Provided herein are compositions and methods for Next Generation Sequencing. Further provided herein are compositions and methods for uniquely labeling molecules. Further provided herein are compositions and methods for synthesizing unique molecular identifiers.
Provided herein are compositions, devices, systems and methods for the generation and use of biomolecule-based information for storage. Further described herein are highly efficient methods for long term data storage with 100% accuracy in the retention of information. Additionally, devices described herein for de novo synthesis of oligonucleic acids encoding information related to the original source information may have a flexible material for oligonucleic acids extension.
Provided herein are methods, systems, and compositions for seamless nucleic acid assembly. Methods, systems, and compositions as provided herein provide for efficient assembly of nucleic acids without primer removal. Methods, systems, and compositions for seamless nucleic acid assembly comprise use of an endonuclease or exonuclease, optionally in conjunction with additional enzymes to assemble nucleic acids or polynucleotides.
Provided herein are methods and compositions relating to variant nucleic acid libraries encoding for antibodies including single domain antibodies. Libraries generated using methods described herein have improved characteristics including improved binding affinity. Libraries described herein include variegated libraries comprising nucleic acids each encoding for a predetermined variant of at least one predetermined reference nucleic acid sequence. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C07K 16/28 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
5.
Methods and Compositions Relating to Adenosine Receptors
Provided herein are methods and compositions relating to adenosine A2A receptor libraries having nucleic acids encoding for a scaffold comprising an adenosine A2A binding domain. adenosine A2A receptor libraries described herein encode for immunoglobulins such as antibodies.
C07K 16/28 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
6.
DEVICE WITH ADDRESSABLE LOCI, AT LEAST ONE ELECTRODE AND A POLYNUCLEOTIDE
Provided herein are compositions, devices, systems and methods for generation and use of biomolecule-based information for storage. Further provided are devices comprising addressable electrodes controlling polynucleotide synthesis (deprotection, extension, or cleavage, etc.) Further provided are compositions for low voltage deprotection of polynucleotides. Further provided is a device comprising a solid support comprising a plurality of addressable loci wherein each locus comprises at least one polynucleotide and a first electrode, and wherein a sample is located on a surface of the solid support.
Provided herein are methods and compositions relating to libraries of optimized antibodies having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein comprise nucleic acids encoding Dickkopf WNT signaling pathway inhibitor 1 (DKK1) antibodies. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
C07K 16/32 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against translation products from oncogenes
Described herein are devices, systems, methods for transferring information encoded by and stored in polynucleotide molecules. The information can be transferred by contacting the plurality of biomolecules residing on a first surface with another second surface, conjugating the biomolecules to the second surface, and cleaving the biomolecules from the first surface.
G11C 13/00 - Digital stores characterised by the use of storage elements not covered by groups , , or
G11C 5/04 - Supports for storage elementsMounting or fixing of storage elements on such supports
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
C40B 50/08 - Liquid phase synthesis, i.e. wherein all library building blocks are in liquid phase or in solution during library creationParticular methods of cleavage from the liquid support
G16B 35/00 - ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
Provided herein are methods and compositions relating to libraries of optimized antibodies having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein comprise nucleic acids encoding SARS-CoV-2 or ACE2 antibodies. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
C07K 16/28 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
C07K 16/00 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies
C07K 16/10 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
A61K 39/00 - Medicinal preparations containing antigens or antibodies
10.
DNA-BASED DIGITAL INFORMATION STORAGE WITH SIDEWALL ELECTRODES
Provided herein are compositions, devices, systems and methods for generation and use of biomolecule-based information for storage. Further provided are devices-having addressable electrodes controlling polynucleotide synthesis (deprotection, extension, or cleavage, etc.) The compositions, devices, systems and methods described herein provide improved storage, density, and retrieval of biomolecule-based information.
C40B 50/14 - Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creationParticular methods of cleavage from the solid support
G06F 16/00 - Information retrievalDatabase structures thereforFile system structures therefor
G06N 99/00 - Subject matter not provided for in other groups of this subclass
G11C 11/00 - Digital stores characterised by the use of particular electric or magnetic storage elementsStorage elements therefor
G11C 11/56 - Digital stores characterised by the use of particular electric or magnetic storage elementsStorage elements therefor using storage elements with more than two stable states represented by steps, e.g. of voltage, current, phase, frequency
G11C 13/00 - Digital stores characterised by the use of storage elements not covered by groups , , or
G11C 13/02 - Digital stores characterised by the use of storage elements not covered by groups , , or using elements whose operation depends upon chemical change
G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
Described herein are devices, systems, methods for processing biomolecules on a plurality of parallel substrates. A device can comprise a first substrate and a second substrate that can be substantially parallel. Each substrate can comprise a functionalized surface facing one another. The device may further comprise one or more fluidic interfaces and one or more spacers separating a plurality of substrates.
