58 results about "Repeated sequence" patented technology

The invention discloses a divalent nucleic acid aptamer fluorescence detection method based on an exonuclease I auxiliary target circulation strategy, and belongs to the field of analysis and detection.The divalent nucleic acid aptamer is a repetitive sequence composed of two monovalent nucleic acid aptamers and can form double-stranded DNA through base complementary pairing with complementary strand cDNA of the divalent nucleic acid aptamer, and the divalent nucleic acid aptamer can be used for fluorescence detection of the divalent nucleic acid aptamer. The method comprises the following steps: taking a bivalent nucleic acid aptamer as a template, forming a DNA silver nanocluster (DNA-AgNCs) under the action of silver nitrate and sodium borohydride, and when the target okadaic acid exists, combining the bivalent nucleic acid aptamer with the target, so that cDNA can be replaced from double-stranded DNA by the target. Exonuclease I is added to perform enzyme digestion on the cDNA and the divalent nucleic acid aptamer, so that the fluorescence intensity of the DNA-AgNCs can be rapidly reduced. The content of the okadaic acid can be judged by detecting the change of the fluorescence intensity. The invention provides a simple, convenient, rapid, high-sensitivity and high-specificity detection method for okadaic acid detection based on a divalent nucleic acid aptamer for the first time.

The invention relates to the technical field of food safety detection, in particular to a food crop pathogenic mycotoxin detection method based on double signal amplification. The core of the method is a section of linear lock-type probe containing a mycotoxin specific nucleic acid aptamer, under the condition that target mycotoxin exists in a sample, the aptamer is combined with the mycotoxin, the probe is induced to generate conformational change, and the probe is closed into annular DNA under the catalysis of DNA ligase; then, the circular DNA is used as a template, isothermal rolling circle amplification is carried out through Phi29 DNA polymerase, and a long-chain DNA product containing a large number of repetitive sequences is generated; subsequently, the long-chain product is used as a molecular scaffold, and two kinds of gold nanoparticles of which the surfaces are modified with different complementary probes are cross-linked at the same time, so that the nanoparticles are quickly gathered, the color of the solution is changed from wine red to blue or purple, and convenient visual detection is realized. The method has the outstanding advantages of ultrahigh sensitivity, rapid detection and the like, and is suitable for on-site rapid screening of mycotoxin pollution.

Nucleic acid error suppression is provided. In various embodiments, DNA is extracted from a collection of plasma samples. A sequence library with duplex adapters is prepared by ligating a duplex adapter having a Unique Molecule Identifier (UMI) to an end of each of a plurality of strands of the extracted DNA and amplifying the extracted DNA with a first polymerase chain reaction (PCR). A subset of the whole genome library is selected and amplified with a second PCR to increase an amount of PCR duplicates. A plurality of duplex reads is sequenced from the amplified subset aligned to a host genome and denoised based on said alignment. A variant presence is detected in at least one of the plurality of duplex reads. A signature of the variant is determined, which is compared to a collection of disease-specific variant signatures. A disease type is determined based on the comparison.

The invention relates to the technical field of biological research data analysis, and discloses a computational biological research data analysis display method, which comprises the following steps of: extracting total RNA (Ribonucleic Acid) from biological tissues or cells, reversely transcribing the RNA into cDNA (Complementary Deoxyribonucleic Acid), constructing a library, and sequencing the library by utilizing a high-throughput sequencing platform to obtain a large number of short sequences. According to the method, the number of the short sequences mapped to the same genome coordinate interval is compared and the threshold value is judged, so that the abnormal repeated area can be effectively identified, whether the gene expression difference result is credible or not is clearly judged, and when the number of the abnormal sequences exceeds the preset repeated sequence threshold value, the influence operation of the repeated sequences is eliminated, and the accuracy of the gene expression difference result is improved. That is to say, completely identical and overlapped short sequences are removed under the condition that the FPKM value is relatively high, and the updating result is compared again, so that the problem of expression quantity distortion caused by repeated reckoning can be corrected.

