Arrays of integrated analytical devices and their methods for production are provided. The arrays are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The devices allow the highly sensitive discrimination of optical signals using features such as spectra, amplitude, and time resolution, or combinations thereof. The devices include an integrated diffractive beam shaping element that provides for the spatial separation of light emitted from the optical reactions.
G01N 21/77 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator
G01N 21/78 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator producing a change of colour
G02B 6/12 - Light guidesStructural details of arrangements comprising light guides and other optical elements, e.g. couplings of the optical waveguide type of the integrated circuit kind
G02B 6/132 - Integrated optical circuits characterised by the manufacturing method by deposition of thin films
G02B 6/136 - Integrated optical circuits characterised by the manufacturing method by etching
H10F 39/00 - Integrated devices, or assemblies of multiple devices, comprising at least one element covered by group , e.g. radiation detectors comprising photodiode arrays
2.
Recombinant Polymerases for Incorporation of Protein Shield Nucleotide Analogs
Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing or nucleic acid amplification. Such properties include enhanced performance with large nucleotide analogs, increased stability, increased readlength, and improved detection of modified bases, and can also include resistance to photodamage, enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased accuracy, altered speed, increased cosolvent resistance, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.
Provided is an analytical system comprising: a plurality of biosensor elements configured to generate sensor data, and a data selection module. The data selection module comprises: a data input array configured to receive sensor data from the plurality of biosensor elements; and a data output array connectable to a downstream data processing module for analyzing the sensor data. The data selection module is for selectively providing the sensor data from the input array to the output array and is configured to: receive sensor mask information, the sensor mask information indicating an identified subset of the plurality of biosensor elements from which sensor data are sought; and selectively provide the identified sensor data from the identified biosensor elements to the data output array.
G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
G01N 33/00 - Investigating or analysing materials by specific methods not covered by groups
G05B 19/04 - Programme control other than numerical control, i.e. in sequence controllers or logic controllers
Methods, compositions, and systems for distributing nucleic acids into array regions are provided. The methods, compositions, and systems utilize nucleic acid condensing agents to increase efficiency of distribution of the nucleic acids into the array regions. Various methods for facilitating distribution of the nucleic acids to the array regions are provided.
05 - Pharmaceutical, veterinary and sanitary products
10 - Medical apparatus and instruments
Goods & Services
assays and reagents for medical diagnosis medical diagnostic instruments for clinical medical genetic sequencing and biochemical analysis and for the analysis of genes, molecules, DNA and RNA samples; analytical array chips for clinical medical genetic sequencing and biochemical analysis and for the analysis of genes, molecules, DNA and RNA samples
Optical analytical devices and their methods of use are provided. The devices are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The devices include optical waveguides for illumination of the optical reactions. The devices further provide for the efficient coupling of optical excitation energy from the waveguides to the optical reactions. Optical signals emitted from the reactions can thus be measured with high sensitivity and discrimination using features such as spectra, amplitude, and time resolution, or combinations thereof. The devices of the invention are well suited for miniaturization and high throughput.
G01N 21/77 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator
G02B 6/024 - Optical fibres with cladding with polarisation-maintaining properties
G02B 6/10 - Light guidesStructural details of arrangements comprising light guides and other optical elements, e.g. couplings of the optical waveguide type
G02B 6/12 - Light guidesStructural details of arrangements comprising light guides and other optical elements, e.g. couplings of the optical waveguide type of the integrated circuit kind
G02B 6/122 - Basic optical elements, e.g. light-guiding paths
G02B 23/24 - Instruments for viewing the inside of hollow bodies, e.g. fibrescopes
G02F 1/365 - Non-linear optics in an optical waveguide structure
7.
PROCESS FOR COGNATE NUCLEOTIDE DETECTION IN A NUCLEIC ACID SEQUENCING WORKFLOW
Method and composition for identifying cognate nucleotides in a Sequencing By Binding™ procedure, wherein one or more labeled nucleotides are detected in ternary complexes but never incorporated. Labeled nucleotides can be incorporable nucleotides that contact preformed blocked primed template nucleic acids. Alternatively, labeled nucleotides are labeled non-incorporable nucleotides. Labeled nucleotides, including labeled non-incorporable nucleotides, can be detected in ternary complexes in the same reaction mixture that incorporates a reversible terminator nucleotide to create a blocked primed template nucleic acid. Detection of ternary complexes can take place in the presence of a catalytic metal ion.
C07H 21/02 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
C07H 99/00 - Subject matter not provided for in other groups of this subclass
Provided includes methods, compositions and systems for circularizing single-stranded nucleic acids and for performing rolling circle amplification reaction with the circularized nucleic acids. The circularization of single-stranded nucleic acids is carried out in the presence of a helicase and optionally a DNA binding protein.
05 - Pharmaceutical, veterinary and sanitary products
10 - Medical apparatus and instruments
Goods & Services
Medical diagnostic assays and reagents, namely, medical diagnostic reagents and assays for use in genetic sequencing and biochemical analysis used to diagnose medical diseases and conditions and to measure and monitor medical treatments Medical instruments and medical analytical array chips, namely, medical diagnostic optical detectors for genetic sequencing, biochemical analysis and the analysis of genes, molecules, DNA and RNA samples, all for medical diagnostic purposes, and medical diagnostic array chips for genetic sequencing, biochemical analysis and for the analysis of genes, molecules, DNA and RNA samples
Labeled nucleotide analogs comprising at least one avidin protein, at least one dye-labeled compound, and at least one nucleotide compound are provided. The analogs are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The analogs are detectable with high sensitivity at desirable wavelengths. They contain structural components that modulate the interactions of the analogs with DNA polymerase, thus decreasing photodamage and improving the kinetic and other properties of the analogs in sequencing reactions. Also provided are nucleotide and dye-labeled compounds of the subject analogs, as well as intermediates useful in the preparation of the compounds and analogs. Compositions comprising the compounds, methods of synthesis of the intermediates, compounds, and analogs, and mutant DNA polymerases are also provided.
C07H 19/207 - Purine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids the phosphoric or polyphosphoric acids being esterified by a further hydroxylic compound, e.g. flavine-adenine dinucleotide or nicotinamide-adenine dinucleotide
C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
C09B 23/06 - Methine or polymethine dyes, e.g. cyanine dyes characterised by the methine chain containing an odd number of CH groups three CH groups, e.g. carbocyanines
C09B 23/08 - Methine or polymethine dyes, e.g. cyanine dyes characterised by the methine chain containing an odd number of CH groups more than three CH groups, e.g. polycarbocyanines
C09B 69/00 - Dyes not provided for by a single group of this subclass
C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
11.
