3585 results about "A-DNA" patented technology

The present disclosure provides new prime editor guide RNAs for prime editing, constructs for prime editing, and methods for using same. In addition, the present disclosure provides compositions and methods for conducting prime editing of a target DNA molecule (e.g., a genome) that enables the incorporation of a nucleotide change and / or targeted mutagenesis (e.g., insertion or deletion). The nucleotide change can include a single-nucleotide change (e.g., any transition or any transversion), an insertion of one or more nucleotides, or a deletion of one or more nucleotides. More in particular, the disclosure provides fusion proteins comprising nucleic acid programmable DNA binding proteins (napDNAbp) and a polymerase (e.g., reverse transcriptase), which is guided to a specific DNA sequence by a prime editor RNA (PEgRNA). The prime editor guide RNA comprises an extension arm that provides a DNA synthesis template sequence which encodes a single strand DNA flap, which is homologous to an endogenous DNA sequence, but which contains the desired one or more nucleotide changes and which, following synthesis by the polymerase (e.g., reverse transcriptase), becomes incorporated into the target DNA molecule.

The invention discloses a DNA binding residue prediction method based on a multi-modal protein language model in the technical field of bioinformatics. The DNA binding residue prediction method based on the multi-modal protein language model comprises the following steps: sequentially using tools to respectively obtain feature files of a protein sequence P to be subjected to DNA binding residue prediction; inputting all the feature files into the ESM3 to obtain an embedded matrix M; the method comprises the following steps: processing a protein sequence into a residue sample, constructing an isovariant graph neural network model according to a protein structure diagram, constructing a data set by utilizing the protein sequence of known DNA binding residues, and training the constructed network; and inputting a residue sample of the protein sequence into the trained model to obtain a DNA binding residue of the protein sequence. According to the DNA binding residue prediction method based on the multi-modal protein language model, the efficiency and accuracy of DNA binding residue prediction are improved.

Systems, methods, and apparatus for generating a DNA / gene sequence output, given a protein sequence input. In one aspect, the protein-to-DNA mapping system includes a protein language model (embedder) that generates a high-dimensional protein embedding from a low-dimensional protein sequence input; and the system includes a protein-to-DNA translator that processes the protein embedding and generates a DNA sequence output, based on the protein embedding. The protein-to-DNA translator is a neural network (e.g., a Seq2Seq model) and is configured with translation coefficients that may be trained with a training dataset, comprising the training protein and DNA embeddings. Training the translation coefficients can include supervised learning that maps the protein embedding (input) to a DNA sequence (target). The systems, methods, and apparatus may increase protein yield / expression, improve protein functionality, enhance gene therapy efficacy, streamline synthetic biology design, and / or broaden functional genomics studies, all leading to reduced costs, better performance, and increased accessibility.

The invention provides a protein expression prediction method based on a convolutional neural network and a residual attention mechanism, and belongs to the field of bioinformatics and artificial intelligence. The method comprises the following steps: performing data cleaning and binary one-hot coding on a DNA sequence, inputting the coded DNA sequence into a feature extraction layer, and extracting local features of DNA; local features are extracted through a convolutional neural network, global features are obtained through a multi-head attention mechanism, and residual connection is combined; and finally, inputting the global features into a full connection layer to generate a protein expression prediction result. Furthermore, an SHAP interpretability method is utilized to interpret the output result of the prediction model, and the contribution of the basic group at each position in the DNA sequence to the predicted value is quantified. According to the method, deep learning and interpretability technologies are combined, the precision and credibility of protein expression prediction are remarkably improved, and the method is suitable for predicting protein expression.

The present invention provides a method and a kit for detecting a target nucleic acid to be detected by using a melting curve. The method includes designing a first primer, a second primer and a detection probe for the target nucleic acid sequence to be detected, performing PCR amplification in a PCR amplification system containing the first primer, the second primer, the detection probe, the sample to be detected, a nicking enzyme and a DNA polymerase, generating a reporter primer that is complementary to the detection probe to form a double-stranded product, obtaining the melting curve of the double-stranded product, and the melting curve of the double-stranded product is the melting curve corresponding to the target nucleic acid to be detected. The method of the present invention is a non-target-dependent melting curve method, and the melting point (T m value) of each double-stranded body can be calculated in advance, solving the problems of melting curve peak shift and easy misjudgment caused by the easy mutation of the target nucleic acid sequence to be detected.

