21 results about "TRNA synthesis" patented technology

The present inventive concept relates to methods of nucleic acid sequencing, and applications and uses of the same. Aspects of the inventive concept include nanopore sequencing on nucleic acids, such as ribonucleic acids (RNAs), including, but not limited to, transfer RNAs (tRNAs). Further aspects include kits for performing the methods, and applications of the methods of the inventive concept as substantively described herein.

The present invention relates to a pharmaceutical composition comprising at least five different suppressor transfer RNAs, where a) at least one of the suppressor transfer RNAs is capable of base-pairing with a UGA stop codon, at least one of the suppressor transfer RNAs is capable of base-pairing with a UAA stop codon, and at least one of the suppressor transfer RNAs is capable of base-pairing with a UAG stop codon; and b) the suppressor transfer RNAs are not all present in equal amounts in the composition, and a pharmaceutically acceptable carrier.

The present invention relates to a modified CCA gene which encodes a CCA-adding enzyme, which modified CCA gene leads to resistance against a positive-strand RNA virus having a transfer RNA-like structure (TLS). The invention further relates to plants and seeds comprising the modified genes, methods for making and identifying such plants and use of the gene.

To provide a method for rescuing a termination codon through genetic reassignment using ACE-tRNA.SOLUTION: In certain embodiments, the invention provides a modified transfer RNA (tRNA) comprising a T-arm, a D-arm, an anticodon arm, and an acceptor arm, wherein the T-arm comprises a T-stem having a nucleotide that interacts with elongation factor 1 alpha 1 (EF1 alpha). EF1 alpha recruits aminoacyl-tRNAs to the ribosome and protects the tRNA from being deacylated. Rational nucleotide substitutions result in tuned tRNA: EF1 α interactions that enhance tRNA delivery to the ribosome and protection from de-acylation.SELECTED DRAWING: None

The present inventive concept relates to methods of nucleic acid sequencing, and applications and uses of the same. Aspects of the inventive concept include nanopore sequencing on nucleic acids, such as ribonucleic acids (RNAs), including, but not limited to, transfer RNAs (tRNAs). Further aspects include kits for performing the methods, and applications of the methods of the inventive concept as substantively described herein.

There is provided a method of quantifying and / or identifying one or more nucleic acids associated with a condition. In one embodiment, the method identifies unannotated transfer RNA-derived fragments (tRFs). In one embodiment, the method identifies boundaries where nucleic acid sequence read ends are frequently detected, using a statistical model, such as Hidden Markov Model. There is also provided a method of determining / predicting a condition of a subject. In one embodiment, the method comprises using a scoring pipeline, such as tScore pipeline, that compares two sample groups, such as a cancer group and a healthy group, to assign quantitative scores to individual sequencing reads that extend to each sample. Also disclosed is a method of determining whether a subject suffers from or is at risk of developing a condition, such as cancer.

In certain embodiments, the present invention provides a modified transfer RNA (tRNA) comprising a T-arm, a D-arm, an anticodon-arm and an acceptor arm, wherein the T-arm comprises nucleotides that interact with the elongation factor 1 alpha protein, and methods of use thereof. In certain embodiments, the present invention provides a modified transfer RNA (tRNA) comprising a T-arm, a D-arm, an anticodon-arm and an acceptor arm, (a) wherein the anticodon-arm comprises a tri-nucleotide anticodon, wherein the anticodon is 5′-UCA-3′ and recognizes TGA stop codons, and wherein the acceptor arm is operably linked to a arginine, tryptophan or glycine; (b) wherein the anticodon-arm comprises a tri-nucleotide anticodon, wherein the anticodon is 5′-UUA-3′ and recognizes TAA stop codons, and wherein the acceptor arm is operably linked to a glutamine or, glutamate; or (c) wherein the anticodon-arm comprises a tri-nucleotide anticodon, wherein the anticodon is 5′-CUA-3′ and recognizes TAG stop codons, and wherein the acceptor arm is operably linked to a tryptophan, glutamate or glutamine.

The engineered transfer RNA (tRNA) molecules for carrying an arginine (Arg) amino acid (including, for example, a suppressor tRNA), the expression cassettes and vectors comprising nucleic acids encoding an engineered tRNA, pharmaceutical compositions comprising the expression cassettes, vectors, and / or the engineered tRNA, and methods of restoring translation and / or disease treatment involving engineered suppressor tRNA molecules are provided.

The present invention relates to a synthetic DNA construct comprising (A) a nucleic acid encoding transfer RNA and (B) a 5' leader sequence, wherein the 5' leader sequence contains a sequence motif for controlling the expression level of the transfer RNA.

