Abstract: Compositions, devices, systems and methods for reducing and/or preventing photo-induced damage of one or more reactants in an illuminated analytical reaction by addition of one or more photo-induced damage mitigating agents to the reaction mixture and allowing the reaction to proceed for a period that is less than a photo-induced damage threshold period.

Abstract: The invention provides a novel class of scaffold-based labeled polymerase enzyme substrates. The polymerase enzyme substrates have a multivalent core or scaffold to which is attached fluorescent dye moieties and nucleoside phosphate moities. The polymerase enzyme substrates have multiple fluorescent dye moities and/or multiple nucleoside phosphate moieties. Preferred multivalent cores comprise trifunctional six membered aromatic moities. The invention also provides for sequencing methods and kits with scaffold-based labeled polymerase enzyme substrates.

Abstract: Engineered nucleotide compositions, having polymerase interacting components that improve the interactivity of the polymerase and the nucleotide, particularly for nucleic acid sequencing applications. Compositions include the interactive polymerases along with the nucleotide analogs. Kits, methods and systems are provided for analysis of nucleic acid synthesis reactions.

Abstract: The invention provides a novel class of cyanine dyes that are functionalized with a linker moiety that facilitates their conjugation to other species and substituent groups which increase the water-solubility, and optimize the optical properties of the dyes. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.

Abstract: In various embodiments, the present invention provides fluorescent dyes that are linked to another species through an adaptor moiety. In an exemplary embodiment, the dye is linked to a polyphosphate nucleic acid through an adaptor. An adaptor can be a component of a linker. These conjugates find use in single molecule DNA sequencing and other applications. In various embodiments, the dye moiety is a cyanine dye. Cyanine dyes that are highly charged, such as those including multiple sulfonate, alkylsulfonate, carboxylate and/or alkylcarboxylate moieties are examples of cyanine dyes of use in the compounds of the invention.

Abstract: The invention provides a novel class of cyanine dyes that are functionalized with a linker moiety that facilitates their conjugation to other species and substituent groups which increase the water-solubility, and optimize the optical properties of the dyes. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.

Abstract: In various embodiments, the present invention provides fluorescent dyes that are linked to another species through an amino acid or peptide linker. In an exemplary embodiment, the dye is linked to a polyphosphate nucleic acid through an amino acid or peptide linker. These conjugates find use in single molecule DNA sequencing and other applications. In various embodiments, the dye moiety is a cyanine dye. Cyanine dyes that are highly charged, such as those including muliple sulfonate, alkylsulfonate, carboxylate and/or alkylcarboxylate moieties are examples of cyanine dyes of use in the compounds of the invention.

Abstract: The invention provides a novel class of cyanine dyes that are functionalized with sulfonic acid groups and a linker moiety that facilitates their conjugation to other species and substituent groups which increase the water-solubility, and optimize the optical properties of the dyes. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.

Abstract: Engineered nucleotide compositions, having polymerase interacting components that improve the interactivity of the polymerase and the nucleotide, particularly for nucleic acid sequencing applications. Compositions include the interactive polymerases along with the nucleotide analogs. Kits, methods and systems are provided for analysis of nucleoc acid synthesis reactions.

Abstract: One or more processor cores of a multiple-core processing device each can utilize a processing pipeline having a plurality of execution units (e.g., integer execution units or floating point units) that together share a pre-execution front-end having instruction fetch, decode and dispatch resources. Further, one or more of the processor cores each can implement dispatch resources configured to dispatch multiple instructions in parallel to multiple corresponding execution units via separate dispatch buses. The dispatch resources further can opportunistically decode and dispatch instruction operations from multiple threads in parallel so as to increase the dispatch bandwidth. Moreover, some or all of the stages of the processing pipelines of one or more of the processor cores can be configured to implement independent thread selection for the corresponding stage.

Abstract: Engineered nucleotide compositions, having polymerase interacting components that improve the interactivity of the polymerase and the nucleotide, particularly for nucleic acid sequencing applications. Compositions include the interactive polymerases along with the nucleotide analogs. Kits, methods and systems are provided for analysis of nucleic acid synthesis reactions.