The present invention provides a method and a kit for detecting a target nucleic acid to be detected through a melting curve. The method includes designing a first primer, a second primer and a detection probe for the target nucleic acid sequence to be detected, performing PCR amplification in a PCR amplification system containing the first primer, the second primer, the detection probe, the sample to be detected, a restriction endonuclease and a DNA polymerase, generating a reporter primer that is complementary to and pairs with the detection probe to form a double-stranded product, obtaining the melting curve of the double-stranded product, and the melting curve of the double-stranded product is the melting curve corresponding to the target nucleic acid to be detected. The method of the present invention is a non-target-dependent melting curve method, and the melting point (T m value) of each double-stranded body can be calculated in advance, solving the problems of melting curve peak shift and easy misjudgment caused by easy mutation of the target nucleic acid sequence to be detected.

The invention relates to a parallel processing synchronous optimization method and system for high-throughput gene sequencing. The method comprises the following steps: performing channel distribution and signal acquisition initialization on a plurality of DNA samples to obtain a signal acquisition parameter matrix; performing feature extraction and clustering analysis on the fluorescence signals collected by each channel to obtain a DNA base feature sequence and a signal classification probability matrix; dynamically adjusting short-term parameters of a sequencing period through a convex optimization algorithm, and optimizing long-term sequencing performance through an integer programming algorithm to obtain a sequencing parameter optimization set and a sequencing period distribution strategy; and inputting the sequencing parameter optimization set and the sequencing period allocation strategy into a double-layer nested control model, and carrying out joint solution through an upper-layer resource allocation network and a lower-layer parameter optimization network to obtain a global optimization control parameter set. According to the method and the device, the sequencing accuracy is improved, and the utilization rate of computing resources is improved.

The invention discloses a kit for detecting tomato brown crinkled fruit virus based on enzyme-mediated dual-amplification nucleic acid amplification and a detection method. The detection system comprises a primer pair DNA (deoxyribonucleic acid) upstream primer (F5) and a DNA downstream primer (R6) for amplifying the tomato brown crinkled fruit virus movement protein gene, a probe (RNA primer (RNA1)) for detecting the MP gene, a nucleic acid amplification group enzyme system (recombinase, single-chain binding protein, polymerase and ATP (adenosine triphosphate) energy regeneration enzyme), a signal amplification group enzyme system (positioning enzyme and cutting enzyme), activating enzyme NTP, a buffer solution and RNase-free Water. The system composed of the freeze-drying protective agent is prepared into the pre-subpackaged freeze-dried balls. The kit disclosed by the invention can realize DNA detection of aM concentration, and besides rapid qualitative detection of the tomato brown crinkled fruit virus, early screening of the tomato brown crinkled fruit virus can also be realized due to high detection sensitivity.

The invention discloses an image encryption method and device based on a chaotic system and electronic equipment, and relates to privacy computing or other related fields, and the method comprises the steps: converting a target image into a three-channel grayscale image, and converting the three-channel grayscale image into a one-dimensional array; obtaining a first random key stream generated by the new four-dimensional chaotic system, and performing pixel value diffusion on the one-dimensional array; merging the diffused image arrays, generating a scrambling function based on chaotic tent mapping, and scrambling pixel positions of the merged arrays; obtaining a second random key stream, selecting a DNA coding rule, and coding the scrambling array into a DNA sequence; obtaining a third random key stream and selecting a DNA operation rule to perform encryption operation on the DNA sequence; and decoding the encrypted sequence into a decimal system, and combining channels to obtain a target encrypted image. Through the method and the device, the technical problem that the encryption information is easily attacked and cracked due to the fact that the sensitive data encryption method in the related technology is limited to the encryption dimension and the key space is solved.

The present application provides guide RNAs and genome-editing complexes or nanoparticles that are useful for specifically targeting a mutated KRAS. Exemplary genome-editing complexes or nanoparticles comprise cell-penetrating peptides, and optionally a DNA nuclease (such as Cas9) or a polynucleotide encoding the DNA nuclease.