This disclosure generally relates to super minimal transposon inverted repeat sequence (ITR) polynucleotides, compositions comprising the polynucleotides and methods of using compositions comprising the polynucleotides for the ex vivo and in vivo delivery of nucleic acids to cells, in particular, in vivo delivery of therapeutic genes to treat genetic disorders or diseases.

The application belongs to the technical field of biology, and discloses a kind of Myzus persicae densovirus, amplification and connector method and its application, Myzus persicae densovirus name is Myzus persicae densovirus 2, abbreviated as MpDV2, preserved in China typical culture preservation center, and the preservation number is V202281.The Myzus persicae densovirus MpDV2 provided in the application is a virus strain that has not been isolated and identified before and has pathogenicity to Myzus persicae, and the full-length sequence of the genome of the Myzus persicae densovirus MpDV2 (including the complete terminal inverted repeat sequence) is disclosed for the first time, and the influence of the virus infection on the growth and development of Myzus persicae and the population dynamics / growth.The Myzus persicae densovirus MpDV2 of the application significantly reduces the intrinsic growth rate (r), net reproduction rate (R0) and week-long growth rate (lambda) of Myzus persicae population, and prolongs the average generation time (T) of the population, and the MpDV2 infection has a significant influence on the growth and development of Myzus persicae and population growth.

The invention relates to the technical field of genome assembly, in particular to a medicinal plant genome assembly method and system based on high-throughput sequencing. The method comprises the following steps: acquiring a target sequencing sequence, and screening a function influence sequence; performing repetitive classification on the target sequencing sequence to obtain a non-repetitive sequence cluster and a repetitive sequence cluster, and dividing the repetitive sequence cluster into a functional repetitive sequence and a non-functional repetitive sequence; determining dynamic association strength by combining expression abundance of functional genes, content detection of medicinal components and base overlapping characteristics of adjacent sequences; constructing an association network; and according to the dynamic association strength in the association network, aiming at the functional association type repetitive sequence, the non-functional association type repetitive sequence and the adjacent non-repetitive sequence, respectively carrying out sequence splicing by adopting a differential assembly path to obtain a complete genome assembly result. According to the method, the problems of splicing errors, fragment breakage and redundancy caused by repeated sequences can be solved, and the assembly accuracy and integrity are remarkably improved.

The invention provides a method for improving the efficiency and detection sensitivity of establishing a CRISPR nucleic acid detection one-step method, and particularly provides a direct Repeat (DR) sequence for forming gRNA and guide RNA containing the DR sequence, the invention finds for the first time, and provides a method for improving the efficiency and detection sensitivity of establishing a CRISPR nucleic acid detection one-step method and a method for establishing the CRISPR nucleic acid detection one-step method for establishing the CRISPR nucleic acid detection one-step method for establishing the CRISPR nucleic acid detection one-step method. When the guide RNA adjusted by the invention is used for detecting target nucleic acid in a one-step detection system, the establishment efficiency and the detection sensitivity of the CRISPR nucleic acid detection one-step method can be remarkably improved.

The application belongs to the field of biological information visualization, and discloses a three-dimensional visualization functional gene browser and system based on Z series closed loop coding, which solves the problems of track disorder, arc winding, dependence on scaling and incomplete coding of existing tools. The application constructs Z series closed loop coding, packs genes and non-gene regions into Z0~ZN units, and adapts repeat sequences and ring chromosomes. L-X-Y three-dimensional coordinates are established, 65 standardized character libraries are constructed, and amino acids are labeled in a six-color degenerate system. Modular labeling is adopted, continuous functional elements are integrated into M modules, three types of background colors are used to classify levels, the trunk area and the independent labeling area are displayed separately, and tracks and arcs are abandoned. The system supports Z unit addressing, three-level interaction, module linkage, variation marking, Hi-C double-end alignment and reverse complementary strand switching, realizes full-link visualization from whole genome to single base, and is suitable for genomics and clinical variation analysis.

