49 results about "Repeat sequence" patented technology

Aspects of the disclosure relate to compositions and methods for the diagnosis and / or treatment of certain neurodegenerative diseases, for example those diseases associated with repeat-associated non-ATG (RAN) translation proteins, such as amyotrophic lateral sclerosis (ALS). In some embodiments, the disclosure relates to recombinant adeno-associated viruses (rAAVs) expressing antibodies and antigen-binding fragments thereof that bind to poly(GA) RAN proteins. In some embodiments, the disclosure relates to methods of treating a RAN protein-associated disease by administering to a subject in need thereof the rAAVs.

The present invention is a precursor crRNA for a type I CRISPR-Cas system having a modified nucleotide, in which at least one nucleotide is a modified nucleotide in a region comprising the 5'arm region of a first repeat sequence, the 5 '-side stem formation region of the first repeat sequence, and the ring formation region of the first repeat sequence.

Split-pegRNA recorder reagents and methods are provided that provide specific molecular interactions within cells induce precise genome editing that inserts an event-specific barcode sequence into the predetermined genomic locus of DNA Tape. The split pegRNAs include (a) a crRNA component, including in 5′ to 3′ order (i) a spacer sequence for a genomic locus of interest; (ii) a crRNA repeat sequence necessary for binding to a CRISPR-Cas protein; and (iii) a first RNA extension; and (b) a petracrRNA component, including in 5′ to 3′ order (i) a second RNA extension; (ii) a petracrRNA antirepeat sequence necessary for binding to a CRISPR-Cas protein; (iii) a gRNA scaffold; wherein the crRNA component and the petracrRNA component are not covalently bound to each other.

A method for improving the replication of covalent closed circular plasmids is provided. [Solution] The method comprises the step of preparing a covalent closed circular plasmid having a Pol I-dependent origin of replication and an insert containing a structured DNA sequence selected from the group consisting of a reverse repeat sequence, a directional repeat sequence, a homopolymer repeat sequence, a eukaryotic origin of replication, or a eukaryotic promoter enhancer sequence, wherein the structured DNA sequence is located at a distance of less than 1000 bp from the Pol I-dependent origin of replication in the direction of replication. The method also comprises the step of modifying the covalent closed circular recombinant molecule so that the Pol I-dependent origin of replication is replaced with a Pol III-dependent origin of replication, thereby improving the replication of the covalent closed circular plasmid with the resulting Pol III-dependent origin of replication. A covalent closed circular recombinant DNA molecule without antibiotic markers is also provided.

It is an object of the present invention to provide a method for modifying multiple DNAs encoding identical or similar proteins using TALE, when the multiple DNAs are present. More specifically, the present invention relates to a method for modifying multiple DNAs encoding identical or similar proteins, wherein the method comprises allowing the TALE portion of one type of TALE-modifier complex comprising at least one repeat sequence containing RVD (repeat variable di-residue) composed of amino acids that recognize or tolerate N, V, H, D, B, R, Y, M, W, S or K, to bind to the binding regions of the multiple DNAs.

Provided herein are methods for determining the microsatellite instability status of samples. In one aspect, the methods include quantifying a number of different repeat lengths present at each of a plurality of microsatellite loci from sequence information to generate a site score for each of the plurality of the microsatellite loci. The methods also include comparing the site score of a given microsatellite locus to a site specific trained threshold for the given microsatellite locus for each of the plurality of the microsatellite loci and calling the given microsatellite locus as being unstable when the site score of the given microsatellite locus exceeds the site specific trained threshold for the given microsatellite locus to generate a microsatellite instability score, which includes a number of unstable microsatellite loci from the plurality of the microsatellite loci.

The present application relates to the technical field of biological research data analysis, and discloses a kind of computing biology research data analysis display method, including extracting total RNA from biological tissue or cell, RNA reverse transcription is cDNA, constructs library, and utilizes high-throughput sequencing platform to sequence library, to obtain a large number of short sequences.The present application can effectively identify abnormal repeat regions by comparing and threshold judging the number of short sequences mapped to the same genomic coordinate interval, so as to determine whether the gene expression difference result is reliable, when the number of abnormal sequences exceeds the preset repeat sequence threshold, by eliminating the influence of repeat sequence operation, i.e. for the case of high FPKM value, remove the completely same and overlapping short sequences, and re-align the updated results, the expression distortion problem caused by repeat counting can be corrected.

To provide more active hyperactive transposons and transposases.SOLUTION: The present invention relates to a polypeptide comprising a piggyBac transposase or a fragment or a derivative thereof having a transposase function comprising at least one amino acid substitution. Further, the present invention relates to a transposable element comprising a piggyBac or piggyBac-like left repeat sequence and left internal repeat sequence, where the left internal repeat sequence comprises at least one nucleotide modification. Furthermore, the present invention relates to a kit comprising the transposase and / or transposable element. In addition, the present invention relates to a targeting system comprising the transposase and / or transposable element.SELECTED DRAWING: None

RNA molecules comprising a guide sequence portion having 17-50 contiguous nucleotides containing nucleotides in the sequence set forth in any one of SEQ ID NOs: 1-2325 and compositions, methods, and uses thereof.