The invention provides an UTR element NHP1 as well as a construction method and application thereof, and relates to the technical field of mRNA. A 5 'UTR with a good expression effect is designed by integrating dominant sequences of a human high-expression gene and a pathogen natural UTR, a chimeric structure NHP1 with high ribosome load is predicted through a calculation model, a DNA sequence of the NHP1 is as shown in SEQ NO 1, and an RNA sequence of the NHP1 is as shown in SEQ NO 2; an EGFP report system is adopted on the DNA level to rapidly screen UTR; the translation efficiency is quantitatively evaluated on the RNA level through luciferase mRNA (N1-methyl pseudouridine modification); and the particle size is controlled by a microfluidic technology, so that the optimized UTR-mRNA is efficiently expressed after being delivered.

The invention discloses a static mixer for oil-water emulsification, and relates to the technical field of oil-water emulsification, the static mixer comprises an oil-water mixing pipe, a dosing pipe is fixed on one side of the top end of the oil-water mixing pipe close to a feed port, support rings are symmetrically fixed in the oil-water mixing pipe, and a DNA-imitated double-helix channel is fixed between the two groups of support rings; the DNA-imitating double-helix channel is fixed between the two groups of supporting rings on the inner side of the oil-water mixing pipe, the shark-imitating placoid scale ribs which are distributed in an array manner are fixed on the inner wall of the DNA-imitating double-helix channel, a unique bionics principle is utilized, an efficient mixing phenomenon in nature is simulated, efficient and uniform mixing of fluid in a steady-state environment is realized, and the oil-water mixing effect is improved. According to the device, fluid can be guided to generate micro vortexes, full contact and collision of oil drops and water drops can be promoted, the emulsification efficiency and stability are remarkably improved, an external power source is not needed, efficient mixing can be achieved by means of energy of the fluid, and the device is compact in overall structure, easy and convenient to install and suitable for various-scale emulsification processes.

The invention provides a DNA binding protein and RNA binding protein classification method based on ESM-2 and a dual-path neural network, and particularly relates to a staged classification method combining the ESM-2 and the dual-path neural network, which is called DRBP-EDP. In the first stage training, the protein sequence is classified as a nucleic acid binding protein or a non-nucleic acid binding protein; further classifying the nucleic acid binding protein as a DNA binding protein or an RNA binding protein in the second stage of training; meanwhile, a fine data set construction method is further constructed, so that a high-quality protein classification data set is created, through the method, the DRBP-EDP model obtains good performance, the classification accuracy of the nucleic acid binding protein and the non-nucleic acid binding protein in the first stage is 90.03%, and the classification accuracy of the non-nucleic acid binding protein in the second stage is 90.03%. In the second stage, the classification accuracy of the DNA binding protein and the RNA binding protein is 89.56%, a new insight and a new method are provided for protein classification, an innovative tool is provided for research on protein functions, and therefore a new opportunity is provided for development of life science.

The invention discloses an SNP (Single Nucleotide Polymorphism) molecular marker combination for constructing an oat DNA (Deoxyribose Nucleic Acid) fingerprint spectrum and application, the SNP molecular marker combination is developed and obtained based on an SLAFseq technology, and has the characteristics of uniformly covering an oat genome, being high in polymorphic information content and being suitable for typing. Compared with other traditional molecular marker technologies, the SNP marker provided by the invention has higher stability, is not easily influenced by experimental conditions and environmental factors, and can be widely applied to oat germplasm resource identification, genetic diversity analysis, DNA fingerprint construction and molecular marker-assisted breeding. The DNA fingerprint spectrum constructed on the basis of the SNP molecular marker can more comprehensively reflect genetic information of a biological individual or population, and is of great significance to research of genetic diversity, evolutionary relationship and the like of species. Therefore, the method can provide technical reference for popularization of oat varieties, property right confirmation and protection, purity identification of oat seed production and the like.

