29 results about "DNA fragmentation" patented technology

The invention relates to the technical field of sequencing, in particular to a Tn5 transposase-based next-generation sequencing method and a DNA library rapid construction kit, and particularly provides a Tn5 transposase-based next-generation sequencing DNA library rapid construction kit, a next-generation sequencing method and a next-generation sequencing DNA library construction method, and the kit comprises a reagent for constructing a next-generation sequencing DNA library. The Tn5 transposase is adopted for double-end Index library building sequencing, the library building process can be simplified, high efficiency and accuracy of high-throughput sequencing can be ensured, DNA fragmentation and linker addition are achieved in a single step by means of the unique characteristics of the Tn5 transposase, the sequencing efficiency and data management flexibility are improved by introducing the double-end Index, and the method is suitable for large-scale popularization and application. Each Index sequence ensures high specificity and traceability, meanwhile, the sequencing method can effectively work under the condition of low initial template quantity, and the application range is expanded.

This invention relates to a DNA fragmentation method and apparatus based on bubble interfacial vibration. The method includes: during the flow of a DNA sample along a flow channel, two bubbles from a bubble pair act symmetrically on both sides of the flow channel, creating a gradually contracting and expanding section within the channel to generate a stretching flow field; the DNA molecular chains in the DNA sample break due to the stretching effect of the stretching flow field as they pass through the contracting and expanding section. This invention can effectively fragment DNA molecules without contaminating them.

1. Name of the product in this design: Sperm Quality Analyzer. 2. Purpose of this design: The product is intended for use by research institutions and medical institutions for sperm concentration detection, motility analysis, sperm morphology identification, and determination of semen pH and DNA fragmentation rate in semen samples. 3. The key design feature of this product is its shape. 4. The image or photograph that best illustrates the design's key points: 3D rendering 2.

This invention discloses a method for repairing DNA damage in FFPE samples, comprising: S1. subjecting FFPE sample DNA to heat denaturation; S2. allowing the DNA to fully renature by slow cooling or ice bath; S3. using random primers to bind to large nicked regions of the DNA fragment; S4. adding a mixed repair enzyme to repair the DNA damage; S5. ligating the DNA repaired in step S4 to obtain large DNA fragments, which are then purified with magnetic beads to obtain the repaired DNA. By using random primer single-strand extension to assist the enzyme reaction system, the efficiency of DNA damage / deletion repair is improved; by using random ligation to assemble fragmented DNA into large DNA fragments, the problem of ineffective amplification caused by excessive DNA fragmentation is solved, without affecting the microarray detection results. The entire DNA repair reaction is performed continuously, without the need for multiple purification operations. Compared with other DNA repair methods, it is simple to operate and low in cost, significantly improving the quality of FFPE sample DNA and increasing its detection pass rate in Infinium CytoSNP-850K whole genome microarray detection.

Analysis of cell free DNA (cfDNA) fragment ends in cancer patients provides a direct relationship between epigenetic alterations and cfDNA fragmentation for non-invasive disease detection and patient treatment. In certain embodiments, methods for cancer diagnosis and treatment include detecting methylation and expression differences in a patient that affect cell free (cfDNA) size and coverage. In certain aspects, include methods for determining circulating cfDNA fragmentation in a provided sample, including determining a genomic sequence to identify cfDNA endpoints; analyzing frequencies of cfDNA breaking points at a plurality of positions in the genome sequence; as a result, a circulating cfDNA fragmentation is determined.

The application discloses a whole-genome DNA cytosine hydroxymethylation modification single-base precision library construction method, relates to the technical field of genomics, epigenetics and molecular biology, and contains the following steps: 5hmC labeling reaction, click chemistry reaction, sample DNA fragmentation, purification of the fragmentation product through magnetic beads, 5hmC fragmented DNA capture, washing of the capture product, reduction reaction, APOBEC enzyme deamination reaction, purification of the deamination product, double-strand conversion reaction, end repair and 3' end A addition reaction, linker ligation, purification of the ligation product and double sorting, library amplification and library purification. The library construction method integrates low data volume, single-base precision and conventional double-strand library construction kit in one under the premise of ensuring data authenticity, and has the technical advantages of high universality and highly repeatable data.

