Abstract: The methods described herein provide a means of producing an array of spatially separated proteins. The method relies on covalently attaching each protein of the plurality of proteins to a structured nucleic acid particle (SNAP), and attaching the SNAPs to a solid support.

Abstract: Described herein are DNA-nanostructures that can be used in an assay to detect and/or quantify an analyte of interest. Aspects of the DNA-nanostructure can include a single DNA molecule composed of hairpin structural motifs, an anchor recognition moiety, and a signal moiety, where the anchor recognition moiety and the signal moiety are in effective proximity to each other such that the tethered diffusion of the signal molecule can be altered based upon binding status of the anchor recognition moiety. Also described herein are methods of making and using the DNA-nanostructures.

Abstract: Provided herein are methods for resetting an array to which a biological sample has been applied that include treating the array with a set of biological sample removal conditions.

Abstract: The invention relates to methods for pairwise sequencing of a polynucleotide template which result in the sequential determination of nucleotide sequence in two distinct and separate regions of the polynucleotide template.

Abstract: Provided herein are high-throughput, high-quality methods of consecutive in situ hybridization for analysis of the genome and/or transcriptome in an individual cell with single-molecule sensitivity. In particular, provided herein are methods comprising visualizing individual genomic loci or transcripts as single detectable signals (e.g., fluorescent spots) which remain in place during consecutive hybridization. In each cycle of consecutive hybridization, detectably labeled probes hybridize to the probe used in the previous cycle, and also introduce the binding sites for the probe of the following cycle. Through consecutive cycles of probe hybridization, imaging, and signal removal, different genomic loci or RNA species can be identified by unique detectable signal profiles (e.g., fluorescent spots with unique color sequences). The number of varied color sequences increases exponentially with the number of hybridization cycles, which enables the genome or transcriptome-wide analysis.

Abstract: The present invention relates to improved processes for production of closed linear deoxyribonucleic acid (DNA), in particular cell-free enzymatic production of closed linear DNA molecules, preferably using a closed linear DNA as a template for DNA synthesis. The invention further relates to a novel closed linear DNA species, suitable for use as a template in the improved processes for production of closed linear DNA. Further, the invention pertains to the intermediate products of the processes, since this enables the production of larger quantities of closed linear DNA from the template than with methods known in the art.

Abstract: Systems and methods of polynucleotide sequencing are provided. Systems and methods optimize control, speed, movement, and/or translocation of a sample (e.g., a polynucleotide) within, through, or at least partially through a nanopore or a type of protein or mutant protein in order to accumulate sufficient time and current blocking information to identify contiguous nucleotides or plurality of nucleotides in a single-stranded area of a polynucleotide.

Abstract: A method for generating amplicon constructs of a target sequence is disclosed, the method comprising providing a target sequence; an oligonucleotide probe, comprising a universal sequence and further comprising, at or towards its 5? end, a target specific sequence capable of hybridising to the reverse complement of a sequence at, or flanking one of the 3? ends of the target sequence; a universal primer, comprising at its 3? end a sequence capable of hybridising to the universal sequence of the oligonucleotide probe and performing a Polymerase Chain Reaction (PCR).

Abstract: Described herein is a method of sequencing, comprising: splitting an asymmetrically tagged library into a plurality of subsamples, tagging the adaptor-ligated DNA in the sub-samples with sequence tags that identify the subsamples, optionally pooling the sub-samples, sequencing polynucleotides from each of the tagged sub-samples, or copies of the same, to produce sequence reads each comprising: i. a sub-sample identifier sequence and ii. the sequence of at least part of a fragment in the sample, wherein some of the sequence reads are derived from the top strand of a fragment in the sample and some of the sequence reads of are derived from the bottom strand of the same fragment.

Abstract: The present invention relates to, among other things, probes, compositions, methods, and kits for simultaneous, multiplexed detection and quantification of protein and/or nucleic acid expression in a user-defined region of a tissue, user-defined cell, and/or user-defined subcellular structure within a cell that are adaptable for use with existing sequencing technologies.