The invention discloses a DNA (Deoxyribose Nucleic Acid) fingerprint spectrum for identifying a feeding oat variety and application thereof, relates to the technical field of biology, and provides 21 molecular markers capable of analyzing and identifying the feeding oat variety. A molecular probe combination, a gene chip and a kit prepared from the 21 SNP molecular markers can play an important role in the aspects of the blood relationship and genetic basis of oat crops, variety certification and determination, counterfeit and shoddy seed identification, management and detection of genetic breeding and crop maps and the like.

The invention relates to a DNA methylation detection method and device and electronic equipment, and the method comprises the following steps: obtaining a DNA sequence to be detected; obtaining original electric signal data and a base sequence corresponding to the DNA sequence to be detected through a nanopore sequencing technology; obtaining a methylation detection result corresponding to the DNA sequence to be detected according to the original electric signal data, the base sequence and a deep learning model; wherein the deep learning model comprises a sequence feature extraction module, a signal feature extraction module, a feature fusion module and a classification module; the sequence feature extraction module comprises a Transform encoder; the signal feature extraction module comprises a Conformer encoder; the feature fusion module comprises a Transform decoder; the classification module comprises a full connection layer; according to the method provided by the invention, the identification accuracy of the methylation site can be improved, high-precision methylation detection is realized, and the problems of gradient disappearance and gradient explosion can be effectively relieved.

An antigen-binding molecule that binds to a target antigen, comprising (i) a target antigen-binding moiety, and (ii) at least one linker-payload moiety, wherein the antigen-binding molecule comprises (a) DNA damage response (DDR) inhibitor moiety, and (b) a DNA topoisomerase I (TOP1) inhibitor moiety.

The invention belongs to the field of gene engineering, and relates to a DNA binding protein based on TraC effect protein, a fusion protein with a cytosine / adenine base editing function, an editing system and nucleic acid molecules or constructs for encoding the DNA binding protein and the fusion protein. The invention also relates to complexes and kits for gene editing comprising the fusion proteins of the invention or the nucleic acid molecules encoding them. The base editing tool disclosed by the invention can realize efficient, accurate and safe base editing in cells of various eukaryotes such as animals and plants. The unique characteristics of the base editing tool enrich the types of existing base editing tools, and the base editing tool has wide application prospects.

An antigen-binding molecule that binds to HER2, comprising (i) a HER2-binding moiety, and (ii) at least one linker-payload moiety, wherein the antigen-binding molecule comprises (a) DNA damage response (DDR) inhibitor moiety, and (b) a DNA topoisomerase I (TOP1) inhibitor moiety.

The present invention relates to the field of biomedical materials. Particularly provided is a DNA-silk fibroin composite hydrogel microsphere. The DNA-silk fibroin composite hydrogel microsphere is prepared from DNA and silk fibroin on the basis of the micro-fluidic technology by means of combination of self-assembly physical crosslinking and photo-crosslinking. The introduction of a silk fibroin network into the composite hydrogel microsphere can provide mechanical performance for a DNA hydrogel network and reduce the production cost. RGD can remarkably improve the cell loading capability of the microsphere. The hydrogel microsphere can simulate a microenvironment of cartilage tissue by means of three-dimensional loading of high-density cells, so as to enhance substance exchange and signaling between cells, and more effectively promote the proliferation and adhesion of bone marrow mesenchymal stem cells and regulating the chondrogenic differentiation, thus promoting cartilage regeneration and repair, and providing an available material for preparing medicaments or medical instruments for cartilage defect repair.

The invention belongs to the technical field of biomedical engineering, and particularly relates to a single-base resolution laminated two-dimensional material nanopore structure, a DNA sequencing device and a DNA sequencing method. The two-dimensional material nanopore structure comprises an insulating layer and conducting layers arranged on the upper side and the lower side of the insulating layer, through nanopores are formed in the insulating layer and the conducting layers, and the pore diameter of the nanopores is 2-5 nm; the insulating layer and the conductive layer are made of two-dimensional materials. The conductive layers on the two sides serve as upper and lower electrodes, and a power supply is connected between the upper and lower electrodes to form a phase conductive path which is provided with a longitudinal current detection element. A plurality of groups of two-dimensional material nanopore structures are stacked, and meanwhile, a plurality of groups of base pair signals are obtained. According to the invention, the advantages of small thickness, high physical strength and the like of the two-dimensional material nanopore are kept by using a few layers of two-dimensional material films, the vibration of the films is reduced by increasing the number of layers and improving the mechanical strength, so that the signal-to-noise ratio is improved, and the spatial resolution of the nanopore sensor is improved by designing the upper electrode and the lower electrode.