Abstract: FRET-labeled compounds are provided for use in analytical reactions. In certain embodiments, FRET-labeled nucleotide analogs are used in place of naturally occurring nucleoside triphosphates or other analogs in analytical reactions comprising nucleic acids, for example, template-directed nucleic acid synthesis, DNA sequencing, RNA sequencing, single-base identification, hybridization, binding assays, and other analytical reactions.

Abstract: One or more processor cores of a multiple-core processing device each can utilize a processing pipeline having a plurality of execution units (e.g., integer execution units or floating point units) that together share a pre-execution front-end having instruction fetch, decode and dispatch resources. Further, one or more of the processor cores each can implement dispatch resources configured to dispatch multiple instructions in parallel to multiple corresponding execution units via separate dispatch buses. The dispatch resources further can opportunistically decode and dispatch instruction operations from multiple threads in parallel so as to increase the dispatch bandwidth. Moreover, some or all of the stages of the processing pipelines of one or more of the processor cores can be configured to implement independent thread selection for the corresponding stage.

Abstract: Compositions, devices, systems and methods for reducing and/or preventing photo-induced damage of one or more reactants in an illuminated analytical reaction by addition of one or more photo-induced damage mitigating agents to the reaction mixture and allowing the reaction to proceed for a period that is less than a photo-induced damage threshold period.

Abstract: The present invention provides methods and compositions for performing illuminated reactions, particularly sequencing reactions, while mitigating and/or preventing photodamage to reactants that can result from prolonged illumination. In particular, the invention provides methods and compositions for incorporating photoprotective agents into conjugates comprising reporter molecules and nucleoside polyphosphates.

Abstract: Engineered nucleotide compositions, having polymerase interacting components that improve the interactivity of the polymerase and the nucleotide, particularly for nucleic acid sequencing applications. Compositions include the interactive polymerases along with the nucleotide analogs. Kits, methods and systems are provided for analysis of nucleic acid synthesis reactions.

Abstract: One or more processor cores of a multiple-core processing device each can utilize a processing pipeline having a plurality of execution units (e.g., integer execution units or floating point units) that together share a pre-execution front-end having instruction fetch, decode and dispatch resources. Further, one or more of the processor cores each can implement dispatch resources configured to dispatch multiple instructions in parallel to multiple corresponding execution units via separate dispatch buses. The dispatch resources further can opportunistically decode and dispatch instruction operations from multiple threads in parallel so as to increase the dispatch bandwidth. Moreover, some or all of the stages of the processing pipelines of one or more of the processor cores can be configured to implement independent thread selection for the corresponding stage.

Abstract: One or more processor cores of a multiple-core processing device each can utilize a processing pipeline having a plurality of execution units (e.g., integer execution units or floating point units) that together share a pre-execution front-end having instruction fetch, decode and dispatch resources. Further, one or more of the processor cores each can implement dispatch resources configured to dispatch multiple instructions in parallel to multiple corresponding execution units via separate dispatch buses. The dispatch resources further can opportunistically decode and dispatch instruction operations from multiple threads in parallel so as to increase the dispatch bandwidth. Moreover, some or all of the stages of the processing pipelines of one or more of the processor cores can be configured to implement independent thread selection for the corresponding stage.

Abstract: Controlled initiation of primer extension in determination of nucleic acid sequence information by incorporation of nucleotides or nucleotide analogs. Preferred aspects include photo-initiated extension through the use of photo-cleavable blocking, groups on termini of primer sequences followed by non-terminating primer extension using nucleotides or nucleotide analogs that are not extension terminators.

Abstract: Fluorescent reporter compounds having a chain terminating (thio)triphosphate nucleotide derivative, a fluorescent dye, and a linker of sufficient length to connect the nucleotide derivative to the fluorescent dye are provided. The fluorescent reporter compounds are used in DNA sequencing reactions and are substantially inactive toward exonuclease digestion.