A computer-implemented framework for designing high-efficiency and high-specificity nucleic acid molecules targeting transfer RNA (tRNA) and its derivatives (tDRs). The framework comprises two primary algorithms. The first, tBOND-G, designs guide RNAs (gRNAs) for Cas13-mediated tRNA cleavage by calculating physical parameters, including target site accessibility and binding energy, and processing them through a Support Vector Machine (SVM) model to predict cleavage efficiency. The second algorithm, tBOND-L, designs therapeutic Locked Nucleic Acid-modified antisense oligonucleotides (LNA-ASOs) that specifically target a tDR without binding to its parent tRNA. This method utilizes a processor to derive an efficiency score based on relative binding affinity and a specificity score based on simulated competitive binding environments.

The present disclosure relates to compositions and methods for treating genetic disorders caused by nonsense mutations using anticodon-engineered transfer RNA (ACE-tRNA) constructs. These DNA-based ACE-tRNA constructs are designed to suppress premature termination codons (PTCs) and restore the expression of full-length, functional proteins. The disclosure further provides formulations of ACE-tRNA constructs with poly(amine-co-ester) (PACE) polymeric nanoparticles to improve stability, protect nucleic acids, and enhance delivery to airway epithelial cells. Also described are functionalized ACE-tRNA Picovectors (sLPVs) incorporating targeting elements such as nuclear localization signals (NLSs), nucleolar localization sequences (NoLSs), and DNA nuclear targeting sequences (DTSs) to improve nuclear import and localization.

In certain embodiments, the present invention provides a modified transfer RNA (tRNA) comprising a T-arm, a D-arm, an anticodon-arm and an acceptor arm, wherein the T-arm comprises nucleotides that interact with the elongation factor 1 alpha protein, and methods of use thereof. In certain embodiments, the present invention provides a modified transfer RNA (tRNA) comprising a T-arm, a D-arm, an anticodon-arm and an acceptor arm, (a) wherein the anticodon-arm comprises a tri-nucleotide anticodon, wherein the anticodon is 5′-UCA-3′ and recognizes TGA stop codons, and wherein the acceptor arm is operably linked to a arginine, tryptophan or glycine; (b) wherein the anticodon-arm comprises a tri-nucleotide anticodon, wherein the anticodon is 5′-UUA-3′ and recognizes TAA stop codons, and wherein the acceptor arm is operably linked to a glutamine or, glutamate; or (c) wherein the anticodon-arm comprises a tri-nucleotide anticodon, wherein the anticodon is 5′-CUA-3′ and recognizes TAG stop codons, and wherein the acceptor arm is operably linked to a tryptophan, glutamate or glutamine.

The present invention relates to a method for the generation of a cDNA library from transfer RNA (tRNA) comprising (a) optionally ligating at least one DNA adapter to 3′-end of tRNA, wherein 3′-end of the DNA adapter is preferably a chain terminator dideoxycytidine, preferably under one or more of the following conditions: (i) crowding reagent at 5% to 35%, preferably 15% to 30%, and most preferably about 25%, (ii) MgCl2 concentration of 1 mM to 15 mM, preferably 3 to 12 mM and most preferably about 10 mM (iii) a temperature of 12° C. to 37° C., preferably of about 25° C. (iv) a pH of 6.0 to 9.0, preferably 6.5 to 8.0 and most preferably about 7.0, (v) reducing agent concentration of 0.1 mM to 10 mM, preferably 0.5 to 5 mM and most preferably about 1 mM, and (vi) a reaction time of at least 30 min, preferably at least 1.5 h and most preferably at least 3 h; and (b) reverse transcription in a primer-dependent reaction, in case step (a) is present, or in a template-switching reaction, in case step (a) is absent, of tRNAs into cDNA by a group II intron reverse transcriptase, under the following conditions: (i) KCl or NaCl at a concentration of 20 mM to 250 mM, preferably 50 to 100 mM and most preferably about 75 mM, (ii) MgCl2 at a concentration of 0.5 mM to 15 mM, preferably 1 to 5 mM and most preferably about 3 mM, (iii) a temperature of 30° C. to 65° C., preferably of about 42° C., and (iv) a reaction time of at least 2 h, preferably at least 8 h and most preferably at least 15 h, and preferably (v) a pH of 6.5 to 9.5, preferably 7.0 to 8.5 and most preferably about 8.0, and / or (vi) a reducing agent (DTT) at a concentration of 1 mM to 12.5 mM, preferably 3 to 8 mM and most preferably about 5 mM.

Disclosed are nucleic acid analysis and sequencing technologies. The disclosure addresses the preparation of transfer RNA (tRNA) constructs suitable for direct RNA sequencing and structural applications by enzymatically ligating multiple tRNA molecules into a single, longer RNA strand using designed RNA oligonucleotides. Disclosed are methods of preparing a sequencing library for a plurality of tRNAs and kits.

The present disclosure relates to compositions and methods for treating genetic disorders caused by nonsense mutations using anticodon-engineered transfer RNA (ACE-tRNA) constructs. These DNA-based ACE-tRNA constructs are designed to suppress premature termination codons (PTCs) and restore the expression of full-length, functional proteins. The disclosure further provides formulations of ACE-tRNA constructs with poly(amine-co-ester) (PACE) polymeric nanoparticles to improve stability, protect nucleic acids, and enhance delivery to airway epithelial cells. Also described are functionalized ACE-tRNA Picovectors (sLPVs) incorporating targeting elements such as nuclear localization signals (NLSs), nucleolar localization sequences (NoLSs), and DNA nuclear targeting sequences (DTSs) to improve nuclear import and localization.