The invention relates to the technical field of molecular biology, in particular to application of a gene marker in early screening of multiple alimentary canal cancer species, an early screening model construction method and a detection device.WGS low-depth sequencing is conducted on plasma sample cfDNA, and three difference characteristics including copy number change, copy number change, cfDNA fragment change, cfDNA fragment change, cfDNA fragment change, cfDNA fragment change, cfDNA fragment change, cfDNA fragment change, cfDNA fragment change, cfDNA fragment change, cfDNA fragment change, cfDNA fragment change and cfDNA fragment change are analyzed according to a high-throughput sequencing result. The method comprises the following steps of: performing training modeling by using a convolutional neural network according to a DNA fragment size ratio and a nucleosome covering mode, realizing high-specificity and high-sensitivity accurate early detection on a plurality of cancers under low sequencing depth, and performing training modeling by using five algorithms, namely a generalized linear model, gradient boosting, a random forest, deep learning and extreme gradient boosting respectively, so as to realize accurate early detection on the plurality of cancers under low sequencing depth. The generalized linear model is subjected to secondary set training to construct multi-feature algorithm integration, and the purpose of tissue traceability detection of multiple cancer species is achieved.

The invention relates to a cartilage organ constructed on the basis of a DNA-silk fibroin hybrid hydrogel sustained-release system as well as a preparation method and application of the cartilage organ. The DNA-silk fibroin hybrid hydrogel sustained-release system is a hydrogel system formed by printing a DNA-silk fibroin hybrid hydrogel sustained-release system premix solution through a digital light processing system, and the DNA-silk fibroin hybrid hydrogel sustained-release system premix solution contains DNA, silk fibroin, acryloylated RGD peptide, acryloylated polyethylene glycol NHS ester, glucosamine, TD-198946 and 2, 4, 6-trimethyl-1, 3-pentanediol. The invention discloses a lithium 2, 6-trimethylbenzoyl phosphate. Compared with the prior art, the glucosamine and the TD-198946 introduced into the DNA-silk fibroin hybrid hydrogel sustained-release system disclosed by the invention can be used for remarkably improving and promoting the cartilage differentiation efficiency of the bone marrow mesenchymal stem cells; the cartilage graft can be transplanted to a cartilage defect position as a cartilage graft to promote cartilage regeneration and repair.

The invention discloses a strain copyright protection system based on a DNA watermark technology. The system comprises a DNA watermark embedding module, a block chain storage and verification module, a strain authentication and tracking module and a security and privacy protection module. The invention further discloses a strain copyright protection method based on the DNA watermarking technology. The method comprises the steps of strain copyright information generation and coding, DNA watermark site selection and editing, strain screening and verification, copyright information uplink and strain use and tracking. According to the method, the copyright information of the strain is coded into the DNA watermark, the DNA watermark is embedded into the genome non-functional region of the strain, and the copyright information is stored and verified in combination with a block chain technology, so that intellectual property protection with high concealment and high safety of the biological strain is realized; illegal copying and tampering of strains are prevented, reliable copyright authentication and tracking functions are provided, and the method has wide application prospects and remarkable market value.

The present invention relates to a molecular imaging probe for tumor diagnosis, and provides a sugar nucleic acid molecular imaging probe, the probe comprises a DNA aptamer sequence and more than one glycosyl nucleoside module, and is labeled by radionuclide, the DNA aptamer sequence can specifically target tumor cells after functional folding; the glycosyl nucleoside module is a glycosyl modified nucleoside derivative, is accurately modified at the 5'end or / and the 3 'end of the aptamer through DNA solid-phase synthesis, has the imaging characteristics of biological safety, high sensitivity and high resolution, and has an excellent diagnosis effect on part of cancers which are difficult to diagnose by a traditional method. The invention also provides a preparation method and a use method of the sugar nucleic acid molecular imaging probe, so that sugar modification of the aptamer is convenient, rapid, accurate, controllable and modularized, and the sugar nucleic acid molecular imaging probe has huge clinical application potential and transformation value in cancer diagnosis.