The invention relates to the technical field of genomics and microbial science, in particular to a myxobacteria T2T genome assembling method. The assembling method mainly comprises the four steps of global assembling, telomere sequence screening, local sequence clustering screening and second-generation data multi-round correction. According to the method provided by the invention, pollution removal strategies of telomere sequence screening and local sequence clustering screening are newly added, so that the problem that tandem repeat sequences in a myxobacteria genome are complex and short is effectively solved, the analysis of a complex region becomes possible, the integrity and continuity of assembly are improved, and the assembly efficiency is improved. The method does not need fingerprint spectrum, Hi-C technology or optical spectrum sequencing technology, reduces the experiment cost, ensures that all the sequences belonging to myxobacteria are extracted, effectively removes the interference of repetitive sequences and deep pronucleus pollution, enables highly similar repetitive sequence fragments to be reduced and positioned to an accurate genome position, and improves the accuracy of the detection result. The integrity and continuity of the genome are obviously improved.

The present application relates to the technical field of biological information, and particularly relates to a repeat sequence detection method, device and equipment and a storage medium, the repeat sequence detection method comprising the following steps: reading double-end current sequences from sequencing data obtained by double-end sequencing, and converting a first sequence segment in the double-end current sequences into a first integer type and a second sequence segment in the double-end current sequences into a second integer type; calculating a double-end sequence positioning characteristic value according to the first integer type, and detecting whether a value at a first position corresponding to the double-end sequence positioning characteristic value in a preset counting array is an occupied value; if the value at the first position is the occupied value, detecting whether the second integer type exists in a double-end sequence array; and if the second integer type exists in the double-end sequence array, determining that the double-end current sequences are repeat sequences. The present application improves the accuracy of repeat sequences.

The invention discloses a QPCR (Quantitative Polymerase Chain Reaction)-based DNA (Deoxyribose Nucleic Acid) methylation rate detection method, which comprises the following steps of: treating a DNA sample to be detected by bisulfite, dividing the DNA sample into a first sample and a second sample which are parallel to each other, and performing substrate amplification on a methylated DNA template and a non-methylated DNA template in the samples through PCR amplification by adopting the same amplification primer under the same condition; then respectively depleting dATP in a sample A reaction system and dGTP in a sample B reaction system through a template and a primer with thymine deoxyribonucleotide repetitive sequences or a template and a primer with cytosine deoxyribonucleotide repetitive sequences, and controlling independent detection of methylation and non-methylation templates through a d3TP system lacking dATP or dGTP; and finally, directly analyzing the fluorescence signal of the methylation template and the fluorescence signal of the non-methylation template, and calculating the methylation rate of the DNA sample to be detected through a methylation rate calculation function.

The invention relates to the field of molecular biology, in particular to a primer pair, a kit and a detection method for detecting a GAA repetitive sequence of an FXN gene. The sequence of the primer pair is as follows: FXN-F: 5 '-CCACCGTGTTATTTGGCC-3'; the primer pair is FXN-R: 5 '-CATGGCCACACCTGCCT-3', and the 5'end of the reverse primer FXN-R of the primer pair is provided with an FAM fluorophore. The method comprises the following steps: extracting DNA (Deoxyribonucleic Acid) and carrying out PCR (Polymerase Chain Reaction) amplification by utilizing the primer pair to obtain a PCR product containing a GAA trinucleotide repetitive sequence; the PCR product is detected through capillary electrophoresis, the GAA repetitive sequence condition of the FXN gene is analyzed according to the electrophoresis detection result, the FXN gene GAA repetitive sequence number is obtained, the whole detection process is short in time consumption, high in efficiency and high in specificity, and the trinucleotide repetitive sequence can be detected without sequencing.

This invention relates to the field of biomedical technology, specifically to a rapid and sensitive detection method for the CGG repeat sequence of the FMR1 gene and its application. It includes a primer combination for detecting the CGG repeat sequence of the FMR1 gene, comprising an upstream primer with the nucleotide sequence shown in SEQ ID NO: 1 and a downstream primer with the nucleotide sequence shown in SEQ ID NO: 2. This invention optimizes the PCR detection procedure, making it more sensitive for samples with high CGG repeat counts, while also enabling accurate quantification and faster detection, significantly shortening the detection time, effectively reducing the workload of operators, and lowering detection costs.