Described herein are methods and compositions relating to enzyme polypeptides and libraries having nucleic acids encoding for the polypeptides comprising variant amino acid sequences. Further described herein are methods of extending polynucleotide molecules using enzyme polypeptides having variant amino acid sequences. Further described herein are methods for preparing sequencing libraries using polymerase polypeptides having variant amino acid sequences.
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C12N 15/52 - Genes encoding for enzymes or proenzymes
C40B 40/06 - Libraries containing nucleotides or polynucleotides, or derivatives thereof
C40B 50/06 - Biochemical methods, e.g. using enzymes or whole viable microorganisms
C12N 15/66 - General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligationUse of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
13.
ANTIBODIES AND VARIANT NUCLEIC ACID LIBRARIES FOR SIRP-ALPHA
Provided herein are methods and compositions relating to SIRPα antibodies and libraries having nucleic acids encoding for a scaffold comprising a SIRPα domain. SIRPα libraries described herein encode for immunoglobulins such as antibodies.
C07K 16/28 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
C12N 15/62 - DNA sequences coding for fusion proteins
Disclosed herein are methods and compositions comprising a polymerase and a phosphorylated nucleoside, wherein the polymerase and the nucleoside are covalently linked by a cleavable linker at the terminal phosphate group. Further disclosed herein are enzymatic polynucleotide synthesis using polymerase and nucleotide conjugation strategies.
Provided herein are compositions relating to Dickkopf WNT signaling pathway inhibitor 1 (DKK1) binders, including bi-specific DKK1 binders. Further described herein are methods of making and using the DKK1 binders.
Described herein are compositions for detecting genomic variants associated with minimal residual disease (MRD). The compositions include libraries comprising a plurality of polynucleotides comprising at least one variant associated with minimal residual disease (MRD). Further described herein are methods of preparing such polynucleotide libraries, and methods of detecting MRD in a sample using such polynucleotide libraries.
C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
Described herein are systems for data storage, including components for receiving, encoding, synthesizing, storing, reading, sequencing, and decoding digital information stored in polynucleotides and libraries of polynucleotides. Further described herein are assemblies for storing information, systems comprising the assemblies, and methods of using the assemblies.
Provided herein are methods and compositions relating to antibodies or antibody fragments that bind B cell maturation agent (BCMA), BCMA libraries having nucleic acids encoding for a scaffold comprising a BCMA domain and chimeric antigen receptor (CAR) comprising BCMA antibody or antigen-binding fragment thereof. BCMA libraries described herein encode for immunoglobulins such as antibodies.
C07K 16/28 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
A61K 39/395 - AntibodiesImmunoglobulinsImmune serum, e.g. antilymphocytic serum
Provided herein are antibodies and antibody fragments relating to SIGLEC-8 and CD117. Provided herein are methods and compositions relating to SIGLEC-8 and/or CD117 libraries having nucleic acids encoding for a scaffold comprising a SIGLEC-8 and/or CD117 domain. SIGLEC-8 and/or CD117 libraries described herein encode for immunoglobulins such as antibodies.
Described herein are systems and methods for extracting biomolecules. Systems for extracting biomolecules can comprise a flow cell, a first reservoir, and a second reservoir. Methods for extracting molecules can comprise introducing liquid to the flow cell, evacuating the liquid from the flow cell, determining an amount of liquid recovered from the cavity, and adjusting a parameter of the system to determine conditions for recovering the maximum amount of liquid from the cavity.
Provided herein are compositions and methods for normalizing sequencing libraries. Further provided herein are adapter conjugates and hybrid circular adapters, composition comprising the same, and methods of generating the same. Further provided herein are methods of using the adapter conjugates, hybrid circular adapters, and compositions comprising the same to normalize genomic DNA libraries for next-generation sequencing.
Provided herein are compositions, devices, systems and methods for constructing and storing polynucleotides encoding information with redox resistant bases. The compositions, devices, systems, and methods described herein provide for storage or synthesis of a library comprising a plurality of polynucleotides with one or more redox resistance bases. Further provided herein are methods to increase DNA synthesis yield and fidelity.