To provide a method of improved detection accuracy for detecting genetic polymorphism including repetitive sequences.SOLUTION: Disclosed is a detection method comprising a step of detecting repetitive sequence polymorphism in a gene having at least four types of repetitive sequence polymorphism using at least four types of detection probes, where the first to fourth detection probes each comprises a 5'-region, an internal region, a 3'-region and a label, where the internal regions of the first to fourth detection probes each comprise a sequence hybridizable with a repetitive sequence of repetition number k, l, m and n respectively, the 5' region is disposed on 5' terminal side of the internal region and comprise a sequence hybridizable with a franking region of the 5' terminus of the gene, the 3' region has a sequence hybridizable with the base sequence of a franking region on 3' terminal side, where the detection step comprises a step of nucleic acid amplification in the presence of a sample, primers and detection probes to detect signals and a step of evaluating repetitive sequence polymorphism on the basis of threshold values.SELECTED DRAWING: Figure 2

The invention discloses a dairy cow early embryo sex identification method, and belongs to the technical field of dairy cow breeding and breeding. The identification method comprises the following steps: (1) culturing a dairy cow embryo to an early blastocyst stage, starting to perform single-embryo single-droplet culture, and after culturing until a blastocyst cavity is formed, punching a blastocyst zona pellucida to promote the blastocyst to shrink and release blastocyst cavity liquid; (2) collecting blastocyst cavity liquid, and extracting embryo free DNA in the blastocyst cavity liquid; (3) by taking the free DNA as a template, designing a primer to amplify a specific repetitive sequence ChrY fragment of the bull Y chromosome; if the amplification product exists, the embryo is identified as a bull, and if the amplification product does not exist, the embryo is identified as a cow. The method can ensure that the embryo free DNA in the obtained blastocyst cavity fluid is only derived from the embryo, and can effectively avoid embryo injury. According to the method disclosed by the invention, the copy number of the amplified target area in the bull Y chromosome is more than 2000 times, a detection signal can be amplified, and the detection accuracy is improved.

The present invention relates to methods of synthesising nucleic acids, in particular to methods of extending an overlapping primer oligonucleotide to generate an oligonucleotide, polynucleotide, gene fragment or gene comprising repeating sequences. The present invention also relates to overlapping primer oligonucleotides for use in nucleic acid synthesis reactions.

A system and method for identification of target sites in a pathogenic genome and combating a pathogenic infection have been provided. The present disclosure utilizes the fact that a conserved stretch of nucleotide sequence in genomic neighborhood of genes important for bacteria can be targeted to disrupt the overall functioning of the pathogen. The method involves identification of nucleotide repeat sequences in the DNA. The method and system also involve administration of a cocktail comprising antimicrobial drugs, biofilm inhibitors and a construct. The genomic neighborhood or vicinity or ‘flanking genes’ refers to regions lying within a predefined number of genes to the identified conserved stretch of nucleotide repeat sequence (or its reverse complement) on the candidate pathogen genome or within a distance of predefined number of bases with respect to the conserved stretch of nucleotide repeat sequence (or its reverse complement) on the candidate pathogen genome.

The invention provides application of an OG7443 gene of trichophyton in identification of trichophyton, a primer pair and an identification method of trichophyton, and relates to the technical field of biology. Based on comparative analysis of genomes of trichophyton and other fungi, the specific marker gene OG7443 which only exists in trichophyton, has single copy and is free of repetitive sequence interference is screened out, and the gene can be used for identification of trichophyton. The primer provided by the invention is designed aiming at the OG7443 gene of trichophyton, has strong specificity and high sensitivity, can accurately distinguish mixed florae possibly existing in a clinical sample, improves the diagnosis accuracy of fungal infection, not only can accelerate the determination of pathogenic bacterium types, but also can improve the diagnosis accuracy of fungal infection. And important technical support can be provided for targeted antifungal treatment and public health prevention and control.