The invention discloses a method for improving collagen yield of mesenchymal stem cells and engineered mesenchymal stem cells for high-yield collagen. The method comprises the following steps: designing at least one guide RNA (Ribonucleic Acid), and gRNA targets a promoter region of a collagen gene; the method comprises the following steps: introducing a composition containing gRNA and an expression vector for coding a CRISPR activation system into MSCs; forming a compound in the MSCs, specifically binding the compound to a collagen gene promoter region, and activating the transcription of the collagen gene; engineering MSCs with the expression quantity higher than that of untreated MSCs are screened and separated. The content of collagen produced by the method disclosed by the invention is obviously increased. Meanwhile, the effect is stable, the cell strain is not easy to lose along with cell division, and the yield of the screened cell strain is highly uniform and stable. More importantly, in the aspect of safety, the core CRISPRa method does not cut DNA, so that off-target damage and chromosome abnormality risks caused by DNA breakage are avoided, the potential risk is smaller, and it is ensured that the improved collagen really has biological functionality.

The invention relates to the field of cell genetic engineering, and discloses a high-sensitivity embryo chromatin analysis method which comprises the following steps: S1, puncturing an embryo zona pellucida through a micromanipulation instrument, sucking 5-8 trophoblast cells, and immersing a sample into 4 DEG C chromatin stabilizing liquid containing 1mM of ethylenediamine tetraacetic acid and bovine serum albumin within 8 seconds after the sample is obtained; s2, processing the sample by adopting a gradient fixation method; s3, sequentially carrying out low-intensity ultrasonication and restriction enzyme combined treatment; s4, carrying out specific labeling by using a double-labeling probe system; s5, implementing two-stage signal amplification in the micro-fluidic chip; and S6, carrying out three-dimensional space conformation analysis by adopting a super-resolution microscope. A silicon nitride microscopic needle penetrates through the zona pellucida at a puncture angle of 75-85 degrees, and the suction speed is controlled to be 0.5 mu L / s in combination with a PID closed loop, so that the DNA fragmentation rate can be reduced to 2.1 + / -0.3% (the proportion of 5kb fragments is 98.5%), and the embryo survival rate is gt; the H3K9 acetylation modification level is improved by 5.3 times, and the chromatin accessibility is improved.

The sperm screening device is sequentially provided with a sperm sampling component, a first filtering component, a sperm screening component, a second filtering component and a sperm collecting component from bottom to top, a sperm storage cavity is formed in the top surface of the sperm sampling part, the sperm screening part is provided with a vertically-through mucus storage cavity, and the sperm collecting part is provided with a vertically-through culture medium storage cavity; the first filtering part is provided with a plurality of first through holes penetrating up and down, and the two ends of the first filtering part are in contact with the sperm storage cavity and the mucus storage cavity respectively; the second filtering part is provided with a plurality of second through holes penetrating up and down, and the two ends of the second filtering part are in contact with the mucus storage cavity and the sperm collecting part respectively. The invention further provides a screening method using the sperm screening device. According to the sperm screening device and the using method thereof, sperms with the ultralow DNA fragmentation rate can be screened out, and the pregnancy rate and the offspring quality can be improved.

The present disclosure relates to the technical field of DNA fragmentation for technologies such as next generation sequencing (NGS) or any other technologies where fragmentation of DNA to a certain uniform size is required. In particular, the present disclosure relates to a variant of a Nucleoside Triphosphate (NTP)-dependent restriction enzyme (McrBC variants selected from McrBL68YC, McrBL68FC, and combinations of certain ratios thereof) for nucleic acid fragmentation for methods that require fragmentation of DNA.

A method for liver cancer detection uses a combination of whole genome mutations and fragmentation characteristics of cfDNA to facilitate cancer screening.

The present invention relates to methods and kits for fragmenting DNA. Methods of DNA fragmentation are provided. The methods include incubating a semi-solid biological sample comprising DNA with an auxiliary domain-directed nuclease having binding affinity and selectivity for a predefined site of the DNA to obtain a DNA fragment of interest, thereby fragmenting the DNA.

