202 results about "Nucleobase" patented technology

Systems and methods for sequencing polynucleotides using nanopores are disclosed. In some embodiments, a polynucleotide including a single-stranded region and a double-stranded region, in which the single-stranded region is disposed through a nanopore. The polynucleotide can be moved relative to the nanopore by electric forces while one or more structural locks keep the polynucleotide close to the nanopore. A characteristic signal based on nanopore ionic current blockade and associated with the regions of the polynucleotide at or near the nanopore recognition zone is measured and used to infer the nucleobase sequence of the polynucleotide. In some examples, the double-stranded region is extended by a polymerase, and the polymerase is removed from the polynucleotide. In some examples, signals measured under different applied voltages provide nonredundant information regarding the polynucleotide sequence.

Some aspects of this disclosure provide strategies, systems, reagents, methods, and kits that are useful for the targeted editing of nucleic acids or the modification of nucleic acids or proteins, including editing a single site within the genome of a cell or subject, e.g., within the human genome. In some embodiments, fusion proteins of nucleic acid programmable DNA binding proteins e.g., GeoCas9 or variants thereof, and effector domains, e.g., deaminase domains, are provided. In some embodiments, methods for targeted nucleic acid editing or protein modification are provided. In some embodiments, reagents and kits for the generation of targeted nucleic acid editing proteins, e.g., fusion proteins of a GeoCas9 and effector domains, are provided.

The present disclosure provides methods for reducing sequencing errors comprising one or any combination of: (i) removing deaminated bases in any nucleic acid molecule throughout a library preparation workflow which includes immobilised splints which bind to the library, the use of a compaction oligonucleotide, optionally with an intervening sequence, formation of closed circular nucleic acids, creating gaps using glycosylase and lyase activities at positions with deaminated bases. The library may be sequenced using pairwise sequencing, e.g. with dark sequencing and / or sequencing using a multivalent labelled probe for the formation of an avidity molecule and soluble primer and polymerase. Method for sequencing concatemers in which the concatermers are contacted with polymerases, soluble primers and a multivalent labelled molecule which forms a complex with the polymerase. Detecting polymerase position and nucleobase bound to the polymerase in the complex. These methods generate higher quality base calls during downstream sequencing workflows.

Nucleic acid molecules, compositions, recombinant AAV (rAAV) particles, kits, and methods are described herein for delivering a base editor (or “nucleobase editor”) to cells, e.g., via AAV vectors. In particular, the disclosure provides compositions, methods, and uses for delivery of adenine base editors and cytosine base editors in a single AAV vector (or genome). Further described herein are improved AAV vectors containing size-minimized regulatory components that enable, e.g., the packaging of base editors. Provided herein are methods and compositions for delivering base editor proteins to a cell or tissue in a single recombinant AAV (rAAV) vector. Contemplated herein are improved methods and compositions for delivering these base editors in vivo, in a single rAAV particle. Further provided herein are base editors and compositions and cells comprising these base editors.

Provided herein are systems, compositions, and methods for generating immunogenic peptides or epitopes from tumor associated antigens (e.g., in vivo or ex vivo). Polynucleotides (e.g., genes) encoding the tumor associated antigens may be edited at selected target sites by nucleobase editors comprising a catalytically-inactive Cas9 and a cytosine deaminase, leading to the expression of heteroclitic or cryptic peptides that are more immunogenic than the native peptide derived from the tumor associated antigens. The heteroclitic or cryptic peptide elicit strong tumor-specific immune response (e.g., T-cell response or B-cell response), which inhibits tumor growth and metastasis.

Some aspects of this disclosure provide strategies, systems, reagents, methods, and kits that are useful for the targeted editing of nucleic acids, including editing a single site within the genome of a cell or subject, e.g., within the human genome. In some embodiments, fusion proteins of Cas9 and nucleic acid editing proteins or protein domains, e.g., deaminase domains, are provided. In some embodiments, methods for targeted nucleic acid editing are provided. In some embodiments, reagents and kits for the generation of targeted nucleic acid editing proteins, e.g., fusion proteins of Cas9 and nucleic acid editing proteins or domains, are provided.

The disclosure provides, for example, double stranded DNA (dsDNA) molecules comprising one or more chemically modified nucleobases. In some embodiments, the dsDNA molecule is circular and comprises a first strand and a second strand, wherein the first strand comprises one or more chemically modified nucleobases, and the second strand is free of chemically modified nucleobases. In some embodiments, the dsDNA molecule comprises a promoter sequence and an effector sequence that encodes an effector.