A genomic data analyzer may be configured to detect and characterize, with a variant calling module, genomic variants from next generation sequencing reads out of a pool of enriched genomic patient samples without suffering from next generation sequencing workflow biases such as those introduced by sequencing errors in particular in repeat patterns regions of the human genome such as homopolymers or heteropolymers. The variant calling module may estimate the probability distribution of the length of the repeat pattern for each patient sample and cross-analyze it against other samples in a single experimental pool to identify best-fit variant models for each pair of samples. The variant calling module may further group samples according to their matching best-fit variant models and identify which group of patient samples carries the wild type reference without the need for control data in the pool. The variant calling module may subsequently characterize the homozygous or heterozygous repeat patterns variants for each patient sample with improved specificity and accuracy even in the presence of next generation sequencing biases.

The invention discloses an oligonucleotide-coated fluorescence in-situ hybridization probe for specifically recognizing a tartary buckwheat Chr1-4 chromosome and application, and belongs to the field of cytological markers. The method comprises the following steps: screening a single-copy oligonucleotide sequence of Chr1-4 from a tartary buckwheat whole genome by using Chorus2 software; filtering and removing repetitive sequences to obtain a Chr1-4 chromosome probe sequence library; screening a specific single copy oligonucleotide sequence of the Chr1-4 chromosome; and adding specific primers at the two ends of each single copy oligonucleotide sequence of Chr1-4, and combining the probes into a buckwheat Chr1-4 Oligo-Painting probe mixing pool. By utilizing the constructed Oligo-Painting probe mixing pool and a fluorescence in-situ hybridization technology, accurate identification and karyotype analysis of the buckwheat chromosomes can be realized, the number, morphology, heritable variation and other structural characteristics of the chromosomes can be known, and an important technical support is provided for cytological analysis of buckwheat crossbreeding.

The application discloses a DNA sequencing and encryption method based on micro-fluidic technology, and the method is characterized in that: through grey correlation weight factor analysis and feature sequence analysis based on an ant colony algorithm, a DNA fragment with a relatively short length and sufficient feature content is optimized to construct a feature information library; DNA detection is completed through fluorescent coding microspheres and high-precision fluorescence detection technology, information is stored in a single-chip microcomputer after microsatellite repeat sequence analysis; finally, the information is transmitted to an MCU by using a Bluetooth module, and the information is stored in a decentralized manner by using an ECC elliptic curve encryption algorithm and a block chain, so that the permanent storage and calling verification of personal identity information are realized. The application can be widely applied to the technical field of micro-fluidic chips.

The invention provides systems and methods for making sequencing libraries that are useful for quantitatively analyzing nucleic acids in a sample. Sample nucleic acids are randomly cleaved at, and PCR handled are attached to, a random cut site. The nucleic acid is amplified into a sequencing library in which a sequencing primer generates a sequence read from adjacent the random cut site. The sequence reads can be mapped to a reference, but they will also include a unique identifier sequence that comes from within the nucleic acid molecule being analyzed, i.e., an intrinsic molecular identifier (IMI). The IMI is unique for each molecule and can thus be used to deduplicate sequence reads originating from the same molecule.

Methods and systems for detecting MSI are provided. Also provided are methods for enriching human genomic DNA for microsatellite loci. Additionally, an oligonucleotide array for detecting MSI is provided. In some embodiments, the method for detecting MSI comprises detecting sequencing reads from a sample for a plurality of microsatellite loci; determining a metric for repeat length distribution (RLD) for each microsatellite locus; comparing the metric to a threshold value for the microsatellite locus; quantifying the number of microsatellite loci having an RLD metric exceeding the threshold value; and comparing the number of microsatellite loci having an RLD metric exceeding the threshold value to a microsatellite instability (MSI) proportion threshold.