HIGH SPEED SCANNING SYSTEM WITH ACCELERATION TRACKING
Disclosed herein is a high throughput optical scanning device and methods of use. The optical scanning device and methods of use provided herein can allow high throughput scanning of a continuously moving object with a high resolution despite fluctuations in stage velocity. This can aid in high throughput scanning of a substrate, such as a biological chip comprising fluorophores. Also provided herein are improved optical relay systems and scanning optics.
G02B 27/64 - Imaging systems using optical elements for stabilisation of the lateral and angular position of the image
G01D 5/347 - Mechanical means for transferring the output of a sensing memberMeans for converting the output of a sensing member to another variable where the form or nature of the sensing member does not constrain the means for convertingTransducers not specially adapted for a specific variable using optical means, i.e. using infrared, visible or ultraviolet light with attenuation or whole or partial obturation of beams of light the beams of light being detected by photocells using displacement encoding scales
H04N 3/08 - Scanning details of television systemsCombination thereof with generation of supply voltages by optical-mechanical means only having a moving reflector
An analytical device including an optically opaque cladding, a sequencing layer including a substrate disposed below the cladding, and a waveguide assembly for receiving optical illumination and introducing illumination into the device. The illumination may be received from a top, a side edge, and a bottom of the device. The waveguide assembly may include a nanoscale aperture disposed in the substrate and extending through the cladding. The aperture defines a reaction cell for receiving a set of reactants. In various aspects, the device includes a sensor element and the illumination pathway is through the sensor element. Waveguides and illumination devices, such as plasmonic illumination devices, are also disclosed. Methods for forming and operating the devices are also disclosed.
G01N 21/75 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated
G01N 21/77 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator
G01N 33/543 - ImmunoassayBiospecific binding assayMaterials therefor with an insoluble carrier for immobilising immunochemicals
G02B 6/122 - Basic optical elements, e.g. light-guiding paths
13.
METHODS AND COMPOSITIONS FOR CAPPING NUCLEIC ACIDS
A method for identifying a nucleic acid template that include (a) providing a plurality of primer-template hybrids, wherein a first hybrid of the plurality includes a first template hybridized to a first primer, and wherein a second hybrid of the plurality includes a second template hybridized to a second primer, the second primer having a ternary complex inhibitor moiety at the 3′ end; (b) delivering polymerases and nucleotides to the plurality, whereby the first hybrid binds a polymerase and nucleotide to form a stabilized ternary complex and whereby the second hybrid does not bind a polymerase and nucleotide to form a stabilized ternary complex; and (c) detecting the stabilized ternary complex to identify the first template.
01 - Chemical and biological materials for industrial, scientific and agricultural use
09 - Scientific and electric apparatus and instruments
Goods & Services
Assays and reagents for scientific or research use; reagent
kits comprised of buffers, enzymes, reagents, nucleotides,
chemical preparations and/or biological compounds for use in
the preparation or performance of ensemble or bulk assays
for scientific or research use; reagent kits comprising
components, namely, buffers, enzymes, reagents, nucleotides,
chemical preparations and/or biological compounds, for
single molecule assays for scientific or research use. Laboratory instruments for scientific research, namely,
optical detectors for genetic sequencing and biochemical
analysis; analytical array chips for genetic sequencing and
biochemical analysis; optical array chips for genetic
sequencing and biochemical analysis; downloadable computer
software for the analysis of biological data.
01 - Chemical and biological materials for industrial, scientific and agricultural use
09 - Scientific and electric apparatus and instruments
Goods & Services
Assays and reagents for scientific or research use; reagent
kits comprised of buffers, enzymes, reagents, nucleotides,
chemical preparations and/or biological compounds for use in
the preparation or performance of ensemble or bulk assays
for scientific or research use; reagent kits comprising
components, namely, buffers, enzymes, reagents, nucleotides,
chemical preparations and/or biological compounds, for
single molecule assays for scientific or research use. Analytical array chips for genetic sequencing and
biochemical analysis; optical array chips for genetic
sequencing and biochemical analysis; downloadable computer
software for the analysis of biological data.
01 - Chemical and biological materials for industrial, scientific and agricultural use
09 - Scientific and electric apparatus and instruments
Goods & Services
(1) Assays and reagents for scientific or research use; reagent kits comprised of buffers, enzymes, reagents, nucleotides, chemical preparations and/or biological compounds for use in the preparation or performance of ensemble or bulk assays for scientific or research use; reagent kits comprising components, namely, buffers, enzymes, reagents, nucleotides, chemical preparations and/or biological compounds, for single molecule assays for scientific or research use.
(2) Laboratory instruments for scientific research, namely, optical detectors for genetic sequencing and biochemical analysis; analytical array chips for genetic sequencing and biochemical analysis; optical array chips for genetic sequencing and biochemical analysis; downloadable computer software for the analysis of biological data; none of the aforementioned goods for use in relation to laboratory robots and surgical robots.
01 - Chemical and biological materials for industrial, scientific and agricultural use
09 - Scientific and electric apparatus and instruments
Goods & Services
(1) Assays and reagents for scientific or research use; reagent kits comprised of buffers, enzymes, reagents, nucleotides, chemical preparations and/or biological compounds for use in the preparation or performance of ensemble or bulk assays for scientific or research use; reagent kits comprising components, namely, buffers, enzymes, reagents, nucleotides, chemical preparations and/or biological compounds, for single molecule assays for scientific or research use.
(2) Analytical array chips for genetic sequencing and biochemical analysis; optical array chips for genetic sequencing and biochemical analysis; downloadable computer software for the analysis of biological data.
Optics collection and detection systems are provided for measuring optical signals from an array of optical sources over time. Methods of using the optics collection and detection systems are also described.
G01N 21/75 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated
G01N 21/77 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator
G01N 33/543 - ImmunoassayBiospecific binding assayMaterials therefor with an insoluble carrier for immobilising immunochemicals
G02B 6/122 - Basic optical elements, e.g. light-guiding paths
01 - Chemical and biological materials for industrial, scientific and agricultural use
09 - Scientific and electric apparatus and instruments
Goods & Services
Assays and reagents for scientific or research use; Reagent kits comprised of buffers, enzymes, reagents, nucleotides, chemical preparations and/or biological compounds for use in the preparation or performance of ensemble or bulk assays for scientific or research use; Reagent kits comprising components, namely, buffers, enzymes, reagents, nucleotides, chemical preparations and/or biological compounds, for single molecule assays for scientific or research use Analytical array chips for genetic sequencing and biochemical analysis; optical array chips for genetic sequencing and biochemical analysis; downloadable computer software for the analysis of biological data
Methods, compositions, and systems are provided for the detection of 5-methyl cytosine modifications in nucleic acid, particularly DNA, samples. A template or plurality of templates is sequenced using single molecule real time sequencing. Feature vectors are produced using specific features. In some aspects, a feature vector having a reduced feature set is provided and these feature vectors are input into a deep learning model.