The invention belongs to the technical field of biological probiotic screening, and particularly relates to a probiotic screening method based on a convolutional neural network, which comprises the following steps: reading an original probiotic related DNA sequence file, matching the DNA sequence file by adopting a regular expression, removing all non-ATCG base characters to obtain a normalized DNA sequence, and screening the normalized DNA sequence; segmenting the screened DNA sequence by adopting a sliding window method to generate a k-mer fragment set; constructing a k-mer frequency vector according to the occurrence frequency of each k-mer fragment in the sequence; performing normalization processing on the k-mer frequency vector; inputting the k-mer frequency vector after normalization processing into the trained convolutional neural network to obtain a DNA sequence classification result; determining whether a strain corresponding to the sequence is a probiotic or not according to a DNA sequence classification result; according to the method, the k-mer frequency characteristics are extracted by adopting the sliding window, and the calculation complexity of a traditional sequence alignment method is reduced from O (n2) to O (n), so that the consumption of calculation resources is reduced.

The invention provides a molecular identity authentication system and method based on DNA origami framework layered assembly. The molecular identity authentication system comprises a disclosed skeleton chain and a plurality of shared staple chains, the shared staple chain comprises staple chains shared by three groups of single bodies and staple chains shared in pairs, and the staple chains are used as secret keys to be distributed to three participants so as to prepare the three groups of single bodies respectively, and then the three groups of single bodies are combined and spliced into a tripolymer with a dot matrix pattern, so that multi-user collaborative layered chain type assembly is realized. According to the molecular identity authentication system based on DNA origami framework layered assembly, the system combination complexity is improved to the information theory security level, so that the biological information security protection capability is improved, and brute force cracking is prevented.

The invention belongs to the technical field of molecular identification of aquatic organisms, and particularly relates to a high-sensitivity large yellow croaker germplasm identification primer combination as well as application and an identification method thereof. The primer composition is a first pair of primers LC-1, and the sequences of the first pair of primers LC-1 are as follows: an upstream primer LC-1F: 5 '-AATTCCACACGACTAATC-3'; the downstream primer LC-1R is 5 '-CTCAGCCGCCGTGCAATC-3', and the downstream primer LC-1R is 5 '- The sequences of the second pair of primers LC-2 are as follows: an upstream primer LC-2F: 5 '-AGGCATTAGGCACAAGG-3', a downstream primer LC-2F: 5 '-AGGCATTAGGCACAAGG-3', a downstream And the downstream primer LC-2R is 5 '-AAACCCCTAGCCTCGAAG-3'. The invention also discloses a kit for detecting the disease resistance of the traditional Chinese medicine. The two large yellow croaker germplasm identification primers provided by the invention have relatively high sensitivity and specificity, can be stably amplified in a DNA sample with extremely low concentration, and overcome the limitation that accurate identification cannot be realized due to low DNA concentration in a traditional method.

This invention relates to recombinant nucleic constructs comprising a DNA binding domain, an endonuclease and a reverse transcriptase and methods of use thereof for modifying nucleic acids in plants.

The invention relates to the technical field of coding and decoding, and discloses a DNA storage coding and decoding method and device, electronic equipment and a storage medium, and the method comprises the steps: carrying out the information filling of to-be-coded data, and obtaining a target binary sequence; encoding and mapping the target binary sequence to obtain a DNA base sequence; identifying a coding error mode of the to-be-coded data according to the DNA base sequence; and according to the coding error mode, selecting a corresponding decoding algorithm to decode the DNA base sequence to obtain decoding data. Through the implementation of the invention, data conversion and information filling are performed on the to-be-coded data, so that the length of the to-be-coded data can meet the length requirement of the polarization code; the coding error mode corresponding to the DNA base sequence is identified for decoding, the decoding accuracy can be effectively improved through different coding error modes, and lossless compiling of the to-be-coded data is realized.