To provide a method for identifying the presence of aneuploidy in the genome of a mammal.SOLUTION: Amplifying a plurality of chromosomal sequences in a cell-free DNA sample with a single primer pair complementary to the chromosomal sequences, wherein the primer pair amplifies a unique amplicon comprising short interspersed repeat sequences, determining at least a portion of the nucleic acid sequence of the plurality of amplicons to produce amplicon sequences, mapping the amplicon sequences to a reference genome, dividing the amplicon sequences into a plurality of genomic intervals, quantifying the number of reads for amplicon sequences mapped to the genomic intervals, and comparing the number of reads of amplicon sequences within a first genomic interval to: Comparing the number of reads of amplicon sequences in the one or more different genomic intervals, thereby identifying the presence of an aneuploidy in the genome of the mammal.SELECTED DRAWING: None

Disclosed is a method for identifying an evaluation target bacterium as a specific bacterial strain, the method comprising the following steps A and B: [step A] a step for performing PCR using a nucleic acid derived from the evaluation target bacterium as a template and using each of at least one set of primers that amplify a genome sequence specific to a bacterial species to which the specific bacterial strain belongs; and [step B] a step for performing PCR using a nucleic acid derived from the evaluation target bacterium as a template and using each of at least two sets of primers that amplify a repeating sequence present in the genome of the bacterial species to which the specific bacterial strain belongs.

The application provides a method for improving biological stress resistance by using a dotP gene, which comprises the following steps: transferring the dotP gene into a host organism, and making the host organism express the dotP gene; the host organism is a plant or a microorganism; the dotP gene encodes a protein (a) or (b): (a) a protein consisting of the amino acid sequence shown in SEQ ID NO. 2; (b) a protein derived from (a) by substituting, deleting or adding n amino acids in the amino acid sequence in (a) and having the activity of a quadruplet repeat sequence protein, wherein n is any integer between 1 and 4. By the technical scheme, the biological stress resistance of the plant or the microorganism is improved, and in particular, the dry resistance of the plant or the microorganism is improved.

The present invention provides a recombinant plasmid which includes: (a) an adeno-associated virus (AAV) genome that includes two AAV ITR sequences and a target gene sequence flanked by the AAV ITR sequences; and (b) stuffer DNA which comprises a nucleotide sequence that does not include an inverted repeat sequence capable of forming a stem loop.

The invention discloses insecticidal dsRNA synthesized according to PM as well as a synthesis method and application thereof, the gene sequence of the dsRNA is shown as SEQ ID NO: 1 or at least comprises a gene sequence with 90% of identity of the sequence shown as SEQ ID NO: 1, and after the dsRNA is introduced into a test insect body through micro-injection, it is found that the accumulated death rate can reach 100.00%, and the lethal effect is remarkable. According to the invention, a recombinant expression vector containing an inverted repeat sequence of the gene is constructed, and high-efficiency expression and accumulation of dsRNA are realized through IPTG induction in escherichia coli. After the dsRNA-containing engineering bacteria are mixed with flour, test insects are fed, and the accumulative fatality rate can reach 64.44%. A metal organic framework (MOF) material is used for loading the obtained dsRNA, the stability and delivery efficiency of the dsRNA can be further improved, the final death rate can reach 71.11% after a test insect compound is fed, and an effective means is provided for application of nucleic acid biopesticide in prevention and control of stored grain pests.

The invention provides a fluorescent sensing probe system and method for detecting ovarian cancer miRNA based on bidirectional primer exchange reaction, and belongs to the technical field of biological analysis and detection.According to the scheme, target miRNA and hairpin specific recognition-mediated bidirectional primer exchange reaction technology is creatively utilized, and through a double-primer system and a bidirectional strand displacement mechanism, the ovarian cancer miRNA can be detected through the fluorescent sensing probe system. The tandem G-rich repetitive sequence can provide hundreds of tandem binding sites for a signal molecule ThT, and a G tetramer-ThT tandem activation signal amplification system is constructed. According to the system, specific recognition of target miRNA and a hairpin and effective combination of a double-primer system and a two-way strand displacement mechanism mediated nucleic acid amplification technology are fully utilized to develop a serum-based'one-tube 'ovarian cancer specific miRNA accurate quantitative detection technology, and efficient, accurate and rapid detection of a novel ovarian cancer biomarker miRNA can be realized.