Disclosed herein are methods and systems for detection and discrimination of optical signals from a densely packed substrate. There have broad applications for biomolecule detection near or below the diffraction limit of optical systems, including in improving the efficiency and accuracy or polynucleotide sequencing applications.
Methods, compositions, and systems are provided for the detection of 5-methylcytosine modifications in nucleic acid, particularly DNA, samples. A template or plurality of templates is sequenced using single molecule real time sequencing. Feature vectors are produced using specific features. In some aspects, a feature vector having a reduced feature set is provided and these feature vectors are input into a deep learning model.
This invention provides analytical devices for use in various applications, including detection of single-molecule analytical reactions. Methods for propagating optical energy within a substrate are provided. Devices comprising waveguide substrates, dielectric omnidirectional reflectors, and optical couplers are provided. Waveguide substrates with improved uniformity of optical energy intensity across one or more waveguides and enhanced waveguide illumination efficiency within an analytic detection region of the arrays are provided.
G01N 21/77 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator
G01N 33/543 - ImmunoassayBiospecific binding assayMaterials therefor with an insoluble carrier for immobilising immunochemicals
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
Goods & Services
Assays and reagents for scientific or research use; reagent
kits for preparation or performance of single molecule
assays for scientific or research use; buffers, enzymes,
reagents, nucleotides, chemical preparations and biological
compounds, each of which is for use in preparation and
performance of single molecule assays for scientific and
research use. Medical diagnostic assays and reagents for testing of
biological samples; reagent kits comprised of medical
diagnostic reagents for testing biological samples; buffers,
enzymes, reagents, nucleotides, chemical preparations and
biological compounds, each of which is for use in medical
diagnostic assays.
26.
METHODS AND COMPOSITIONS FOR STABILIZING CONCATEMERS
This application describes methods, compositions, and kits for forming stabilized concatemers using staple molecules. Additionally, this application provides methods of using stabilized concatemers to improve the results of downstream applications, including sequencing applications.
This application describes methods, compositions, and kits for enriching cells based on DNA sequences. The method may include one or more of cloning nucleic acids into a population of cells, culturing the cells, obtaining nucleic acids from a portion of the cultured cells, sequencing the obtained nucleic acids, identifying a set of one or more barcode sequences that distinguish a population of cultured cells that have a desired library sequence, and enriching one or more cultured cells that comprise the identified set of one or more barcode sequences.
Labeled nucleotide analogs comprising at least one avidin protein, at least one dye-labeled compound, and at least one nucleotide compound are provided. The analogs are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The analogs are detectable with high sensitivity at desirable wavelengths. They contain structural components that modulate the interactions of the analogs with DNA polymerase, thus decreasing photodamage and improving the kinetic and other properties of the analogs in sequencing reactions. Also provided are nucleotide and dye-labeled compounds of the subject analogs, as well as intermediates useful in the preparation of the compounds and analogs. Compositions comprising the compounds, methods of synthesis of the intermediates, compounds, and analogs, and mutant DNA polymerases are also provided.
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
C07H 19/10 - Pyrimidine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids
C07H 19/207 - Purine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids the phosphoric or polyphosphoric acids being esterified by a further hydroxylic compound, e.g. flavine-adenine dinucleotide or nicotinamide-adenine dinucleotide
The present disclosure relates to a deblocking agent and compositions thereof for cleaving an NO bond in an amineoxy group at the 3' position of a non-extendable polynucleotide, the deblocking agent being a carbonyl phosphonate and/or sulfonate, or salt thereof. The present disclosure further relates to methods of activating and/or extending a non-extendable polynucleotide using the deblocking agent of the present disclosure. The present disclosure also relates to methods of sequencing a target nucleic acid comprising the methods of activating a non-extendable polynucleotide of the present disclosure.
01 - Chemical and biological materials for industrial, scientific and agricultural use
09 - Scientific and electric apparatus and instruments
Goods & Services
Assays and reagents for scientific or research use; Reagent kits comprised of buffers, enzymes, reagents, nucleotides, chemical preparations and/or biological compounds for use in the preparation or performance of ensemble or bulk assays for scientific or research use; Reagent kits comprising components, namely, buffers, enzymes, reagents, nucleotides, chemical preparations and/or biological compounds, for single molecule assays for scientific or research use Laboratory instruments for scientific research, namely, optical detectors for genetic sequencing and biochemical analysis; analytical array chips for genetic sequencing and biochemical analysis; optical array chips for genetic sequencing and biochemical analysis; downloadable computer software for the analysis of biological data; none of the aforementioned goods for use in relation to laboratory robots and surgical robots.
01 - Chemical and biological materials for industrial, scientific and agricultural use
09 - Scientific and electric apparatus and instruments
Goods & Services
Assays and reagents for scientific or research use; Reagent kits comprised of buffers, enzymes, reagents, nucleotides, chemical preparations and/or biological compounds for use in the preparation or performance of ensemble or bulk assays for scientific or research use; Reagent kits comprising components, namely, buffers, enzymes, reagents, nucleotides, chemical preparations and/or biological compounds, for single molecule assays for scientific or research use Analytical array chips for genetic sequencing and biochemical analysis; optical array chips for genetic sequencing and biochemical analysis; downloadable computer software for the analysis of biological data
01 - Chemical and biological materials for industrial, scientific and agricultural use
09 - Scientific and electric apparatus and instruments
Goods & Services
Assays and reagents for scientific or research use; Reagent kits comprised of buffers, enzymes, reagents, nucleotides, chemical preparations and/or biological compounds for use in the preparation or performance of ensemble or bulk assays for scientific or research use; Reagent kits comprising components, namely, buffers, enzymes, reagents, nucleotides, chemical preparations and/or biological compounds, for single molecule assays for scientific or research use Analytical array chips for genetic sequencing and biochemical analysis; optical array chips for genetic sequencing and biochemical analysis; downloadable computer software for the analysis of biological data
33.
DENSLEY-PACKED ANALYTE LAYERS AND DETECTION METHODS
Disclosed herein are methods and systems for detection and discrimination of optical signals from a densely packed substrate. These have broad applications for biomolecule detection near or below the diffraction limit of optical systems, including in improving the efficiency and accuracy of polynucleotide sequencing applications.
Disclosed herein are methods and systems for detection and discrimination of optical signals from a densely packed substrate. These have broad applications for biomolecule detection near or below the diffraction limit of optical systems, including in improving the efficiency and accuracy of polynucleotide sequencing applications.
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
C12Q 1/689 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
Reaction mixtures are provided having at least a first reactant and a second reactant that produce signals in response to excitation illumination. The signals produced by the reactants have peaks at the same wavelengths, but have distinct signal intensities. In some embodiments, the reactants are FRET-labeled.