The disclosure provides, for example, a double stranded DNA (dsDNA) molecule comprising chemically modified nucleotides. In some embodiments, the dsDNA molecule comprises an upstream DNA end form which is a closed end, a downstream DNA end form which is a closed end, and a double stranded region comprising a sense strand and an antisense strand, in which the sense strand comprises one or more chemically modified nucleobases, and the antisense strand is free of chemically modified nucleobases.

The invention comprises a process for the production of a linear P-linked oligonucleotide bearing an alkyl phosphonate group at 5′-terminus of the formula Iwherein R1 is a C1-4-alkyl group, R2 is fluoro, hydroxyl or C1-4-alkoxy, X is sulfur or oxygen, the term Nucleobase stands for an optionally modified adenine, cytosine, guanine or uracil and the term oligo strand stands for the remaining P-linked oligo nucleotide strand, and wherein the oligo strand comprises at least one uracil nucleobase.The process is performed under conditions that the level of alkyl transfer impurities and the level of cyanoethyl (CNET) impurities in the linear P-linked oligonucleotide of formula I, is substantially reduced.

Described herein are nucleic acid molecules, compositions, recombinant AAV (rAAV) particles, kits, and methods for delivering a base editor (or a "nucleobase editor") to a cell, for example via an AAV vector. In particular, the present disclosure provides compositions, methods and uses for delivery of adenine base editors and cytosine base editors in a single AAV vector (or genome). Further described herein are improved AAV vectors comprising a minimised size regulatory component, for example, a regulatory component that can enable packaging of a base editor. Provided herein are methods and compositions for delivering a base editor protein to a cell or tissue in a single recombinant AAV (rAAV) vector. Improved methods and compositions for in vivo delivery of these base editors in a single rAAV particle are contemplated herein. Further provided herein are base editors, and compositions and cells comprising these base editors.

Disclosed are conjugates of an oligonucleotide and a peptide covalently bonded or linked via a linker to the oligonucleotide, the peptide including at least one cationic domain comprising at least 4 amino acid residues and at least one hydrophobic domain comprising at least 3 amino acid residues, provided that the peptide includes a total of 7 to 40 amino acid residues and does not include any artificial amino acid residues; and the oligonucleotide including a total of 12 to 40 contiguous nucleobases, where at least 12 contiguous nucleobases are complementary to a target sequence in a human dystrophin gene.

The present disclosure provides oligonucleotides comprising at least one radical of a central nervous system receptor ligand at a nucleobase, the 2' position of a nucleoside, or the 3' position of a nucleoside. The present disclosure also provides pharmaceutical compositions and kits comprising said oligonucleotides, methods of delivering said oligonucleotides, methods of modulating the activity of a protein using such oligonucleotides, and methods of treating, preventing, or diagnosing diseases (e.g., central nervous system diseases, neurodegenerative diseases, and neurocognitive diseases) in a. subject in need thereof using said oligonucleotides or pharmaceutical compositions thereof. The present disclosure also provides oligonucleosides that may be useful for making the oligonucleotides.

The disclosure provides, for example, double stranded DNA (dsDNA) molecules comprising one or more chemically modified nucleobases. In some embodiments, the dsDNA molecule is circular and comprises a first strand and a second strand, wherein the first strand comprises one or more chemically modified nucleobases, and the second strand is free of chemically modified nucleobases. In some embodiments, the dsDNA molecule comprises a promoter sequence and an effector sequence that encodes an effector.

Some aspects of this disclosure provide strategies, systems, reagents, methods, and kits that are useful for the targeted editing of nucleic acids, including editing a single site within the genome of a cell or subject, e.g., within the human genome. In some embodiments, fusion proteins of Cas9 and nucleic acid editing proteins or protein domains, e.g., deaminase domains, are provided. In some embodiments, methods for targeted nucleic acid editing are provided. In some embodiments, reagents and kits for the generation of targeted nucleic acid editing proteins, e.g., fusion proteins of Cas9 and nucleic acid editing proteins or domains, are provided.

Some aspects of this disclosure provide strategies, systems, reagents, methods, and kits that are useful for the targeted editing of nucleic acids or the modification of nucleic acids or proteins, including editing a single site within the genome of a cell or subject, e.g., within the human genome. In some embodiments, fusion proteins of nucleic acid programmable DNA binding proteins e.g., GeoCas9 or variants thereof, and effector domains, e.g., deaminase domains, are provided. In some embodiments, methods for targeted nucleic acid editing or protein modification are provided. In some embodiments, reagents and kits for the generation of targeted nucleic acid editing proteins, e.g., fusion proteins of a GeoCas9 and effector domains, are provided.