The present invention provides an in situ imaging method that can realize the visualization of specific modifications of target nucleic acids in cells. This method only requires three single-stranded nucleic acids with different functions: a single-stranded nucleic acid scaffold equipped with a component for recognizing specific modifications of nucleic acids, a single-stranded nucleic acid primer-1 that can specifically target the target nucleic acid sequence, and a single-stranded nucleic acid primer-2, so as to complete the targeting of specific modifications and specific nucleic acid sequences and form a signal amplification system for rolling circle amplification. It is simple and economical and has extremely high commercial potential. After in situ rolling circle amplification, a long single-stranded nucleic acid with a repeated sequence is formed, which can enrich specific fluorescent probes for imaging, and the imaging signal point therein is the spatial position of the specific modification site of the target nucleic acid. The present invention can be used in conjunction with protein immunofluorescence, can realize the simultaneous imaging of multiple nucleic acids, and can realize the imaging of nucleic acids located in different subspaces, making this method a multifunctional solution that can be applied in multiple scenarios.

The invention discloses three tandem repeat PAV markers related to thousand seed weight of highland barley and application of the three tandem repeat PAV markers. The three PAV markers adopt an oligonucleotide probe sleeve # 8 as a probe, detection is carried out through chromosome fluorescence in situ hybridization in the mitosis metaphase of root tip cells, variations with repetitive sequence insertion fragments are respectively named as 1H-C, 3H-A and 6H-2, and types without insertion fragments are respectively named as 1H-D, 3H-B and 6H-1. Results show that the thousand seed weights of varieties containing 1H-C, 3H-A and 6H-2 are obviously higher than those of other polymorphic chromosomes respectively. The invention provides a cytological marker for thousand seed weight detection for highland barley breeding, and is beneficial to improving highland barley marker-assisted selective breeding efficiency. The influence of chromosome structure variation on the thousand seed weight of highland barley is disclosed, and important information is provided for mining environment adaptability genes and gene clusters.

The present disclosure relates to nucleic acid probes and kits for determining the length of a region of tandem repeats in a subject's genome and methods of using the DNA probes for determining the length of a region of tandem repeats in a subject's genome. In some embodiments, the region of tandem repeats in telomeres.

The present invention discloses detection primers for Relish-SSR molecular markers related to the resistance of whiteleg shrimp to Vibrio parahaemolyticus and their applications. The present invention discovered a continuous glutamine repeat sequence (microsatellite) with polymorphism in the Relish gene of whiteleg shrimp, the polymorphism of which affects the polyglutamine structure encoded by the Relish gene, and can affect the anti-Vibrio parahaemolyticus trait of shrimp by regulating the expression of downstream antimicrobial peptides, that is, the present invention obtains a Relish-SSR molecular marker related to the anti-Vibrio parahaemolyticus shape of whiteleg shrimp. On the basis of the molecular marker, the present invention also provides corresponding detection primers, etc., which can be used for the identification of the anti-Vibrio parahaemolyticus trait of whiteleg shrimp or the screening of whiteleg shrimp with high resistance to Vibrio parahaemolyticus. The SSR molecular markers described in the present invention can also be used for population genetic structure analysis and molecular marker-assisted breeding, which is beneficial to the breeding of disease-resistant varieties of whiteleg shrimp.

Nucleic acid preparation and analysis techniques described. In an embodiment, techniques for generating tandem repeats include using adaptor sets having two types of adaptors with respective complementary regions present. When an adaptor of each type is present on end of a nucleic acid fragment, the complementary regions can bind to one another to generate tandem repeats of an insert, e.g., a fragment generated from a target nucleic acid.