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
C07H 19/207 - Purine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids the phosphoric or polyphosphoric acids being esterified by a further hydroxylic compound, e.g. flavine-adenine dinucleotide or nicotinamide-adenine dinucleotide
C12Q 1/6818 - Hybridisation assays characterised by the detection means involving interaction of two or more labels, e.g. resonant energy transfer
G01N 33/542 - ImmunoassayBiospecific binding assayMaterials therefor with immune complex formed in liquid phase with steric inhibition or signal modification, e.g. fluorescent quenching
G01N 33/58 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving labelled substances
36.
RECOMBINANT POLYMERASES FOR INCORPORATION OF PROTEIN SHIELD NUCLEOTIDE ANALOGS
Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing or nucleic acid amplification. Such properties include enhanced performance with large nucleotide analogs, increased stability, increased readlength, and improved detection of modified bases, and can also include resistance to photodamage, enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased accuracy, altered speed, increased cosolvent resistance, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.
Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.
Provided are methods and systems for detecting formation of nucleotide-specific ternary complexes comprising a DNA polymerase, a nucleic acid, and a nucleotide complementary to the templated base of the primed template nucleic acid. The methods and systems facilitate determination of the next correct nucleotide without requiring chemical incorporation of the nucleotide into the primer. This advantageously improves signal-to-noise ratios and increases the quality of results obtainable in a sequencing-by-binding protocol, and enables extended read lengths. These results can even be achieved in procedures employing unlabeled, native nucleotides.
Provided herein are engineered DNA polymerases comprising modifications improving accuracy and processivity of the polymerase including modifications in the Motif A region, optionally, along with additional modifications in the palm and/or exonuclease domains of the polymerase. Also provided are nucleic acids encoding the engineered DNA polymerases comprising modifications in motif A of the polymerase, optionally, with additional modifications. Methods, vectors, kits, and compositions comprising the nucleic acids and compositions, methods and kits comprising the engineered polymerases are also provided.
Methods and systems for single molecule sequencing using concatemers of copies of sense and antisense strands. Concatemers are provided, for example, by carrying out rolling circle amplification on a circular molecule having sense and antisense regions to produce repeated copies of the sense and antisense regions connected by linking regions. The circular molecules can be produced by ligating hairpin adapters to each end of a double-stranded nucleic acid having a sense and antisense strand. The ligations can be carried out, for example using blunt end ligation. In some cases, a single molecule consensus sequence for a single template molecule is obtained. A single read from each template molecule can be obtained by comparing the sequence information of the sense and antisense regions.
C12Q 1/689 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
Goods & Services
(1) Assays and reagents for scientific or research use; reagent kits for preparation or performance of single molecule assays for scientific or research use; buffers, enzymes, reagents, nucleotides, chemical preparations and biological compounds, each of which is for use in preparation and performance of single molecule assays for scientific and research use.
(2) Medical diagnostic assays and reagents for testing of biological samples; reagent kits comprised of medical diagnostic reagents for testing biological samples; buffers, enzymes, reagents, nucleotides, chemical preparations and biological compounds, each of which is for use in medical diagnostic assays.
42.
MODIFIED BIOTIN-BINDING PROTEINS FOR IMMOBILIZATION
Compositions comprising covalently modified and mutated biotin-binding proteins, particularly biotin-binding proteins having a negative charge at physiological pH, are provided. Methods of producing such proteins are also provided, as are methods of immobilizing, sequencing, and making nucleic acids employing such proteins.
C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
C07K 14/36 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from bacteria from ActinomycesPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from bacteria from Streptomyces (G)
Integrated target waveguide devices and optical analytical systems comprising such devices are provided. The target devices include an optical coupler that is optically coupled to an integrated waveguide and that is configured to receive optical input from an optical source through free space, particularly through a low numerical aperture interface. The devices and systems are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The devices provide for the efficient and reliable coupling of optical excitation energy from an optical source to the optical reactions. Optical signals emitted from the reactions can thus be measured with high sensitivity and discrimination. The devices and systems are well suited for miniaturization and high throughput.
G01N 21/77 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator
G02B 6/124 - Geodesic lenses or integrated gratings
G02B 6/12 - Light guidesStructural details of arrangements comprising light guides and other optical elements, e.g. couplings of the optical waveguide type of the integrated circuit kind
G02B 6/42 - Coupling light guides with opto-electronic elements
Labeled nucleotide analogs comprising at least one avidin protein, at least one dye-labeled compound, and at least one nucleotide compound are provided. The analogs are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The analogs are detectable with high sensitivity at desirable wavelengths. They contain structural components that modulate the interactions of the analogs with DNA polymerase, thus decreasing photodamage and improving the kinetic and other properties of the analogs in sequencing reactions. Also provided are nucleotide and dye-labeled compounds of the subject analogs, as well as intermediates useful in the preparation of the compounds and analogs. Compositions comprising the compounds, methods of synthesis of the intermediates, compounds, and analogs, and mutant DNA polymerases are also provided.
C07H 19/10 - Pyrimidine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids
C07H 19/207 - Purine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids the phosphoric or polyphosphoric acids being esterified by a further hydroxylic compound, e.g. flavine-adenine dinucleotide or nicotinamide-adenine dinucleotide
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.
C07D 209/14 - Radicals substituted by nitrogen atoms, not forming part of a nitro radical
C07D 401/14 - Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing three or more hetero rings
C07D 405/14 - Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing three or more hetero rings
C07H 19/10 - Pyrimidine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids
C07K 5/09 - Tripeptides the side chain of the first amino acid containing more amino groups than carboxyl groups, or derivatives thereof, e.g. Lys, Arg
C07K 5/11 - Tetrapeptides the side chain of the first amino acid containing more amino groups than carboxyl groups, or derivatives thereof, e.g. Lys, Arg
C09B 23/01 - Methine or polymethine dyes, e.g. cyanine dyes characterised by the methine chain
C09B 23/06 - Methine or polymethine dyes, e.g. cyanine dyes characterised by the methine chain containing an odd number of CH groups three CH groups, e.g. carbocyanines
C09B 23/08 - Methine or polymethine dyes, e.g. cyanine dyes characterised by the methine chain containing an odd number of CH groups more than three CH groups, e.g. polycarbocyanines
C09B 23/10 - Methine or polymethine dyes, e.g. cyanine dyes characterised by the methine chain containing an even number of CH groups
C09B 23/16 - Methine or polymethine dyes, e.g. cyanine dyes the polymethine chain containing hetero atoms
A method of characterizing a nucleic acid that includes steps of (a) contacting a primer-template nucleic acid hybrid with a polymerase and a mixture of nucleotides to produce an extended primer hybrid and to form a stabilized ternary complex including the extended primer hybrid, the polymerase and a nucleotide cognate of the next base in the template, wherein the mixture contains nucleotide cognates of four different base types, wherein the nucleotide cognate of the first base type has a reversible terminator, and wherein nucleotide cognates of the second, third and fourth base types are extendable; (b) detecting the stabilized ternary complex to distinguish the next base from other base types in the template; and (c) determining the presence of a base multiplet in the template nucleic acid, the base multiplet including the first base type followed by the next base.