The present invention provides novel triazolopyrimidines derived from nucleobase thymine, and methods of producing the same, as well as various biologically active substances obtained by the methods, particularly antitumor agents. The triazolopyrimidine compounds represented by the following formulas (I) to (VIII) (wherein R represents a hydrogen atom, an alkyl group, or an aryl group) and methods of producing the same.

Described is a compound for substituting amino acids of proteins or peptides, wherein the compound has the formula (1)wherein the stereocenter C1* represents CH that either results in the D- or L-form of the compound of formula (1); A− is a negatively charged ion compensating the positive charge; X1 is H or an amine protecting group; X2 is OH, an ester residue or an amide residue or an activated carboxylic acid derivate to be used for the formation of an amide bond; Y1, Y2 and Y3 are independently from each other a C1-C6 alkyl, and Z1 and Z2 are independently from each other a nucleobase, a C1 to C16 alkyl group, an aromatic residue or a heteroaromatic residue, wherein the aromatic residue or the heteroaromatic residue contains one 5, 6, or 7-membered ring or two condensed 5, 6, or 7-membered rings sharing two carbon atoms, wherein the aromatic residue or the heteroaromatic residue can be substituted by a linear or branched C1 to C16 alkyl group and / or a further aromatic group. Furthermore, a method for preparing this compound and proteins and peptides containing this compound are disclosed.

The invention features the use of an adenylate deaminase base editor to destroy the scissor acceptor site of a disease-related gene, including compositions and methods for treating genetic diseases, particularly for treating, alleviating or ameliorating the asthenic effect of amyotrophic lateral sclerosis (ALS) and spinal bulbar muscular atrophy (SBMA). Provided herein are compositions and methods for using improved new base editors (e.g., adenosine base editors) comprising a polynucleotide programmable nucleotide binding domain and a nucleobase editing domain that cooperate with a guide polynucleotide, e.g., adenosine base editors, for example, adenosine base editors, for example, adenosine base editors, for example, adenosine base editors, for example, adenosine base editors, for example, adenosine base editors. The present invention relates to a method for modifying a target gene associated with a hereditary disease or disorder, such as ALS or SBMA, by modifying the target gene using a base editor system provided herein to disrupt normal transcription of a gene associated with the hereditary disease or disorder.

The disclosure relates to improved sequencing reactions. Specifically, the disclosure provides methods which allow for identification of sequencing reads that originated from the same DNA molecule based at least in part on (i) one or more locations into which a dNTP comprising a modified nucleobase was incorporated (such as during an end-repair step), (ii) one or more locations of one or more inappropriately converted nucleobases and / or one or more locations of one or more inappropriately unconverted nucleobases, and / or (iii) one or more additional sequencing errors (such as those introduced during an amplification step), such as one or more additional sequencing errors affecting one or more CpH positions.

To provide a C9orf72 oligonucleotide, a composition, and a method for treatment of C9orf72-associated conditions, disorders, or diseases including amyotrophic lateral sclerosis and frontotemporal dementia.SOLUTION: Provided is an oligonucleotide comprising at least one modification of a sugar, a base, or an internucleotidic linkage, wherein the base sequence of the oligonucleotide is or comprises at least 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 contiguous bases of a base sequence that is at least 80% identical with or complementary to a base sequence of a C9orf72 gene or a transcript thereof, and wherein a nucleobase at a 3' end of the oligonucleotide is optionally replaced by a replacement nucleobase selected from I, A, T, U, G, and C.SELECTED DRAWING: None

Provided are systems for strand-specific editing of DNA, including mitochondrial DNA in humans. The systems provided herein comprise a nickase and a single-stranded (ss) DNA deaminase each, or together, associated with a double-stranded DNA binding polypeptide such that DNA editing occurs in an editing region. Also provided herein are components of the systems for editing DNA taught herein, and methods of use thereof.

The present invention provides a composition and a method of using a base editor comprising a polynucleotide programmable nucleotide binding domain and a nucleobase editing domain that binds a guide polynucleotide. The invention also provides a base editor system for editing nucleobases of a target nucleotide sequence.