Described herein are systems and methods for quality control of polynucleotides. The provided systems and methods for quality control are performed before, during, or after synthesis or storage of the polynucleotides. Further provided herein are system and methods for performing quality control of a surface, for example for synthesis or storage of polynucleotides.
Provided herein are methods and compositions relating to enzymes and libraries having nucleic acids encoding for an enzyme comprising modified sequences. Further provided herein are methods for enzyme optimization. Further provided herein are enzymes for sequencing library generation.
C12N 9/00 - Enzymes, e.g. ligases (6.)ProenzymesCompositions thereofProcesses for preparing, activating, inhibiting, separating, or purifying enzymes
C12N 15/00 - Mutation or genetic engineeringDNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purificationUse of hosts therefor
Provided herein are compositions, devices, systems and methods for single molecule sensing. Further provided are devices for nucleic acid sequencing. The compositions, devices, systems and methods described herein provide improved retrieval of biomolecule-based information.
Provided herein are methods and compositions relating to PSMA libraries having nucleic acids encoding for a scaffold comprising a prostate-specific membrane antigen (PSMA) binding domain. PSMA libraries described herein encode for immunoglobulins such as antibodies.
C07K 16/30 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells
27.
OLIGONUCLEIC ACID VARIANT LIBRARIES AND SYNTHESIS THEREOF
Disclosed herein are methods for the generation of highly accurate oligonucleic acid libraries encoding for predetermined variants of a nucleic acid sequence. The degree of variation may be complete, resulting in a saturated variant library, or less than complete, resulting in a selective library of variants. The variant oligonucleic acid libraries described herein may designed for further processing by transcription or translation. The variant oligonucleic acid libraries described herein may be designed to generate variant RNA, DNA and/or protein populations. Further provided herein are method for identifying variant species with increased or decreased activities, with applications in regulating biological functions and the design of therapeutics for treatment or reduction of disease.
C40B 50/06 - Biochemical methods, e.g. using enzymes or whole viable microorganisms
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides
C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
C40B 50/08 - Liquid phase synthesis, i.e. wherein all library building blocks are in liquid phase or in solution during library creationParticular methods of cleavage from the liquid support
C40B 50/14 - Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creationParticular methods of cleavage from the solid support
G01N 33/50 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing
Provided herein are methods and compositions relating to libraries of optimized antibodies having nucleic acids encoding for an antibody comprising modified sequences. Further provided herein are methods for antibody optimization with machine learning.
C07K 16/00 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies
C07K 16/28 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
Systems, methods, and compositions for identifying genomic variants and methylation analysis, including synthetic polynucleotide libraries, are provided. The synthetic polynucleotide libraries may comprise a plurality of polynucleotides. The polynucleotides may comprise sequences corresponding to a genetic abnormality in a genome. The stoichiometry of each of the plurality of polynucleotides is controlled. Systems, methods, and compositions described herein may include standards for determining the analytical sensitivity and/or accuracy of instruments configured to measure nucleic acid variant frequencies. Standards may comprise RNA-fusions and/or CNV mutations related to cancer.
Synthetic polynucleotide libraries may include a plurality of polynucleotides. The polynucleotides may comprise DNA and may be configured to hybridize with one or more regions of target nucleic acids. The target nucleic acids may comprise a cDNA library. The cDNA library may comprise at least one exon-exon boundary between a first exon and a second exon.
C07K 16/28 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
32.
POLYNUCLEOTIDES, REAGENTS, AND METHODS FOR NUCLEIC ACID HYBRIDIZATION
Provided herein are compositions, methods and systems relating to libraries of polynucleotides such that the libraries allow for accurate and efficient hybridization after binding to target sequences. Further provided herein are probes, blockers, additives, buffers, and methods that result in improved hybridization. Such compositions and methods are useful for improvement of Next Generation Sequencing applications, such as reducing off-target binding or reducing workflow times.
Devices for the manufacturing of high-quality building blocks, such as oligonucleotides, are described herein. Nano-scale devices allow for selective control over reaction conditions. Further, methods and devices described herein allow for the rapid construction of large libraries of highly accurate nucleic acids.