Systems and methods for mapping a plurality of sequence reads to a genomic region are provided. A plurality of sequence reads mappable to the genomic region are obtained. An initial Markov model for the genomic region is obtained. The initial Markov model comprises at least (i) a first repeat for a first repeat region, (ii) a second repeat for a second repeat region, and (iii) an intermediate region linking the first repeat to the second repeat. The initial Markov model is refined using the plurality of sequence reads, thereby obtaining a refined Markov model. For each respective sequence read in the plurality of sequences, the respective sequence read is used to find a highest probability path through the Markov model. This highest probability path is then used to map the respective sequence read to the genomic region.
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
Goods & Services
Assays and reagents for scientific or research use; reagent
kits for preparation or performance of single molecule
assays for scientific or research use; buffers, enzymes,
reagents, nucleotides, chemical preparations and/or
biological compounds for scientific or research use. Assays and reagents for medical and diagnostic use; reagent
kits for medical and diagnostic use; buffers, enzymes,
reagents, nucleotides, chemical preparations and/or
biological compounds for medical and diagnostic use.
49.
Substrates and optical systems and methods of use thereof
This invention provides devices for use in various analytical applications including single-molecule analytical reactions. Methods for detecting analytes optically by propagating optical energy by waveguides within a substrate are provided. Analytical devices are provided which have both shallow and deep waveguides in which illumination light is transported through the deep waveguides and coupled into the shallow waveguides. The shallow waveguides provide evanescent field illumination to analytes, such as single-molecule analytes, within nanometer scale wells. Integrated devices including integrated detectors such as CMOS detectors are included.
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
G01N 21/77 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator
G01N 33/543 - ImmunoassayBiospecific binding assayMaterials therefor with an insoluble carrier for immobilising immunochemicals
50.
DIGITAL ANALYSIS OF MOLECULAR ANALYTES USING SINGLE MOLECULE DETECTION
Methods and systems are provided for small molecule analyte detection using digital signals, key encryption, and communications protocols. The methods provide detection of a large numbers of proteins, peptides, RNA molecules, and DNA molecules in a single optical or electrical detection assay within a large dynamic range.
Disclosed herein are methods and systems for detection and discrimination of optical signals from a densely packed substrate. These have broad applications for biomolecule detection near or below the diffraction limit of optical systems, including in improving the efficiency and accuracy of polynucleotide sequencing applications.
Labeled nucleotide analogs comprising at least one avidin protein, at least one dye-labeled compound, and at least one nucleotide compound are provided. The analogs are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The analogs are detectable with high sensitivity at desirable wavelengths. They contain structural components that modulate the interactions of the analogs with DNA polymerase, thus decreasing photodamage and improving the kinetic and other properties of the analogs in sequencing reactions. Also provided are nucleotide and dye-labeled compounds of the subject analogs, as well as intermediates useful in the preparation of the compounds and analogs. Compositions comprising the compounds, methods of synthesis of the intermediates, compounds, and analogs, and mutant DNA polymerases are also provided.
C07H 19/207 - Purine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids the phosphoric or polyphosphoric acids being esterified by a further hydroxylic compound, e.g. flavine-adenine dinucleotide or nicotinamide-adenine dinucleotide
C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
C09B 23/06 - Methine or polymethine dyes, e.g. cyanine dyes characterised by the methine chain containing an odd number of CH groups three CH groups, e.g. carbocyanines
C09B 23/08 - Methine or polymethine dyes, e.g. cyanine dyes characterised by the methine chain containing an odd number of CH groups more than three CH groups, e.g. polycarbocyanines
C09B 69/00 - Dyes not provided for by a single group of this subclass
The present disclosure provides compositions, methods and systems for sequencing a template nucleic acid using a polymerase based, nucleic acid binding reaction involving examination of the interaction between a polymerase and template nucleic acid in the presence of one or more unlabeled nucleotides. The methods rely, in part, on identifying a base of a template nucleic acid during nucleic acid synthesis by controlling the sequencing reaction conditions. Template nucleic acid bases may be identified during an examination step followed by an optional incorporation step.
Methods, compositions, and systems are provided that allow for reliable sequencing of the initial sequence region of a sequence of interest. The methods of the invention allow for more reliable barcoding of subpopulations of nucleic acids to be sequenced.
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Assays and reagents for scientific and research use; reagent kits consisting primarily of reagents for preparation and performance of single molecule assays for scientific and research use; buffers, enzymes, reagents, nucleotides, chemical preparations and biological compounds, each of which is for use in preparation and performance of single molecule assays for scientific and research use
05 - Pharmaceutical, veterinary and sanitary products
Goods & Services
Medical diagnostic assays and reagents for testing of biological samples; reagent kits comprised of medical diagnostic reagents for testing biological samples; buffers, enzymes, reagents, nucleotides, chemical preparations and biological compounds, each of which is for use in medical diagnostic assays
Disclosed herein are blocked asymmetric hairpin adaptors that include a spacer that prevents extension by a strand-displacing polymerase. Such adaptors can be utilized for creating libraries of templates that can be processed into template concatemers and/or interrogated by various sequencing methods.
A sensor having a first electrode and a second electrode operably connected by a conduction channel, wherein a polymerase, primed template nucleic acid and nucleotide form a stabilized ternary complex that is immobilized in or on the conduction channel, whereby association and dissociation of the ternary complex is detected due to changes in electrical properties of the sensor. Identification of the nucleotide type that participates in the complex indicates the identity of the next template base in the template. Repeated cycles of extending the primer and detecting stabilized ternary complexes can allow determination of the sequence of nucleotides for the template.
Disclosed herein are methods of detecting at least one target biomolecule in at least one single cell comprising lysing the single cell or cells and performing a cell identification assay and target identification assay. Also disclosed herein are methods for preparing a sample for undergoing single cell analysis, wherein the single cell analysis comprises performing a cell identification assay and a target identification assay.
Disclosed herein are methods and systems for detection and discrimination of optical signals from a densely packed substrate. These have broad applications for biomolecule detection near or below the diffraction limit of optical systems, including in improving the efficiency and accuracy of polynucleotide sequencing applications.
Disclosed herein are methods and systems for detection and discrimination of optical signals from a densely packed substrate. These methods and systems may have broad applications for biomolecule detection near or below the diffraction limit of optical systems, including in improving the efficiency and accuracy of polynucleotide sequencing applications.