This disclosure relates to the modified 3' region elements that confer improved therapeutic properties including, but not limited to, increased stability, increased expression, and / or a reduced innate immune response when introduced into a population of cells, even in the absence of a 5'-cap. The disclosure also provides polynucleotides (e.g., RNA molecules) containing modified 3' regions. In some embodiments of the disclosure, the modified 3' regions contain modified adenosines (e.g., 2'-0-methoxy- adenosine, 2'-fluoro-adenosine, or locked nucleic acid (LNA)-adenosine) and / or a modified thymidine (e.g., inverted deoxythymidine). In some embodiments of the disclosure, the modified 3' region may contain one or more modified internucleoside linkages (e.g., a phosphorothioate linkage) or modified nucleobase (e.g., N1-methyl-pseudouridine). The polynucleotides of the disclosure may be used to express a desired polypeptide in a subject, such as a subject having a disease or condition associated with a deficiency in the corresponding endogenous polypeptide.

The invention relates to antisense molecules and methods for modulating splicing of polyomavirus T antigen pre-mRNA. In one aspect the invention relates to an antisense oligonucleotide 12 to 30, preferably 17, 18, 19 or 20 to 30 nucleobases in length which comprises a sequence that is the reverse complement of a contiguous stretch of at least 12 nucleobases of a polyomavirus T-antigen pre-mRNA and which antisense oligonucleotide can modulate splicing of said T-antigen pre-mRNA in a cell.

A method for DNA synthesis using protected nucleosides is disclosed. The nucleosides may be nucleoside triphosphates or nucleoside phosphoramidites with nucleobases attached to electrochemically-cleavable linkers. Removal of a protecting group by application of a voltage in solution triggers a cyclization reaction that cleaves the electrochemically-cleavable linkers. The electrochemically-cleavable linkers may include an amide linkage and an amide that forms a lactam or an ester linkage and a protected alcohol that forms a lactone when the protecting group is removed. The voltage used to cleave the electrochemically-cleavable linkers may be generated by activation of individual electrodes on a microelectrode array. The microelectrode array can be a substrate for solid-phase synthesis of oligonucleotides. Activation of specific electrodes removes the protecting groups at those electrodes and thus enables spatially-controlled extension of the oligonucleotides. Protected nucleosides linked to protecting groups by electrochemically-cleavable linkers are also disclosed.

A system and method for identifying nucleobases in a template polynucleotide is disclosed. In an embodiment, such a method may include providing a substrate comprising a plurality of template polynucleotides in a cluster. The method may further include generating light to stimulate fluorescence emission from the cluster. The method may further include receiving a first signal emitted at a first intensity from a first plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a first site. The method may further include receiving a second signal emitted at a second intensity from a second plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a second site. The method may further include identifying the nucleobases hybridized at the first and second sites of the template polynucleotide based on a combination of the first and second signals.

Provided herein is a method of detecting the presence or absence of a single naturally- or synthetically-modified nucleobase in a polynucleotide molecule, which is achieved by first contacting the polynucleotide molecule with one or more reagents capable of attaching a detectable moiety to at least one nucleobase of the polynucleotide molecule or to a nucleobase adjacent to the modified nucleobase, thereby forming a labeled nucleobase, while the presence or absence of the modified nucleobase is determined by the attachment. The polynucleotide molecule is then assayed using a nanopore device to detection the presence or absence of the labeled nucleobase, wherein the detectable moiety attached to at least one nucleobase in the polynucleotide molecule has a molecular weight that ranges from 40 to 1,000 Daltons, and the average pore diameter in the nanopore device is no more than 5 nanometers.

This disclosure relates to reagents such as antisense oligonucleotides that bind to nucleic acids encoding cryptic exons, thereby inhibiting or preventing ELAVL3 cryptic splicing, and to their use in the treatment or prevention of TDP-43-related neurodegenerative or neurological diseases or conditions associated therewith. In some embodiments, the antisense oligonucleotide is a nucleobase polymer capable of reducing the level or expression of intracellular ELAVL3 cryptic exon RNA and increasing or restoring the expression of functional ELAVL3 protein without substantially incorporating the cryptic exon RNA peptide sequence.

Disclosed herein are improved methods and compositions of de novo synthesis of nucleic acids by cyclic extension using nucleotides that have an N-linked or O-linked scar or protecting group, and subsequent removal of the scar or protecting group. During polymerase-nucleotide conjugate-based polynucleotide synthesis or after the synthesis is completed, nucleobases having a scar from linker cleavage can be converted back into native form by removal of the scars from the nucleobases. Secondary structure formation in the nascent chain, which may inhibit extension reactions, is suppressed by the use of monomers with protected nucleobases that prevent Watson-Crick base pairing and / or other structures. After the synthesis is completed, the nucleobases can be converted back into native form by palladium-based removal of the protecting groups.

The invention features base editors having reduced non-target deamination, methods of using the base editors, and assays for characterizing base editors as having decreased non-target deamination, e.g. compared to programmed, on-target deamination.