Provided herein are methods, systems, and compositions for efficient nucleic acid assembly with improved representation and distribution. Provided herein are methods, systems, and compositions for efficient nucleic acid assembly of nucleic acids encoding genes for use in various downstream processes.
Described herein are systems and methods for encoding digital data into oligonucleotides and decoding the oligonucleotides back into digital data. The encoding and decoding schemes include an inner codec for transforming the digital data into bases, and vice versa. The encoding and decoding schemes also include an outer codec comprising an error correction scheme.
Disclosed herein are methods for the generation of highly accurate nucleic acid libraries encoding for predetermined variants of a nucleic acid sequence. Further provided herein are method for identifying variant species with increased or decreased activities, with applications in regulating biological functions and the design of therapeutics for treatment or reduction of disease.
Described herein are systems and methods for encoding digital data into oligonucleotides and decoding the oligonucleotides back into digital data. The encoding and decoding schemes include an inner codec for transforming the digital data into bases, and vice versa. The encoding and decoding schemes also include an outer codec comprising an error correction scheme.
H03M 13/00 - Coding, decoding or code conversion, for error detection or error correctionCoding theory basic assumptionsCoding boundsError probability evaluation methodsChannel modelsSimulation or testing of codes
H03M 7/00 - Conversion of a code where information is represented by a given sequence or number of digits to a code where the same information is represented by a different sequence or number of digits
38.
METHODS AND DEVICES FOR DE NOVO OLIGONUCLEIC ACID ASSEMBLY
Methods and devices are provided herein for surfaces for de novo nucleic acid synthesis which provide for low error rates. In addition, methods and devices are provided herein for increased nucleic acid mass yield resulting from de novo nucleic acid synthesis.
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
B01J 19/00 - Chemical, physical or physico-chemical processes in generalTheir relevant apparatus
C07H 1/00 - Processes for the preparation of sugar derivatives
C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
C23C 16/455 - Chemical coating by decomposition of gaseous compounds, without leaving reaction products of surface material in the coating, i.e. chemical vapour deposition [CVD] processes characterised by the method of coating characterised by the method used for introducing gases into the reaction chamber or for modifying gas flows in the reaction chamber
Disclosed herein are methods and compositions for cleavage of nucleic acids from a surface of a solid support. Further described herein are cleavage methods compatible with enzymatic and chemical nucleic acid synthesis methods.
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
Testing the many hypotheses from genomics and systems biology experiments demands accurate and cost-effective gene and genome synthesis. Here we describe a microchip-based technology for multiplex gene synthesis. Pools of thousands of ‘construction’ oligonucleotides and tagged complementary ‘selection’ oligonucleotides are synthesized on photo-programmable microfluidic chips, released, amplified and selected by hybridization to reduce synthesis errors ninefold. A one-step polymerase assembly multiplexing reaction assembles these into multiple genes. This technology enabled us to synthesize all 21 genes that encode the proteins of the Escherichia coli 30S ribosomal subunit, and to optimize their translation efficiency in vitro through alteration of codon bias. This is a significant step towards the synthesis of ribosomes in vitro and should have utility for synthetic biology in general.
Disclosed herein are methods and compositions for cleavage of nucleic acids from a surface of a solid support. Further described herein are cleavage methods compatible with enzymatic and chemical nucleic acid synthesis methods.
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
C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
Provided herein are methods and compositions relating to libraries of optimized antibodies having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein comprise nucleic acids encoding Dickkopf WNT signaling pathway inhibitor 1 (DKK1) antibodies. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
C07K 16/32 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against translation products from oncogenes
Provided herein are compositions, devices, systems and methods for single molecule sensing. Further provided are devices for nucleic acid sequencing. The compositions, devices, systems and methods described herein provide improved retrieval of biomolecule-based information.
Provided herein are compositions and methods for identifying post-transcriptional nucleic acid modifications. Further provided herein are synthetic blocking libraries. Further provided herein are methods for designing synthetic blocking libraries, and application towards methylome analysis.
C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
Provided herein are compositions and methods for identifying post-transcriptional nucleic acid modifications. Further provided herein are synthetic blocking libraries. Further provided herein are methods for designing synthetic blocking libraries, and application towards methylome analysis.
C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
46.