The invention provides a crop variety analysis method, device and equipment based on a simple repetitive sequence, and relates to the technical field of crop analysis, the method comprises the following steps: determining a target primer group according to a pre-screened simple repetitive sequence site of a target crop; performing polymerase chain reaction amplification on the target primer group to obtain an amplification product corresponding to the target primer group; performing electrophoretic separation on the amplification product to obtain a target fluorescence signal image corresponding to the amplification product; extracting target image features of the target fluorescence signal image; inputting the target image features into a pre-trained random forest classifier to obtain a variety analysis result of the target crop output by the random forest classifier; the random forest classifier is obtained by training based on the training image features and the corresponding variety identifiers. According to the method, feature extraction is performed on the target fluorescence signal image, and the target image features are input into the pre-trained random forest classifier, so that crop variety analysis can be accurately, efficiently and reliably realized.

The invention relates to a plasmid-free gene editing system based on T7RNA polymerase and application of the plasmid-free gene editing system, and belongs to the technical field of gene editing. The plasmid-free gene editing system constructed by the invention comprises a T7 RNA polymerase, a Cas12a nuclease, a selection marker gene and a short double-stranded DNA expression cassette, wherein the short double-stranded DNA expression cassette sequentially comprises a T7 promoter, a first forward repetitive sequence, a spacer sequence and a second forward repetitive sequence. According to the plasmid-free gene editing system, T7RNA polymerase is expressed in host bacteria, short double-stranded DNA is transcribed to generate guide RNA, Cas12a nuclease is driven to achieve rapid and efficient gene editing, the problems that in the prior art, linear fragment transformation is complex and tedious, and part of strains lack genetic plasmids are solved, iterative editing and multi-site editing are supported at the same time, and the plasmid-free gene editing system is suitable for large-scale popularization and application. And a brand-new convenient tool is provided for gene editing of non-model fungi.

A CRISPR-Cas system and applications thereof are provided, also related to a Cas protein, a fusion protein and a guide polynucleotide. The Cas protein has at least 50% sequence identity compared to the sequence set forth in any one of SEQ ID NOs: 1-184, 426-428. The fusion protein comprises the Cas protein fused to a protein domain and / or a polypeptide tag. The guide polynucleotide comprises a direct repeat sequence having at least 70% sequence identity to any one of SEQ ID NOs: 185-199, 245-247, 287-303, 369 and 370-373, and a guide sequence engineered to hybridize to a target nucleic acid. The CRISPR-Cas system comprises a Cas protein having at least 90% sequence identity compared to the sequence set forth in any one of SEQ ID NOs: 1-184, 426-428, or a nucleic acid encoding thereof, and a guide polynucleotide or a nucleic acid encoding thereof.

Staple nucleic acids capable of forming guanine quadruplex structure on a target nucleic acid even when four guanine repeat sequences are not present on the target nucleic acid. The oligonucleotide (second generation-type Staple nucleic acid) can supply guanine repeat sequences so that a guanine quadruplex structure can be formed on a target nucleic acid by a total of four guanine repeat sequences, consisting of guanine repeat sequences on the target nucleic acid and guanine repeat sequences on the oligonucleotide.

The invention discloses a construction method and application of an AAV single-molecule sequencing library and a kit, and belongs to the technical field of biological medicine detection. In order to solve the technical problem that ligase steric hindrance is caused by a secondary structure of an AAV inverted repeat (ITR), a Cas9-RNP compound specifically targeting an ITR stem region (Stem Region) is used for carrying out directional cutting on a single-chain genome, a closed-loop hairpin structure is removed, and a blunt-end double-chain DNA handle of 10-50 bp is reserved at the tail end. In cooperation with a forced dissociation step of the enzyme, the method eliminates connection steric hindrance and significantly improves the linker connection efficiency. According to the method, double-end cyclization is not needed, sequencing can be achieved only through single-end connection, and therefore a complete genome, a truncated body and a covalent head-to-tail concatemer can be captured without bias, and the method can be used for accurately measuring the physical packaging capacity limit of the AAV carrier.

Provided herein are methods for determining the microsatellite instability status of samples. In one aspect, the methods include quantifying a number of different repeat lengths present at each of a plurality of microsatellite loci from sequence information to generate a site score for each of the plurality of the microsatellite loci. The methods also include comparing the site score of a given microsatellite locus to a site specific trained threshold for the given microsatellite locus for each of the plurality of the microsatellite loci and calling the given microsatellite locus as being unstable when the site score of the given microsatellite locus exceeds the site specific trained threshold for the given microsatellite locus to generate a microsatellite instability score, which includes a number of unstable microsatellite loci from the plurality of the microsatellite loci.