The invention relates to methods and compositions for the detection and quantification of nucleotide sequence variants, such as genetic polymorphisms, with decreased error and increased sensitivity, including single molecule detection. Detection of genetic polymorphisms, including single nucleotide polymorphisms (SNPs), is highly useful for the study of physiology, disease, phylogeny and forensics. Current methods for the detection and identification of nucleic acid sequence variants, such as genetic polymorphisms, lack the sensitivity to accurately detect low incidence mutations, sequence variants or alleles. Detection techniques for highly multiplexed single molecule identification and quantification of analytes using optical systems are disclosed. Analytes include, but are not limited to, nucleic acid, such as DNA and RNA molecules, with and without modifications. Techniques described herein include use of specific and non-specific probes complementary to nucleic acids of interest for detailed characterization of nucleotide sequence variants and highly multiplexed single molecule identification and quantification.
Optical analytical devices and their methods of use are provided. The devices are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The devices include optical waveguides for illumination of the optical reactions. The devices further provide for the efficient coupling of optical excitation energy from the waveguides to the optical reactions. Optical signals emitted from the reactions can thus be measured with high sensitivity and discrimination using features such as spectra, amplitude, and time resolution, or combinations thereof. The devices of the invention are well suited for miniaturization and high throughput.
G01N 21/77 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator
G02B 6/024 - Optical fibres with cladding with polarisation-maintaining properties
G02B 6/10 - Light guidesStructural details of arrangements comprising light guides and other optical elements, e.g. couplings of the optical waveguide type
G02B 6/12 - Light guidesStructural details of arrangements comprising light guides and other optical elements, e.g. couplings of the optical waveguide type of the integrated circuit kind
G02B 6/122 - Basic optical elements, e.g. light-guiding paths
G02F 1/365 - Non-linear optics in an optical waveguide structure
B82Y 15/00 - Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
B82Y 20/00 - Nanooptics, e.g. quantum optics or photonic crystals
G02B 23/24 - Instruments for viewing the inside of hollow bodies, e.g. fibrescopes
65.
METHODS AND COMPOSITIONS FOR LOADING OF POLYMERASE COMPLEXES
The present disclosure provides methods, compositions, and systems for distributing polymerase compositions into array regions. In particular, the described methods, compositions, and systems utilize density differentials and/or additives to increase efficiency in the distribution of polymerase compositions to a surface as compared to methods utilizing only diffusion control.
Methods, compositions, and systems for distributing nucleic acids into array regions are provided. The methods, compositions, and systems utilize nucleic acid condensing agents to increase efficiency of distribution of the nucleic acids into the array regions. Various methods for facilitating distribution of the nucleic acids to the array regions are provided.
Disclosed herein is a high throughput optical scanning device and methods of use. The optical scanning device and methods of use provided herein can allow high throughput scanning of a continuously moving object with a high resolution despite fluctuations in stage velocity. This can aid in high throughput scanning of a substrate, such as a biological chip comprising fluorophores. Also provided herein are improved optical relay systems and scanning optics.
H04N 5/232 - Devices for controlling television cameras, e.g. remote control
G01D 5/347 - Mechanical means for transferring the output of a sensing memberMeans for converting the output of a sensing member to another variable where the form or nature of the sensing member does not constrain the means for convertingTransducers not specially adapted for a specific variable using optical means, i.e. using infrared, visible or ultraviolet light with attenuation or whole or partial obturation of beams of light the beams of light being detected by photocells using displacement encoding scales
G02B 27/64 - Imaging systems using optical elements for stabilisation of the lateral and angular position of the image
H04N 3/08 - Scanning details of television systemsCombination thereof with generation of supply voltages by optical-mechanical means only having a moving reflector
Disclosed herein are methods and systems for detection and discrimination of optical signals from a densely packed substrate. There have broad applications for biomolecule detection near or below the diffraction limit of optical systems, including in improving the efficiency and accuracy or polynucleotide sequencing applications.
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
Goods & Services
(1) Assays and reagents for scientific or research use; reagent kits for preparation or performance of single molecule assays for scientific or research use; buffers, enzymes, reagents, nucleotides, chemical preparations and/or biological compounds for scientific or research use.
(2) Assays and reagents for medical and diagnostic use; reagent kits for medical and diagnostic use; buffers, enzymes, reagents, nucleotides, chemical preparations and/or biological compounds for medical and diagnostic use.
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
09 - Scientific and electric apparatus and instruments
10 - Medical apparatus and instruments
Goods & Services
Assays and reagents for scientific or research use; reagent
kits for preparation or performance of ensemble or bulk
assays for scientific or research use; reagent kits
comprising components for single molecule assays for
scientific or research use. Assays and reagents for medical diagnosis. Laboratory instruments for scientific research, namely,
optical detectors for genetic sequencing and biochemical
analysis; analytical array chips; optical array chips for
genetic sequencing and biochemical analysis; downloadable
computer software for the analysis of biological data. Medical diagnostic instruments for clinical medical genetic
sequencing and biochemical analysis and for the analysis of
genes, molecules, DNA and RNA samples; medical analytical
array chips for clinical medical genetic sequencing and
biochemical analysis and for the analysis of genes,
molecules, DNA and RNA samples.
71.
SIZE SELECTION PURIFICATION USING A THERMOPLASTIC SILICA NANOMATERIAL
The present disclosure is directed to a method for purifying a sample containing nucleic acids to obtain isolated nucleic acids of a desired size range, either above a size cut-off, below a cut-off, or within a defined band of sizes, including: a) combining a nucleic acid-containing sample with a binding buffer to provide a binding mixture; b) contacting the binding mixture with a silica nanomembrane, wherein the silica nanomembrane adsorbs nucleic acids from the binding mixture within a desired size-range; and c) separating the bound nucleic acid from the remaining sample. Kits including a silica nanomembrane, a binding buffer and one or wash buffers are also provided herein.
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
B01J 20/10 - Solid sorbent compositions or filter aid compositionsSorbents for chromatographyProcesses for preparing, regenerating or reactivating thereof comprising inorganic material comprising silica or silicate
72.
Labeled nucleotide analogs, reaction mixtures, and methods and systems for sequencing
Labeled nucleotide analogs comprising at least one avidin protein, at least one dye-labeled compound, and at least one nucleotide compound are provided. The analogs are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The analogs are detectable with high sensitivity at desirable wavelengths. They contain structural components that modulate the interactions of the analogs with DNA polymerase, thus decreasing photodamage and improving the kinetic and other properties of the analogs in sequencing reactions. Also provided are nucleotide and dye-labeled compounds of the subject analogs, as well as intermediates useful in the preparation of the compounds and analogs. Compositions comprising the compounds, methods of synthesis of the intermediates, compounds, and analogs, and mutant DNA polymerases are also provided.
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
C07H 19/10 - Pyrimidine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids
C07H 19/207 - Purine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids the phosphoric or polyphosphoric acids being esterified by a further hydroxylic compound, e.g. flavine-adenine dinucleotide or nicotinamide-adenine dinucleotide
Compositions, methods, and systems are provided for fluorescent polymerase enzyme substrates comprising protein shields for improving enzyme photostability in single molecule real time sequencing. Fluorescent polymerase enzyme substrates of the invention have a protein shield between the fluorescent dye moieties and nucleotide moieties of the polymerase enzyme substrate. The polymerase enzyme substrates have a nucleotide component and a dye component, each attached to a protein. The attachments can be covalent. The protein can, for example, prevent the direct interaction of the fluorescent dye moiety with the enzyme when carrying out nucleotide synthesis, preventing photodamage to the enzyme. The polymerase enzyme substrates of the invention can have multiple dyes and multiple nucleotide moieties.