METHYLATION-MEDIATED ADAPTER REMOVAL ON NUCLEIC ACID SEQUENCES
Restriction enzymes or restriction endonucleases are enzymes that cleave DNA into fragments at recognition sites known as restriction sites. Restriction enzymes, generally found in bacteria and archaea, provide an innate immune response that cleaves foreign DNA via restriction digestion. Provided herein are methods, systems, and compositions for efficient nucleic acid assembly with improved representation and distribution. Provided herein are methods, systems, and compositions for efficient nucleic acid assembly of nucleic acids encoding genes for use in various downstream processes.
C12Q 1/683 - Hybridisation assays for detection of mutation or polymorphism involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
C12N 15/66 - General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligationUse of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
Provided herein are methods and compositions relating to libraries of optimized antibodies (e.g., multispecific antibodies) having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein comprise nucleic acids encoding SARS-CoV-2 or ACE2 antibodies.
Provided herein are methods and compositions relating to neuropilin-1 (NRP1) libraries having nucleic acids encoding for immunoglobulins that bind to NRP1. Libraries described herein include variegated libraries comprising nucleic acids each encoding for a predetermined variant of at least one predetermined reference nucleic acid sequence. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
C07K 16/28 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
Provided herein are methods and compositions relating to cytokine variant libraries having nucleic acids encoding for immunoglobulins that bind to cytokines. Libraries described herein include variegated libraries comprising nucleic acids each encoding for a predetermined variant of at least one predetermined reference nucleic acid sequence. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
C07K 16/24 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against cytokines, lymphokines or interferons
50.
COMBINATORIAL DNA ASSEMBLY FOR MULTISPECIFIC ANTIBODIES
Disclosed herein are methods for the generation of highly accurate nucleic acid libraries encoding for predetermined variants of a nucleic acid sequence. Further provided herein are method for identifying variant species with increased or decreased activities, with applications in regulating biological functions and the design of therapeutics for treatment or reduction of disease.
De novo synthesized large libraries of nucleic acids are provided herein with low error rates. Further, devices for the manufacturing of high-quality building blocks, such as oligonucleotides, are described herein. Longer nucleic acids can be synthesized in parallel using microfluidic assemblies. Further, methods herein allow for the fast construction of large libraries of long, high-quality genes. Devices for the manufacturing of large libraries of long and high-quality nucleic acids are further described herein.
B01J 19/00 - Chemical, physical or physico-chemical processes in generalTheir relevant apparatus
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C40B 50/18 - Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creationParticular methods of cleavage from the solid support using a particular method of attachment to the solid support
C12N 15/66 - General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligationUse of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
C12N 15/74 - Vectors or expression systems specially adapted for prokaryotic hosts other than E. coli, e.g. Lactobacillus, Micromonospora
53.
BISPECIFIC SARS-COV-2 ANTIBODIES AND METHODS OF USE
Provided herein are methods and compositions relating to improved bispecific antibodies capable of binding and neutralizing SARS-CoV-2 variants. SARS-CoV-2 has been shown to mutant frequently, especially the Spike protein, making it resistant to both natural and acquired immunity. The bispecific antibodies of the invention have multiple binding domains to the Spike glycoprotein in order to target multiple mutations and enhance immunity against SARS-CoV-2. Further methods include methods of treating an individual for SARS-CoV-2, and immunizing an individual against SARS-CoV-2 prior to exposure. The antibodies of the invention can also be used for diagnosing individual with SARS-CoV-2.
Provided herein are methods and compositions relating to glucagon-like peptide-1 receptor (GLP1R) libraries having nucleic acids encoding for a scaffold comprising a GLP1R binding domain. Libraries described herein include variegated libraries comprising nucleic acids each encoding for a predetermined variant of at least one predetermined reference nucleic acid sequence. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
C40B 40/10 - Libraries containing peptides or polypeptides, or derivatives thereof
C07K 16/28 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
C40B 40/08 - Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
55.
SARS-COV-2 ANTIBODIES AND RELATED COMPOSITIONS AND METHODS OF USE
Provided herein are methods and compositions relating to libraries of optimized antibodies having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein comprise nucleic acids encoding SARS-CoV-2 or ACE2 antibodies. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
Provided herein are compositions, devices, systems and methods for the generation and use of biomolecule-based information for storage. Further described herein are highly efficient methods for long term data storage with 100% accuracy in the retention of information. Additionally, devices described herein for de novo synthesis of oligonucleic acids encoding information related to the original source information may have a flexible material for oligonucleic acids extension.