A method for improving the replication of a covalently closed circular plasmid is provided. The method includes providing a covalently closed circular plasmid having a Pol I-dependent origin of replication, and an insert including a structured DNA sequence selected from inverted repeat sequences, direct repeat sequences, homopolymeric repeat sequences, eukaryotic origins of replication or eukaryotic promoter enhancer sequences, wherein the structured DNA sequence is located at a distance of less than 1000 bp from the Pol I-dependent origin of replication in the direction of replication. The method also includes modifying the covalently closed circular recombinant molecule such that the Pol I-dependent origin of replication is replaced with a Pol III-dependent origin of replication, whereby the resultant Pol III-dependent origin of replication covalently closed circular plasmid has improved replication. An antibiotic marker free covalently closed circular recombinant DNA molecule is also provided.

The present application relates to the technical field of molecular marker, and more particularly to a kind of SSR molecular marker combination and its application in detecting pecan variety.The SSR molecular marker combination includes: SSR12-1 and SSR6-2;The SSR12-1 is located at Chr12:22685469bp-22685482bp, and repeat sequence is CT, and repeat 7 times;The SSR6-2 is located at Chr06:7785735bp-7785761bp, and repeat sequence is CTT, and repeat 9 times.The molecular marker provided by the present application can accurately and quickly identify pecan variety, and the result is stable and reliable, and it has important significance for the identification of pecan genetic resources.

The application discloses a double-end sequencing sample mark weight method, comprising the following steps: aligning the double-end read length corresponding to the DNA fragment in the double-end sequencing sample to the position corresponding to the whole genome reference sequence respectively, the double-end read length of the fragment being at adjacent positions, obtaining the alignment information of the double-end read length, adding an auxiliary field in the alignment information of each read length, and the auxiliary field containing the starting position of the other end read length corresponding to the read length; sorting the read length according to the reference sequence site after the alignment is completed, and saving the ordered read length in a SAM file; sequentially reading the read length from the ordered SAM file, taking the read length at the same alignment position as a group of candidate read length repeats, screening the fragment repeat sequence from the candidate read length repeat sequence according to the auxiliary field; deleting the repeat sequence or marking the repeat sequence, and writing into a new SAM file, so that the application reduces the data reading throughput in the double-end sequencing sample mark weight process, reduces the running time, and improves the running efficiency.

The invention provides a method for synthesizing a DNA sequence comprising repeat units, including designing and synthesizing an extension primer and a blocking primer based on the repeat unit, performing a PCR amplification reaction by using the repeat unit (as an amplification template), the extension primer, and the blocking primer in a PCR reaction system, to obtain the DNA sequence comprising repeat units. The invention also provides a kit for this method. The method of the invention has the characteristics such as controllable copy number for repeat synthesis, simple synthesis steps, and low cost, and is very suitable for high-throughput production in industry.

The present application relates to a kind of primer group, kit and method for detecting ATXN8OS and ATXN8 gene (CTA·TAG) n And (CTG·CAG) n Trinucleotide repeat number, belong to gene detection technical field.The primer group includes first primer pair and second primer pair;The forward primer sequence of the first primer pair is as shown in SEQ ID NO.1, and the reverse primer sequence is as shown in SEQ ID NO.2;The forward primer sequence of the second primer pair is as shown in SEQ ID NO.1, and the reverse primer sequence is as shown in SEQ ID NO.3.The present application is realized by the design of two primer pairs, complementary verification is realized, detection result is comprehensive and reliable, make up the technical deficiency of one generation sequencing and two generation sequencing in long fragment, high GC content repeat sequence detection, and detection cost is low, detection cycle is short.

This invention provides an adeno-associated virus (AVV) complex for RUNX3 gene expression containing an asymmetrically deformed inverse repeat sequence (ITR). The AAV complex has the advantage of improved productivity and gene expression efficiency compared to existing AVV complexes, as one of the two ITRs is a deformed asymmetric ITR, which increases the self-renewal efficiency in the host cell and increases the efficiency of transgene expression.

The invention belongs to the technical field of microbial engineering, and particularly relates to an engineering bacterium for efficiently expressing tandem repeat protein as well as a construction method and application of the engineering bacterium. By optimizing precursor amino acid supply, the engineering bacterium for efficiently expressing tandem repeat protein is provided, GHK tripeptide tandem protein and mussel mucin are taken as examples, the yield of tandem repeat protein expressed by the engineering bacterium is increased by enhancing a biosynthetic pathway of an amino acid substrate, the expression bottleneck is relieved, and the expression efficiency is improved. The intracellular synthesis efficiency of the target peptide is remarkably improved, and the production cost is reduced. On the basis of the prior art, the method focuses on yield increase, and provides a solution with higher industrial potential for efficient biosynthesis of oligopeptide.

An adeno-associated virus (AAV) complex platform is disclosed that includes an asymmetrically modified terminal inverted repeat (ITR). The AAV complex has an asymmetric ITR in which any one of two ITRs is modified, and thus has the advantages of increased productivity and transgene expression efficiency, and reduced genetic toxicity. Also disclosed are compositions comprising the adeno-associated virus complexes and gene therapy methods.