Abstract: The present invention relates to methods and systems for isolation of species in semi-permeable capsules and processing of encapsulated species through series of steps and/or reactions. To produce capsules, first aqueous two-phase system (ATPS) droplets are generated using microfluidics system and then the hydrogel shell layer is hardened by inducing polymerization. As exemplified in this invention to achieve concentric ATPS droplet formation density-matched PEGDA and Dextran polymer solutions can be used. Once a capsule is formed, its composition can be changed by adding new reagents or replacing out old ones (e.g. by resuspending capsules in desired aqueous solution). The hydrogel shell of semi-permeable capsules can be dissolved at selected step during multi-step procedures in order to release the encapsulated species. The present invention exemplifies the isolation of individual cells within capsules and using the encapsulated cells for genotypic and phenotypic analysis.

Abstract: Emulsion compositions are provided herein. Also provided herein are kits containing one or more emulsion compositions or components for making such emulsion compositions. Also provided herein are methods of using such emulsion compositions, such as for amplification of target nucleic acids in emulsion droplets.

Abstract: The present invention provides water soluble photoactive macromolecular complexes and methods for detecting an analyte in a sample by using a binding agent conjugated to a water soluble photoactive macromolecule.

Abstract: The present invention provides, among other aspects, functionalized chromophoric polymer dots comprising a hydrophobic core and a hydrophilic cap, and bioconjugates thereof. Also provided are improved methods for preparing functionalized chromophoric polymer dots. Methods for in vivo imaging and molecular labeling are also disclosed.

Abstract: Embodiments of the present disclosure relate to methods of preparing growing polynucleotides using nucleotide molecules with a 3? AOM blocking group. Also provided herein are kits related to such methods.

Abstract: Provided herein are methods and systems for sensitive and multiplexed in situ analysis of samples such as biological samples using cleavable hapten linked targeting agents and cleavable detectably-labeled hapten-binding agents. In particular, provided herein are methods for multiplexed single-cell in situ biomolecule profiling in samples, including fixed or fresh tissues, and also allows the investigation of the different cell compositions and their spatial organizations in intact tissues through consecutive cycles of probe hybridization, fluorescence imaging, and signal removal.

Abstract: Reaction mixtures are provided having at least a first nucleotide analog and a second nucleotide analog that produce signals in response to excitation illumination. The signals produced by the analogs have peaks at the same wavelengths, but have distinct signal intensities. The distinct intensities allow for identification of the analogs in nucleic acid sequencing. In some embodiments, FRET-labeled compounds are provided. In certain embodiments, FRET-labeled nucleotide analogs are used, for example, in DNA sequencing or RNA sequencing.

Abstract: Methods are disclosed for detecting peripheral mitochondrial DNA damage and dysfunction. Methods are also disclosed that utilize blood samples to detect a neurodegenerative disease, such as Parkinson's disease, and determine the efficacy of therapy.

Abstract: Systems for detecting fluorescence from a molecule comprising an ion-impermeable film comprising at least one ion-conducting nanopore; a first and second liquid reservoir separated by the film; a means to induce movement of the molecule from the first reservoir to the second reservoir via the nanopore; a light source capable of exciting the molecule to emit fluorescence, wherein the light source shines into the second reservoir; a metallic layer adhered to the film by an adhesion layer and comprising a nanowell structure located adjacent to the nanopore; and a detector configured to detect the fluorescence emitted by the molecule are provided. Methods of use of the systems are also provided.

Abstract: This disclosure provides systems and methods for sequencing nucleic acids using nucleotide analogues and translocation of tags from incorporated nucleotide analogues through a nanopore. In aspects, this disclosure is related to composition, method, and system for sequencing a nucleic acid using tag molecules and detection of translocation through a nanopore of tags released from incorporation of the molecule.

Abstract: The present disclosure is directed to designing dyes and methods to alter the parameters controlling the dipole-dipole coupling of dyes bound to a nucleotide oligomer architecture, which are used to propagate excitons for use in next generation room temperature quantum information systems. The disclosed dyes and methods are directed to changing the dye stability, symmetry, overlap, and steric hindrance of the dyes to fine tune aggregate systems.

Abstract: A flow cell includes a support and a heteropolymer attached to the support. The heteropolymer includes an acrylamide monomer including an attachment group to react with a functional group attached to a primer, and a monomer including a stimuli-responsive functional group. The monomer including the stimuli-responsive functional group may be pH-responsive, temperature-responsive, saccharide-responsive, nucleophile-responsive, and/or salt-responsive.

Abstract: Some embodiments of the present application relate to novel modified nucleotide linkers for increasing the efficiency of nucleotide incorporation in Sequencing by Synthesis applications. Methods of preparing these modified nucleotide linkers are also provided herewith.

Abstract: Compositions and methods for optically-verified, sequence-controlled polymer synthesis are described.

Abstract: Provided herein, in some embodiments, are methods, compositions and kits for large-scale production of long single-stranded DNA in solution.

Abstract: Methods and systems and related compositions for separating through a solid matrix a mixture comprising a nucleic acid together with a target compound having a water solubility equal to or greater than 0.01 mg per 100 mL, which can be used for managing fluid flow, biochemical reactions and purification of the nucleic acid or other target analytes.

Abstract: The present disclosure provides a solid phase method of making oligonucleotides via sequential coupling cycles including at least one coupling of a dinucleotide dimer subunit to a free 3?-terminal group of a growing chain. The oligonucleotides include at least two nucleoside subunits joined by a N3??P5? phosphoramidate linkage. The method may include the steps of (a) deprotecting the protected 3? amino group of a terminal nucleoside attached to a solid phase support, said deprotecting forming a free 3? amino group; (b) contacting the free 3? amino group with a 3?-protected amino-dinucleotide-5?-phosphoramidite dimer in the presence of a nucleophilic catalyst to form an internucleoside N3??P5? phosphoramidite linkage; and (c) oxidizing (e.g., sulfurizing) the linkage. The compositions produced by the subject methods may include a reduced amount of one or more (N?x) oligonucleotide products. Also provided are pharmaceutical compositions including the subject oligonucleotide compositions.

Abstract: The present disclosure relates to compositions and methods based on polypeptide-tagged nucleotide, and the use of such polypeptide-tagged nucleotides in nanopore devices and methods.

Abstract: In an example, a flow cell includes a substrate, a selectively removable porous molecular network on the substrate and defining exposed substrate regions, and sequencing surface chemistry on at least some of the exposed regions. The sequencing surface chemistry is selected from the group consisting of i) an activated pad, a polymer layer attached to the activated pad, and a primer attached to the polymer layer; or ii) a nanostructure and an enzyme attached to the nanostructure.

Abstract: Provided herein are compositions, methods and systems relating to libraries of polynucleotides such that the libraries allow for accurate and efficient hybridization after binding to target sequences. Further provided herein are probes, blockers, additives, buffers, and methods that result in improved hybridization. Such compositions and methods are useful for improvement of Next Generation Sequencing applications, such as reducing off-target binding or reducing workflow times.