Provided herein are methods and compositions relating to libraries of optimized antibodies having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein comprise nucleic acids encoding SARS-CoV-2 or ACE2 antibodies. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
Nucleic acid sequencing with high fidelity and low cost has a central role in biotechnology and medicine, and in basic biomedical research. Provided herein are compositions and methods for Next Generation Sequencing. Further provided herein are compositions and methods for uniquely labeling molecules. Further provided herein are compositions and methods for synthesizing unique molecular identifiers.
Provided herein are compositions, devices, systems and methods for the generation and use of biomolecule-based information for storage. Additionally, devices described herein for de novo synthesis of nucleic acids encoding information related to the original source information may be rigid or flexible material. Further described herein are highly efficient methods for long term data storage with 100% accuracy in the retention of information. Also provided herein are methods and systems for efficient transfer of preselected polynucleotides from a storage structure for reading stored information.
G06F 21/78 - Protecting specific internal or peripheral components, in which the protection of a component leads to protection of the entire computer to assure secure storage of data
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
Provided herein are compositions, devices, systems and methods for single molecule sensing. Further provided are devices for nucleic acid sequencing. The compositions, devices, systems and methods described herein provide improved retrieval of biomolecule-based information.
Provided herein are methods and compositions relating to neuropilin-1 (NRP1) libraries having nucleic acids encoding for immunoglobulins that bind to NRP1. Libraries described herein include variegated libraries comprising nucleic acids each encoding for a predetermined variant of at least one predetermined reference nucleic acid sequence. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
C07K 16/28 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
A61K 39/395 - AntibodiesImmunoglobulinsImmune serum, e.g. antilymphocytic serum
Provided herein are compositions, devices, systems and methods for DNA oligomer synthesis. Further provided are devices comprising addressable electrodes controlling polynucleotide synthesis (deprotection, extension, or cleavage, etc.). The compositions, devices, systems and methods described herein provide improved synthesis, storage, density, and retrieval of biomolecule-based information.
Provided herein are methods and compositions relating to libraries of optimized antibodies having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein comprise nucleic acids encoding Dickkopf WNT signaling pathway inhibitor 1 (DKK1) antibodies. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
Provided herein are methods and compositions relating to cytokine variant libraries having nucleic acids encoding for immunoglobulins that bind to cytokines. Libraries described herein include variegated libraries comprising nucleic acids each encoding for a predetermined variant of at least one predetermined reference nucleic acid sequence. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
C07K 16/24 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against cytokines, lymphokines or interferons
Provided herein are methods and compositions relating to libraries of optimized antibodies having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein comprise nucleic acids encoding Dickkopf WNT signaling pathway inhibitor 1 (DKK1) antibodies. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
A61K 38/17 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from animalsPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from humans
C07K 7/06 - Linear peptides containing only normal peptide links having 5 to 11 amino acids
C07K 14/47 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from animalsPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from humans from vertebrates from mammals
C07K 16/22 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against growth factors
66.
NUCLEIC ACID BASED DATA STORAGE USING ENZYMATIC BIOENCRYPTION
Provided herein are compositions, devices, systems and methods for the generation and use of secured biomolecule-based information for storage. Further described herein are compositions, devices, systems and methods for bioencryption or biodecryption of information. Conversion of a digital sequence to a nucleic based sequence includes a step of selection of one or more bioencryption methods.
G06F 21/62 - Protecting access to data via a platform, e.g. using keys or access control rules
H04L 9/32 - Arrangements for secret or secure communicationsNetwork security protocols including means for verifying the identity or authority of a user of the system
G16B 50/00 - ICT programming tools or database systems specially adapted for bioinformatics
Provided herein are compositions, devices, systems and methods for DNA oligomer synthesis. Further provided are devices comprising addressable electrodes controlling polynucleotide synthesis (deprotection, extension, or cleavage, etc.). The compositions, devices, systems and methods described herein provide improved synthesis, storage, density, and retrieval of biomolecule-based information.
C07H 19/20 - Purine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids
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
Provided herein are methods and compositions relating to libraries of optimized antibodies. Libraries described herein comprise nucleic acids encoding SARS-CoV-2 or ACE2 antibodies. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
Provided herein are compositions, devices, systems and methods for DNA oligomer synthesis. Further provided are devices comprising addressable electrodes controlling polynucleotide synthesis (deprotection, extension, or cleavage, etc.). The compositions, devices, systems and methods described herein provide improved synthesis, storage, density, and retrieval of biomolecule-based information.