The invention discloses a method for efficiently and quickly constructing a specific library, and relates to the technical field of second-generation gene sequencing improvement. Traditional library construction steps (such as DNA fragmentation, terminal repair, linker connection, amplification and the like) are integrated into a reaction system, a specific primer and an index primer are connected through an accompanying primer under the action of ligase, then specific PCR is performed, and reaction conditions are optimized, so that all the steps can be completed in one tube of reagent and one PCR reaction. The library construction process is greatly simplified, the library construction time is shortened, aerosol pollution is greatly reduced, and the library construction efficiency and quality are improved.

The invention relates to the technical field of methylation sequencing, in particular to a low-cost methylation library preparation method for simultaneously performing bisulfite conversion and DNA fragmentation. Compared with a method for fragmenting the genome DNA by using an ultrasonic breaking method, the method disclosed by the invention has the advantage that the cost for fragmenting the genome DNA in the methylation library preparation process is greatly reduced.

The application discloses a culture solution containing lupeol for improving in-vitro maturation efficiency of pig oocytes and application thereof. The application adds lupeol, especially 4 muM lupeol, to an in-vitro maturation culture solution of oocytes, which can effectively improve the oxidation-reduction state of oocytes, significantly reduce the intracellular ROS level, and meanwhile, improve the GSH content, thereby maximally relieving oxidative stress damage in the in-vitro maturation process, significantly improving the maturation rate of pig oocytes in the meiotic metaphase II, and effectively reducing the DNA fragmentation ratio, which indicates that the lupeol has excellent effects of promoting nuclear maturation and protecting genetic material. The lupeol is added to the in-vitro maturation culture solution of oocytes, which is easy to operate and can be applied to the existing culture process, and can stably improve the efficiency and quality of pig in-vitro embryo production, and has important application value for pig germplasm resource preservation, rapid propagation of excellent breeds and development of animal husbandry.

The invention relates to a microfluidic device, method, and use for the continuous, label-free isolation of motile, morphologically normal spermatozoa from semen samples This invention offers a gentle, reliable, and efficient platform for sperm selection, serving as an alternative to centrifugation-based techniques in ART laboratories. By maintaining the structural and genetic integrity of sperm, it improves fertilization success, embryo quality, and pregnancy outcomes. The platform also reduces variability between technicians and limits exposure to reactive oxygen species (ROS), ensuring consistent clinical performance. Beyond its application in fertility treatments, the system can be used as a diagnostic tool to assess sperm motility disorders, susceptibility to oxidative stress, and DNA fragmentation dynamics under different environmental conditions or drug exposures.

The invention discloses a lentiviral vector integration site detection method based on Tn5 transposase mediation. According to the method, a pre-assembled Tn5 transposase-UMI joint compound is utilized, genome DNA fragmentation and molecular marking are completed simultaneously in a single-step reaction, and accurate quantitative detection of integration sites is achieved through carrier specific PCR amplification and high-throughput sequencing. Compared with the prior art, the method has the advantages that the operation steps are simplified from 6-8 steps to 4-5 steps, the detection period is shortened by 60%, PCR deviation is eliminated through the UMI molecular marker, and the detection precision is remarkably improved. The method is particularly suitable for safety evaluation of gene therapy products.

The present invention relates to cell lines in which DNA fragmentation is inhibited, uses of cell lines in which DNA fragmentation is inhibited for the production of Adeno-associated virus (AAV), related methods of producing AAV, and methods of producing AAV, comprising the step of exposing the cells in which AAV is produced to an inhibitor of DNA fragmentation during the AAV production phase.

A system and method for identifying genomic regions with higher fragmentation rates than the local and global backgrounds as part of diagnosing early stage cancer is provided. The method includes steps of: de-novo characterizing genome-wide cell-free DNA fragmentation regions with higher fragmentation rates than the local and global backgrounds from whole-genome sequencing by weighing the fragment coverages in each region by a ratio of average fragment sizes in the region versus that in the whole chromosome to generate a score; and identifying DNA fragmentation regions of interest based upon comparing the score with a threshold. The system and method can utilize identified DNA fragmentation hotspots for the detection and localization of multiple early-stage cancers (or certain other non-malignant disease).