Abstract: An object of the present invention is to provide a biomolecule measuring device that can decrease the influence of crosstalk between chambers. A biomolecule measuring device according to the present invention supplies, to electrodes equipped on chambers, voltages modulated differently to each other.

Abstract: A method for identifying a predefined target organism includes extracting a nucleic acid from a sample to form an extracted nucleic acid, amplifying the extracted nucleic acid to form a nucleic acid amplicon, tagging the nucleic acid amplicon with a capture probe and a detector partner to form a detector partner-nucleic acid amplicon-capture probe complex, and performing a detection assay on the detector partner-nucleic acid amplicon-capture probe complex to identify whether the predefined target organism is present in the sample.

Abstract: The invention relates to adaptors for sequencing nucleic acids. The adaptors may be used to generate single stranded constructs of nucleic acid for sequencing purposes. Such constructs may contain both strands from a double stranded deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) template. The invention also relates to the constructs generated using the adaptors, methods of making the adaptors and constructs, as well as methods of sequencing double stranded nucleic acids.

Abstract: As demonstrated herein, when composite transcription factor binding sites do not function synergistically, mammalian promoters can be constructed according to simple design rules. Host-cell transcriptional machinery components were analyzed in silico to identify transcription factors with desired expression dynamics. Cognate binding sites were then comprehensively tested in homotypic and heterotypic architectures to assess modularity and determine the transcriptional activity exhibited by a single copy of each site. When elements were specifically selected to prevent combinatorial interactions, heterotypic promoter activities could be accurately modeled simply as a function of constituent binding site copy numbers. As binding site order, spacing, and orientation had minimal effect on promoter activity, blocks could be optimally combined and arranged in silico according to context-specific design-criteria.

Abstract: The invention is a method of sequencing polymers in which the sequence of one or more polymers is determined through an emergent property of the binding interactions of a repertoire of molecular probes to the polymer(s).

Abstract: A method for collecting microorganisms when contained in a fluid includes (i) introducing the fluid into a cavity of a collecting device via at least one admission duct, (ii) capturing the microorganisms when contained in the fluid with a set of beads retained in the cavity as the fluid passes through the set of beads, (iii) evacuating the fluid from the cavity via at least one evacuating duct, (iv) introducing a reaction liquid into the cavity via at least one admission channel, (v) collecting the microorganisms from the set of beads with the reaction liquid as the reaction liquid passes through the set of beads, and (vi) evacuating the reaction liquid from the cavity via at least one evacuating channel.

Abstract: The present disclosure relates to a set of at least 100 single-stranded oligonucleotide probes directed against (or complementary to) portions of a genomic target sequence of interest. The present disclosure also relates to a method of detecting a genomic target sequence of interest using the set of oligonucleotide probes and a method of generating the set of oligonucleotide probes. Further, the present disclosure relates to a kit comprising the set of oligonucleotide probes and at least one further component.

Abstract: The invention generally relates to compositions for maximizing capture of affinity-labeled molecules on solid supports. The disclosed methods and compositions were developed to maximize depletion of ribosomal RNA from total RNA samples, which is useful to improve the quality of RNA preparations used for applications such as massively parallel sequencing. The RNA depletion method is based on using long affinity-labeled RNA molecules that are complementary to all or part of the target ribosomal RNAs, as subtractive hybridization probes.

Abstract: A method for determining the presence of a copy number imbalance in genomic DNA of a test sample is provided. The method can separately measure hybridization of a single test sample to a first hybridization array and hybridization of a plurality of reference samples to a plurality of other, respective test arrays. A determination of copy number can be based on the best fit reference array, relative to the test array. The best fit can be determined based on the closest or most similar signal-to-noise ratio of the measured signals.

Abstract: The present invention relates to, among other things, probes, compositions, methods, and kits for simultaneous, multiplexed detection and quantification of protein and/or nucleic acid expression in a user-defined region of a tissue, user-defined cell, and/or user-defined subcellular structure within a cell that are adaptable for use with existing sequencing technologies.