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 19/20 - Purine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids
C07H 21/00 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
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
70.
MULTISPECIFIC SARS-COV-2 ANTIBODIES AND METHODS OF USE
Provided herein are methods and compositions relating to libraries of optimized antibodies (e.g., multispecific antibodies) having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein comprise nucleic acids encoding SARS-CoV-2 or ACE2 antibodies.
Provided herein are compositions, devices, systems and methods for polynucleotide sequencing. Further provided are devices comprising surfaces for continuous sequencing. The compositions, devices, systems and methods described herein provide improved storage, density, and retrieval of biomolecule-based information.
Provided herein are compositions, devices, systems and methods for polynucleotide sequencing. Further provided are devices comprising surfaces for continuous sequencing. The compositions, devices, systems and methods described herein provide improved storage, density, and retrieval of biomolecule-based information.
Provided herein are methods, systems, and compositions for assembly of covalently closed double stranded nucleic acids. Provided herein are methods, systems, and compositions for assembly covalently closed double stranded nucleic acids for use in various downstream processes.
Provided herein are methods and compositions relating to libraries of optimized antibodies having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein include variegated libraries comprising nucleic acids each encoding for a predetermined variant of at least one predetermined reference nucleic acid sequence. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
De novo synthesized large libraries of nucleic acids are provided herein with low error rates. Further, devices for the manufacturing of high-quality building blocks, such as oligonucleotides, are described herein. Longer nucleic acids can be synthesized in parallel using microfluidic assemblies. Further, methods herein allow for the fast construction of large libraries of long, high-quality genes. Devices for the manufacturing of large libraries of long and high-quality nucleic acids are further described herein.
B01J 19/00 - Chemical, physical or physico-chemical processes in generalTheir relevant apparatus
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C40B 50/18 - Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creationParticular methods of cleavage from the solid support using a particular method of attachment to the solid support
C12N 15/66 - General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligationUse of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
C12N 15/74 - Vectors or expression systems specially adapted for prokaryotic hosts other than E. coli, e.g. Lactobacillus, Micromonospora
76.
SARS-COV-2 ANTIBODIES AND RELATED COMPOSITIONS AND METHODS OF USE
Provided herein are methods and compositions relating to libraries of optimized antibodies having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein comprise nucleic acids encoding SARS-CoV-2 or ACE2 antibodies. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
C07K 16/10 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
C07K 16/28 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids
Provided herein are methods and compositions relating to libraries of optimized antibodies having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein comprise nucleic acids encoding SARS-CoV-2 or ACE2 antibodies. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
Provided herein are methods, systems, and compositions for assembly of covalently closed double stranded nucleic acids. Provided herein are methods, systems, and compositions for assembly covalently closed double stranded nucleic acids for use in various downstream processes.
Provided herein are compositions, devices, systems and methods for the generation and use of biomolecule-based information for storage. Additionally, devices described herein for de novo synthesis of nucleic acids encoding information related to the original source information may be rigid or flexible material. Further described herein are highly efficient methods for long term data storage with 100% accuracy in the retention of information. Also provided herein are methods and systems for efficient transfer of preselected polynucleotides from a storage structure for reading stored information.
G06F 21/78 - Protecting specific internal or peripheral components, in which the protection of a component leads to protection of the entire computer to assure secure storage of data
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
80.
Methods and compositions relating to covid antibody epitopes
Provided herein are methods and compositions relating to libraries of optimized antibodies having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein comprise nucleic acids encoding SARS-CoV-2 or ACE2 antibodies. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
Provided herein are methods and compositions relating to glycan libraries having nucleic acids encoding for a scaffold comprising a glycan domain. Glycan libraries described herein encode for immunoglobulins such as antibodies.
Provided herein are methods and compositions relating to libraries of optimized antibodies having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein comprise nucleic acids encoding SARS-CoV-2 or ACE2 antibodies. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
Provided herein are compositions and methods for identifying genomic variants. Further provided herein are standards useful for determining the analytical sensitivity and/or accuracy of instruments configured to measure nucleic acid variant frequencies.
Provided herein are methods and compositions relating to ion channel libraries having nucleic acids encoding for a scaffold comprising a natural peptide toxin. Ion channel libraries described herein encode for immunoglobulins such as antibodies.
Provided herein are methods and compositions relating to ion channel libraries having nucleic acids encoding for a scaffold comprising a natural peptide toxin. Ion channel libraries described herein encode for immunoglobulins such as antibodies.