The invention provides a single-cell genome amplification library building method, which comprises the following steps of: splitting a single cell; dNA fragmentation: a cleavage product is subjected to DNA fragmentation with at least two restriction endonucleases, most recognition sites of the first restriction endonucleases are located in a high-CG region of the genome, and recognition sites of the second restriction endonucleases do not have CG; sequentially carrying out terminal repair A addition, linker addition and User enzyme treatment on the fragmented product; and library amplification: adding a sequence tag into the User enzyme treatment product, and carrying out DNA amplification, thereby completing single cell genome amplification and library construction in one step. The invention also provides a single cell genome amplification library building kit, which comprises a fragmentation enzyme combination, and the fragmentation enzyme combination comprises a second restriction enzyme without CG in first restriction enzyme recognition sites of which most recognition sites are located in a genome high CG region. According to the method and the kit, the sequencing success rate after library establishment can be greatly improved.

The present invention relates to the technical field of DNA fragment data processing, and in particular to a method for processing DNA fragmentation gene detection data based on artificial intelligence. The method divides DNA fragmentation detection data into several local data blocks, performs continuous homology analysis on each local data block, uses an attention mechanism to assign dynamic weights to the ring and branch structures in a multi-scale topological feature matrix, extracts base association patterns of base sequences in the DNA fragmentation detection data through one-dimensional convolution, and obtains sequence features. The weighted topological features and sequence features are tensor-joined in a latent space. A multi-layer perceptron performs coarse-grained classification on the fused high-order feature vectors, and outputs preliminary classification results. A lightweight neural network submodule is constructed based on the preliminary classification results to obtain the final classification results. The present invention effectively improves the accuracy and interpretability of the classification results.

The present application belongs to the technical field of non-invasive prenatal testing, and particularly relates to a preparation method of a pregnant woman simulated plasma standard product capable of fetal concentration enrichment through fragment size. The present application provides a preparation method of a pregnant woman plasma free DNA simulation sample. The method combines specific DNA fragmentation processing technology to prepare a simulation sample with high fidelity and stability and capable of accurately simulating the fetal free DNA and pregnant woman free DNA distribution proportion in real pregnant woman plasma, for quality control and evaluation of non-invasive prenatal diagnosis technology. The method can accurately prepare the pregnant woman simulated plasma DNA with the corresponding fetal concentration according to the requirement, and the prepared pregnant woman simulated plasma can meet the requirement of the application of fetal concentration enrichment test, and at the same time, the cfDNA fragment distribution in the pregnant woman plasma is restored in the maximum range.

The invention belongs to the technical field of assisted reproduction, and particularly relates to a sperm optimization device and optimization method for assisted reproduction. The sperm optimization device for assisted reproduction comprises an outer chamber and an inner chamber, the outer chamber is communicated with the inner chamber through a plurality of micro through holes; the outer chamber is used for storing sperms needing to be optimized, and the inner chamber is used for storing sperm washing liquid (DEFB119). According to the sperm optimization device and optimization method for assisted reproduction, a sperm optimization system composed of the inner chamber, the outer chamber and the micro through holes is constructed, DEFB119 is adopted as a sperm detergent, the sperm optimization cumulative gradient can be formed in the inner chamber based on natural selection of DEFB119, and combined screening of sperms is achieved; and the optimized sperms are low in DNA fragmentation rate, complete in form, good in activity and suitable for further assisted reproduction work.

Small cell lung cancer (SCLC) exhibits distinct molecular subtypes characterized by activation of transcription factors (TFs) such as ASCL1, NEUROD1, POU2F3, and REST, but clinical translation has been limited by tissue scarcity. Here, a cell-free DNA (cfDNA) targeted sequencing assay is disclosed that analyzes DNA fragmentation patterns to infer nucleosome profiles at TF binding sites and gene transcription start sites (TSSs) and also detects exonic mutations in certain genes. Application to plasma cfDNA from SCLC patient-derived xenograft models faithfully captured signatures of TF activity and gene expression and revealed a subset of highly informative nucleosome profiling loci including TSSs of key genes including ATOH1, POU2AF2, and targets of SCLC subtype defining TFs. Prediction models of ASCL1, NEUROD1, and REST activity achieved AUCs (0.82-1.00) in SCLC patient samples while a predictor of SCLC vs NSCLC histology achieved an AUC of 0.99. Targeted cfDNA nucleosome profiling can enable SCLC subtyping to improve patient care.