C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
C07K 14/36 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from bacteria from ActinomycesPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from bacteria from Streptomyces (G)
C09B 23/08 - Methine or polymethine dyes, e.g. cyanine dyes characterised by the methine chain containing an odd number of CH groups more than three CH groups, e.g. polycarbocyanines
C09B 69/10 - Polymeric dyesReaction products of dyes with monomers or with macromolecular compounds
A method for determining sequences from sense and antisense strands of a nucleic acid, including (a) providing a nucleic acid cluster attached to a solid support, wherein the nucleic acid cluster includes a sense strand and an antisense strand of a concatemer, the concatemer including multiple copies of a sequence unit, the sequence unit including a target sequence and a primer binding site; (b) hybridizing a primer to a primer binding site in the antisense strand; (c) extending the primer along the antisense strand to determine the sequence from at least a portion of the target sequence in the antisense strand; (d) hybridizing a second primer to a primer binding site in the sense strand; and (e) extending the second primer along the sense strand to determine the sequence from at least a portion of the target sequence in the sense strand.
01 - Chemical and biological materials for industrial, scientific and agricultural use
09 - Scientific and electric apparatus and instruments
Goods & Services
Assays and reagents for scientific or research use; reagent
kits for preparation or performance of single molecule
assays for scientific or research use; reagent kits
comprising components for single molecule assays for
scientific or research use. Laboratory instruments for scientific research, namely,
optical detectors for genetic sequencing and biochemical
analysis; analytical array chips; optical array chips for
genetic sequencing and biochemical analysis; downloadable
computer software for the analysis of biological data.
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Assays and reagents for scientific and research use; Reagent kits consisting primarily of reagents for preparation and performance of single molecule assays for scientific and research use; buffers, enzymes, reagents, nucleotides, chemical preparations and biological compounds, each of which is for use in preparation and performance of single molecule assays for scientific and research use
05 - Pharmaceutical, veterinary and sanitary products
Goods & Services
Medical diagnostic assays and reagents for testing of biological samples; reagent kits comprised of medical diagnostic reagents for testing biological samples; buffers, enzymes, reagents, nucleotides, chemical preparations and biological compounds, each of which is for use in medical diagnostic assays
79.
Fluidic apparatus and methods useful for chemical and biological reactions
Provided herein is a method of performing a nucleic acid sequencing reaction using a sequencing system comprising a reagent cartridge coupled to a detection apparatus, and a pump coupled to the reagent cartridge. The reagent cartridge includes a plurality of reagent reservoirs and a main channel. The detection apparatus includes a flow cell that is coupled to the reagent cartridge when the reagent cartridge interacts transiently with the detection apparatus.
Arrays of integrated analytical devices and their methods for production are provided. The arrays are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The devices allow the highly sensitive discrimination of optical signals using features such as spectra, amplitude, and time resolution, or combinations thereof. The devices include an integrated diffractive beam shaping element that provides for the spatial separation of light emitted from the optical reactions.
G01N 21/77 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator
G01N 21/78 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator producing a change of colour
G02B 6/132 - Integrated optical circuits characterised by the manufacturing method by deposition of thin films
G02B 6/136 - Integrated optical circuits characterised by the manufacturing method by etching
G02B 6/12 - Light guidesStructural details of arrangements comprising light guides and other optical elements, e.g. couplings of the optical waveguide type of the integrated circuit kind
Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.
01 - Chemical and biological materials for industrial, scientific and agricultural use
09 - Scientific and electric apparatus and instruments
Goods & Services
(1) Assays and reagents for use in the fields of biological, biochemical and diagnostic analysis for scientific and research use; reagent kits for preparation or performance of single molecule assays for scientific or research use; reagent kits comprising components for single molecule assays for scientific or research use
(2) Laboratory instruments for scientific research, namely, optical detectors for genetic sequencing and biochemical analysis; analytical array chips; optical array chips for genetic sequencing and biochemical analysis; downloadable computer software for the analysis of biological data in the fields of genomics, sequencing, disease research, therapeutics research, biology, biochemistry, and biotechnology
83.
SYSTEMS AND METHODS OF DETECTING DENSELY-PACKED ANALYTES
Disclosed herein are methods and systems for detection and discrimination of optical signals from a densely packed substrate. These may have broad applications for biomolecule detection near or below the diffraction limit of optical systems, including in improving the efficiency and accuracy of polynucleotide sequencing applications.
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
09 - Scientific and electric apparatus and instruments
10 - Medical apparatus and instruments
Goods & Services
(1) Assays and reagents for scientific or research use; reagent kits for preparation or performance of ensemble or bulk assays for scientific or research use; reagent kits comprising components for single molecule assays for scientific or research use.
(2) Assays and reagents for medical diagnosis.
(3) Laboratory instruments for scientific research, namely, optical detectors for genetic sequencing and biochemical analysis; analytical array chips; optical array chips for genetic sequencing and biochemical analysis; downloadable computer software for the analysis of biological data.
(4) Medical diagnostic instruments for clinical medical genetic sequencing and biochemical analysis and for the analysis of genes, molecules, DNA and RNA samples; medical analytical array chips for clinical medical genetic sequencing and biochemical analysis and for the analysis of genes, molecules, DNA and RNA samples.
85.
DISTINGUISHING SEQUENCES BY DETECTING POLYMERASE DISSOCIATION
A method for determining the presence of an allele, including (a) binding a polymerase to a double stranded nucleic acid that includes a primer hybridized to a template, the template including a first allele of a locus; (b) adding a nucleotide to the primer via catalytic activity of the polymerase, thereby producing an extended nucleic acid; (c) dissociating the polymerase from the extended nucleic acid; (d) detecting dissociation of the polymerase from the extended nucleic acid; and (e) comparing the dissociation of the polymerase from the extended nucleic acid to dissociation of the polymerase from a second double stranded nucleic acid, the second double stranded nucleic acid including a primer hybridized to the same position of the locus as the primer of the extended nucleic acid.
Protected fluorescent reagent compounds and their methods of synthesis are provided. The compounds are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The compounds contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements.