Provided herein are methods and compositions for reducing the expression and / or activity of an oncogenic transfer RNA (tRNA). Composition for treating cancer in the subject are disclosed, comprising an inhibitor of an oncogenic transfer RNA (tRNA) to a subject in need thereof, wherein the oncogenic tRNA comprises an inhibitory nucleic acid such as ARG-TCT-4-1, an siRNA, an shRNA, an miRNA, an antisense oligonucleotide, or a nucleic acid modification such as a locked nucleic acid, a phosphorothioate modification, a 2′—O-methyl modification, a 2′—O-methoxyethyl modification, a 2′-fluoro modification, a phosphorodiamidate modification, or a mesylphosphoramidate modification. The disclosed compositions are disclosed as treating cancers such as a sarcoma, a glioblastoma, an adrenocortical carcinoma, a cholangiocarcinonma, a melanoma, a glioma, a diffuse glioma, a mature B cell neoplasm, a non-small cell lung cancer, an esophagogastric adenocarcinoma, a pheochromocytoma, a hepatocellular carcinoma, an endometrial carcinoma, a pancreatic adenocarcinoma, a breast carcinoma, an invasive breast carcinoma, a head and neck squamous cell carcinoma, a bladder urothelial carcinoma, a colorectal adenocarcinoma, an ovarian epithelial tumor, a prostate adenocarcinoma, a cervical squamous cell carcinoma, a renal non-clear cell carcinoma, or a renal clear cell carcinoma.

Provided is a trackable, robust and universal prime editing system TRU-PE, which comprises a vector. The vector comprises a gene encoding a guide RNA (gRNA) targeting a target gene locus, a tRNA (Transfer RNA), and a gene encoding a selection marker. The selection marker does not comprise a resistance gene. In the system, cells expressing editing elements are enriched by means of fluorescence guidance, such that the editing efficiency can be significantly improved when DNA or viral delivery methods are used. By using a split-PE design and a pegRNA architecture processed by hCtRNA, the TRU-PE system achieves simultaneous editing of up to 10 gene loci, with the editing efficiency being improved by up to 20 fold, effectively expanding the application range in hard-to-transfect cell types and complex gene loci. The gene editing system overcomes the application bottlenecks of prime editing technology in terms of size, delivery efficiency and multiplex editing. Moreover, the system is compatible with a variety of prime editor architectures and has wide applicability.

The present invention is directed to methods including determining in a sample obtained or derived from a subject: (a) an abundance of transfer RNA fragments (tRFs) including the motif RGTTCRA (RGTTCRA-tRFs); a ratio between the abundance of the RGTTCRA-tRFs and an abundance of all tRFs in a sample; or both, or a method including determining in a sample the ratio between the abundance of RGTTCRA-tRFs and mitochondrial tRFs, for diagnosing, determining severity, treating, testing novel therapeutics, or any combination thereof, of mitochondrial-related disease in a subject in need thereof.

The invention provides a child brain injury detection marker and application thereof, and belongs to the technical field of in-vitro diagnosis. The pediatric brain injury detection marker provided by the invention is 3 'tiRNA-50-SerCGA-4 which is a lysis product for transferring RNA in body fluid, the expression level of the 3' tiRNA-50-SerCGA-4 is confirmed to be related to pediatric brain injury for the first time, and the pediatric brain injury detection marker provided by the invention has the advantages of high specificity and high sensitivity, and can be used for detecting pediatric brain injury. The non-invasive or minimally invasive detection of the child brain injury can be realized, and the method has a wide application prospect.

The disclosure relates generally to suppressor tRNAs engineered to enhance suppression of premature termination and their use in treatment of disorders associated with a premature terminal codon, such as muscular dystrophy and cardiology disorders.

The invention discloses a method for capturing an FFPE sample space transcriptome and application of the method. The method comprises the following steps: exposing mRNA on an FFPE slice by using a de-crosslinking reagent, transferring RNA to a space transcriptome capture chip, carrying out reverse transcription, melting, synthesizing two chains, carrying out PCR (Polymerase Chain Reaction) amplification enrichment and purification, constructing a library, and carrying out sequencing analysis. The decrosslinking reagent comprises any one of the following components: (1) a NaCl solution; (2) a PBS buffer solution containing urea and Tween; (3) preparing a protease K solution; and (4) a sodium citrate buffer solution. Compared with the traditional method, the method disclosed by the invention has the advantages that the integrity of RNA (Ribonucleic Acid) can be better reserved, the RNA with polyA which is not completely degraded is efficiently enriched, and finally, the space transcriptome capture analysis of a low-quality FFPE sample is realized.