The application discloses an enzyme composition for low-preference DNA fragmentation and a reaction solution thereof. The enzyme composition comprises an endonuclease, a nucleotide kinase and a DNA polymerase, the endonuclease comprises any one of DNase I, heat-stable high-salt-tolerant endonuclease HL-SAN or endonuclease IV or a combination of at least two of them, the nucleotide kinase comprises T4 polynucleotide kinase, and the DNA polymerase comprises any one of Taq DNA polymerase, a Klenow fragment of DNA polymerase I or T4 DNA polymerase or a combination of at least two of them. The application develops a one-tube method for genome fragmentation, end repair and A-tailing module, including an enzyme composition and a reaction solution thereof. In view of the problems and deficiencies of the current enzyme library construction, the components are optimized and explored, and a suitable connection module is combined, so that the finally obtained product has low preference, the output library has higher uniformity, and has a wide application prospect in second-generation sequencing.

The present invention refers to the fertility field. Particularly, the present invention refers to an in vitro method for the diagnosis of male infertility, or for the identification of the fertility status of a subject compared to a reference group, to an in vitro method for recommending a fertility treatment to a subject, and to an in vitro method for assessing DNA fragmentation in a biological sample that has been obtained from a subject, which comprises assessing the expression of gamma-H2AX and H2AX in a sperm sample that has been obtained from a subject, and processing the expression values to obtain a normalized expression value of gamma-H2AX with respect to the expression of H2AX.

The invention relates to a microfluidic device, method, and use for the continuous, label-free isolation of motile, morphologically normal spermatozoa from semen samples This invention offers a gentle, reliable, and efficient platform for sperm selection, serving as an alternative to centrifugation-based techniques in ART laboratories. By maintaining the structural and genetic integrity of sperm, it improves fertilization success, embryo quality, and pregnancy outcomes. The platform also reduces variability between technicians and limits exposure to reactive oxygen species (ROS), ensuring consistent clinical performance. Beyond its application in fertility treatments, the system can be used as a diagnostic tool to assess sperm motility disorders, susceptibility to oxidative stress, and DNA fragmentation dynamics under different environmental conditions or drug exposures.

The present invention relates to the diagnostic of inflammatory diseases. The inventors described methods using NET biomarkers as diagnostic biomarkers for inflammatory diseases. COVID-19, Lupus or mCRC are used here as illustrative models for investigating an inflammatory disease. Examples in highlighting variation of the respective correlation of NET biomarkers in this invention rely on the determination of the NET main constituents: (i), DNA as determined by examining the amount of circulating DNA (cirDNA) that corresponds to the amount of NET as being degradation by-products that are released into the circulation; (ii) NE; and (iii), MPO; as well as the detection of a blood compound being indirectly associated to NET formation like the anti-cardiolipin auto-antibody. The invention provides threshold values of NE, MPO, cir-nDNA, and cir-mtDNA blood concentrations and of MNR that can be combined to diagnose / screen individuals. Thus the invention relates to a method for diagnosing a subject for an inflammatory disease comprising the steps of i) determining in a sample obtained from the subject the level of at least one marker selected in the group consisting in NET protein markers, cir-nDNA, cir-mtDNA and / or a cir-DNA fragmentation index.

The utility model discloses a multi-reaction device for targeted NGS totally-closed efficient automatic library building, which comprises a base, reaction holes and reagent storage holes are defined in the base, the reaction holes are used for placing samples to be detected, the reagent storage holes are used for placing reaction reagents, a reagent transfer mechanism is used for sucking the reaction reagents and putting the reaction reagents into the reaction holes, and the reaction holes are used for placing the reaction reagents. The sealing shell covers the base in a sealing mode, and the reagent transferring mechanism is arranged in the sealing shell. A series of operations such as DNA extraction, DNA fragmentation, terminal repair, linker connection and library amplification in the library construction process can be carried out in the reaction hole of the base, so that the automation of library construction is realized, the experiment time is shortened, the labor cost is reduced, and high efficiency is realized; meanwhile, result errors caused by human factors are reduced, experimental results are more accurate, and repeatability of library building operation is achieved; in a sealed environment, the formation of aerosol can be isolated, and the aerosol is prevented from polluting a library amplification product.