C07H 19/10 - Pyrimidine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids
C07F 9/6558 - Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom containing at least two different or differently substituted hetero rings neither condensed among themselves nor condensed with a common carbocyclic ring or ring system
C07F 9/6561 - Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom containing systems of two or more relevant hetero rings condensed among themselves or condensed with a common carbocyclic ring or ring system, with or without other non-condensed hetero rings
C09B 23/06 - Methine or polymethine dyes, e.g. cyanine dyes characterised by the methine chain containing an odd number of CH groups three CH groups, e.g. carbocyanines
C09B 23/08 - Methine or polymethine dyes, e.g. cyanine dyes characterised by the methine chain containing an odd number of CH groups more than three CH groups, e.g. polycarbocyanines
C09B 69/10 - Polymeric dyesReaction products of dyes with monomers or with macromolecular compounds
Provided herein include a method for modifying polymerase-nucleic acid complexes, including (a) providing a plurality of surface-immobilized polymerase-nucleic acid complexes in a vessel, wherein the nucleic acid includes a primed-template nucleic acid, wherein at least a subset of the surface-immobilized polymerase-nucleic acid complexes include ternary complexes further including nucleotides; and (b) washing the surface with an aqueous solution including a diol, sulfoxide or polyol, thereby removing the nucleotides from the vessel and retaining the surface-immobilized polymerase-nucleic acid complexes in the vessel.
Optics collection and detection systems are provided for measuring optical signals from an array of optical sources over time. Methods of using the optics collection and detection systems are also described.
G01N 21/75 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated
G01N 21/77 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator
G01N 33/543 - ImmunoassayBiospecific binding assayMaterials therefor with an insoluble carrier for immobilising immunochemicals
G02B 6/122 - Basic optical elements, e.g. light-guiding paths
89.
METHODS AND COMPOSITIONS FOR DELIVERY OF MOLECULES AND COMPLEXES TO REACTION SITES
The present invention provides methods, compositions, and systems for distributing molecules and complexes into reaction sites. In particular, the methods, compositions, and systems of the present invention result in an active loading of molecules and complexes into reaction sites with improved efficiency over loading by passive diffusion methods alone.
A method of determining a nucleic acid sequence that includes steps of: (a) contacting a primed template nucleic acid with a series of mixtures for forming ternary complexes, wherein each of the mixtures includes a polymerase and nucleotide cognates for at least two different base types suspected of being present at the next template position of the template nucleic acid; (b) monitoring the next template position for ternary complexes formed by the series of mixtures, wherein a signal state indicates presence or absence of ternary complex formed at the next template position by each individual mixture, thereby determining a series of signal states that encodes a base call for the next template position; and (c) decoding the series of signal states to distinguish a correct base call for the next template position from an error in the base call.
Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.
Optical analytical devices and their methods of use are provided. The devices are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The devices include integrated illumination elements and optical waveguides for illumination of the optical reactions. The devices further provide for the efficient coupling of optical excitation energy from the waveguides to the optical reactions. Optical signals emitted from the reactions can thus be measured with high sensitivity and discrimination using features such as spectra, amplitude, and time resolution, or combinations thereof. The devices of the invention are well suited for miniaturization and high throughput.
G01N 21/77 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator
05 - Pharmaceutical, veterinary and sanitary products
10 - Medical apparatus and instruments
Goods & Services
Reagents for use in biochemical analysis for medical diagnostic use Medical diagnostic instruments, namely, optical detectors for genetic sequencing and biochemical analysis of genes, molecules, DNA and RNA samples
95.
Systems, devices, and methods for improved optical waveguide transmission and alignment
Provided herein are systems, devices, and methods for improved optical waveguide transmission and alignment in an analytical system. Waveguides in optical analytical systems can exhibit variable and increasing back reflection of single-wavelength illumination over time, thus limiting their effectiveness and reliability. The systems are also subject to optical interference under conditions that have been used to overcome the back reflection. Novel systems and approaches using broadband illumination light with multiple longitudinal modes have been developed to improve optical transmission and analysis in these systems. Novel systems and approaches for the alignment of a target waveguide device and an optical source are also disclosed.
G02B 6/12 - Light guidesStructural details of arrangements comprising light guides and other optical elements, e.g. couplings of the optical waveguide type of the integrated circuit kind
G01N 21/77 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator
G02B 6/122 - Basic optical elements, e.g. light-guiding paths
G02B 6/124 - Geodesic lenses or integrated gratings
G02B 6/42 - Coupling light guides with opto-electronic elements
G02B 27/09 - Beam shaping, e.g. changing the cross-sectioned area, not otherwise provided for
G02B 6/34 - Optical coupling means utilising prism or grating
96.
Recombinant polymerases with increased phototolerance
Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties include increased resistance to photodamage, and can also include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.
01 - Chemical and biological materials for industrial, scientific and agricultural use
09 - Scientific and electric apparatus and instruments
Goods & Services
Assays and reagents for scientific or research use; Reagent kits comprised of buffers, enzymes, reagents, nucleotides, chemical preparations and/or biological compounds for use in the preparation or performance of ensemble or bulk assays for scientific or research use; Reagent kits comprising components, namely, buffers, enzymes, reagents, nucleotides, chemical preparations and/or biological compounds, for single molecule assays for scientific or research use Laboratory instruments for scientific research, namely, optical detectors for genetic sequencing and biochemical analysis; analytical array chips for genetic sequencing and biochemical analysis; optical array chips for genetic sequencing and biochemical analysis
98.
FLOW CELLS AND METHODS FOR THEIR MANUFACTURE AND USE
A flow cell that includes (a) a gasket interposed between a first substrate and a second substrate, wherein the gasket, the first substrate and the second substrate are impermeable to aqueous liquid and liquid adhesive, wherein the gasket has a footprint on the first substrate that delineates a channel for containing the aqueous liquid; (b) a via in the gasket, the via containing a solidified liquid adhesive that bonds the first substrate to the second substrate, wherein the solidified liquid adhesive in the via is separated from the channel by the gasket; and (c) a channel port connecting the channel to the exterior of the flow cell, wherein the channel port is permeable to the aqueous liquid.
Provided herein are methods of purifying a sample containing nucleic acids to obtain isolated nucleic acids of a desired size range and methods of sequencing nucleic acids of a desired size range. The methods include a) combining a nucleic acid-containing sample with a precipitation buffer in a container to provide a precipitation mixture in which the precipitation buffer comprises water, a buffer, a salt, and polyvinyl pyrrolidinone (PVP) and/or Ficoll. The methods also include precipitating the nucleic acids in the precipitation mixture to provide a precipitated nucleic acid portion and a remaining sample portion. The precipitated nucleic acid portion predominantly comprises nucleic acid molecules above a selected size cutoff value and the remaining sample portion predominantly comprises nucleic acid molecules below the selected size cutoff value. The methods also include separating the precipitated nucleic acid portion from the remaining sample portion. Related compositions and kits are also provided herein.
Arrays of integrated analytical devices are provided. The arrays are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. In particular, the arrays provide increased efficiency of optical collection and decreased background signal as the lateral dimensions of the unit cell of devices within the array are decreased, for example as they are decreased to 2 μm, or even less.
