to an integrated device in which at least one storage bin is shaped and/or positioned relative to the photodetector to facilitate receipt of some charge carriers (e.g., fluorescent emission charge carriers) and/or photons and to impede receipt of other charge carriers (e.g., noise charge carriers) and/or photons.