C12N 15/66 - General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligationUse of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
C40B 50/00 - Methods of creating libraries, e.g. combinatorial synthesis
Provided herein are methods and compositions relating to glycan libraries having nucleic acids encoding for a scaffold comprising a glycan domain. Glycan libraries described herein encode for immunoglobulins such as antibodies.
Provided herein are methods and compositions relating to CD3 libraries having nucleic acids encoding for a scaffold comprising a CD3 domain. CD3 libraries described herein encode for immunoglobulins such as antibodies.
C07K 16/28 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
C07K 16/18 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
Provided herein are compositions and methods for identifying genomic variants. Further provided herein are standards useful for determining the analytical sensitivity and/or accuracy of instruments configured to measure nucleic acid variant frequencies.
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving virus or bacteriophage
Provided herein are compositions and methods for identifying genomic variants. Further provided herein are standards useful for determining the analytical sensitivity and/or accuracy of instruments configured to measure nucleic acid variant frequencies.
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving virus or bacteriophage
Provided herein are methods, systems, and compositions for seamless nucleic acid assembly. Methods, systems, and compositions as provided herein provide for efficient assembly of nucleic acids without primer removal. Methods, systems, and compositions for seamless nucleic acid assembly comprise use of an endonuclease or exonuclease, optionally in conjunction with additional enzymes to assemble nucleic acids or polynucleotides.
Provided herein are compositions, devices, systems and methods for generation and use of biomolecule-based information for storage. Further provided are devices comprising addressable electrodes controlling polynucleotide synthesis (deprotection, extension, or cleavage, etc.) Further provided are compositions for low voltage deprotection of polynucleotides.
Provided herein are methods, systems, and compositions for seamless nucleic acid assembly. Such methods, systems, and compositions for seamless nucleic acid assembly include those for in vitro recombination cloning, single-stranded hierarchal DNA assembly, or overlap extension PCR without primer removal.
Provided herein are methods and compositions relating to TIGIT libraries having nucleic acids encoding for a scaffold comprising a TIGIT domain. TIGIT libraries described herein encode for immunoglobulins such as antibodies.
C07K 16/28 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
Provided herein are compositions, devices, systems and methods for generation and use of biomolecule-based information for storage. Further provided are devices comprising addressable electrodes controlling polynucleotide synthesis (deprotection, extension, or cleavage, etc.) Further provided are compositions for low voltage deprotection of polynucleotides.
Provided herein are methods and compositions relating to TIGIT libraries having nucleic acids encoding for a scaffold comprising a TIGIT domain. TIGIT libraries described herein encode for immunoglobulins such as antibodies.
C07K 16/28 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
C40B 40/08 - Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
C07K 16/00 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies
C40B 30/04 - Methods of screening libraries by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
Provided herein are methods and compositions relating to CD3 libraries having nucleic acids encoding for a scaffold comprising a CD3 domain. CDS libraries described herein encode for immunoglobulins such as antibodies. In some instances, the invention encompasses an antibody or antibody fragment that binds to the CD3 (Cluster of Differentiation 3) protein complex, comprising an immunoglobulin heavy chain comprising an amino acid sequence at least about 90% sequence identity to any one of SEQ ID NOs: 25-32. In some instances, the CD3 antibody or immunoglobulin sequence comprises a light chain variable domain comprising at least about 70% sequence identity to any one of SEQ ID NOs: 33-36. Methods of use thereof include methods of treating cancer or viral infection comprising administering the antibody or antibody fragment to a subject in need thereof.
C07K 16/28 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
Provided herein are methods and compositions relating to G protein-coupled receptor (GPCR) libraries having nucleic acids encoding for a scaffold comprising a GPCR binding domain. Libraries described herein include variegated libraries comprising nucleic acids each encoding for a predetermined variant of at least one predetermined reference nucleic acid sequence. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
C07K 16/28 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
C07K 16/00 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
Provided herein are compositions and methods for identifying genomic variants. Further provided herein are compositions and methods for capture of genomic sequences. Further provided herein are compositions and methods for capturing genomic DNA comprising single nucleotide polymorphisms.
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
C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
Provided herein are compositions and methods for identifying genomic variants. Further provided herein are compositions and methods for capture of genomic sequences. Further provided herein are compositions and methods for capturing genomic DNA comprising single nucleotide polymorphisms.
