8 results about "Degenerate primer" patented technology

This invention relates to a primer set and method for high-throughput assessment of drug resistance levels in rodent populations. The invention provides a set of universal degenerate primers for amplifying the Vkorc1 gene in multiple rodent species. The primer set includes primers for amplifying exon 1, exon 2, and exon 3 of the Vkorc1 gene, respectively. By designing universal degenerate primers and coupling them with next-generation sequencing technology, this invention can simultaneously amplify the Vkorc1 gene coding region of at least 15 rodent species across genera and families. This significantly improves the species universality and detection throughput of rodent drug resistance monitoring, reduces the cost of large-scale screening, overcomes the limitation of Sanger sequencing in accurately analyzing heterozygotes with insertions and deletions, and enhances the ability to discover new resistance mutations. It provides a standardized and low-cost technical solution for efficient assessment of rodent drug resistance.

The present disclosure relates to an integrated system for generating optimized primer probe pair design for one or more quantitative polymerase chain reaction (qPCR) assays using a sequence alignment free design approach. The system includes a processor; and a computer-readable medium storing instructions which, when executed by the processor, cause the processor to: receive data including a genomic dataset; generate one or more k-mers from the genomic dataset; cluster the one or more k-mers to identify one or more targeted genomic regions; generate a plurality of primer-probe pair candidates corresponding to the one or more targeted genomic regions, wherein the one or more primer-probe pairs include degenerate primers; and perform one or more in silico operations using the one or more primers, wherein the one or more in silico operations comprise at least one of primer-probe pair optimization, specificity testing, secondary structure analysis, and in silico PCR simulation.

The invention discloses a bacterial cadmium response element screening method, and belongs to the technical field of biology. According to the invention, a strain of Microbacterium oxydans SC-30 is screened, the tolerance to Cd < 2 + > is relatively high, and the minimum inhibitory concentration (MIC) value is 5.72 mmol / L, so that the cadmium resistance of microorganisms is greatly broken through. Degenerate primers of bacterium sources cadR and cadC are further designed to be used for obtaining a Cd < 2 + > response element in a microbacterium oxydans SC-30 strain, then cadR and cadC gene sequences in the strain SC-30 are obtained, the sizes of the cadR and cadC gene sequences are 438 bp and 2097 bp, and the cadR and cadC gene sequences have the highest homology with cadR4 and cadC1 gene sequences in Pseudomonas putida, and the cadR4 and cadC1 gene sequences have the highest homology with the cadR4 and cadC1 gene sequences in Pseudomonas putida, and the cadR4 and cadC1 gene sequences are 54.90% and 55.85% respectively.

The invention relates to a method for detecting DNA modification, in particular to a construction method of a DNA library with modified nucleotide, a detection method, a kit set and application. According to the scheme provided by the invention, the necessity of designing degenerate primers is avoided, the design difficulty of multiple primers is greatly reduced, the specificity of multiple PCR amplification is improved, and the formation of primer dimers is reduced.

The invention discloses a detection method for distinguishing human genetic materials based on a nanopore sequencing technology and a DNA bar code technology. The detection method is characterized by comprising the following steps: (1) extracting total nucleic acid of a sample to be detected; (2) carrying out PCR (Polymerase Chain Reaction) amplification on a sample to be detected by adopting the degenerate primer; and (3) sequencing the PCR product based on a nanopore sequencing technology, and determining whether the to-be-detected sample contains the human genetic material based on a sequencing result. Primer design and optimization are carried out according to the COI gene of human mtDNA, compared with a general identification primer for mammals, the capture capacity of the human COI gene is improved, meanwhile, a sequencing experiment process suitable for on-site rapid detection is developed, enough data can be obtained by computer sequencing for 10 minutes, and then comparison with a known sequence is carried out.

The application discloses a primer set for detecting a whole genome of a pig HEV, a kit comprising the primer set and application. The primer set comprises nucleotide sequences as shown in SEQ ID NO. 1-62, the primer set is designed for amplification fragments of 450 bp of a whole gene of the pig HEV and 650 bp of a non-conserved region, is divided into two sets of shingle degenerate primers, comprises five primer groups of A, B, C, D and E, and five amplification primer pools are constructed by using the five primer groups, so that the primer set can cover the complete genome of different strain types of the pig HEV. The application also establishes a method for sequencing the whole genome of the pig hepatitis E virus by using multiplex targeted RT-PCR and nanopore sequencing based on the primer set. The method is rapid, sensitive and specific, can be used for rapidly obtaining the whole genome information of the pig hepatitis E virus in a sample, and provides a reliable technical means for tracing the pig hepatitis E virus and accurately determining the genotype.

This invention provides a sex-specific molecular marker for kelp and its application, wherein the nucleotide sequence of the male marker fragment is SEQ ID NO:1, and the nucleotide sequence of the female marker fragment is SEQ ID NO:2. The gene sequence fragments obtained by this invention are derived from conserved homologous genes in the sex-determining regions of brown algae. The primer sequences for the selected sex identification markers are derived from the regions with the highest similarity in the coding sequences of the homologous genes. This method enables rapid identification of the sex of kelp gametophytes using only a pair of degenerate primers, offering high efficiency, high accuracy, and high interspecies compatibility. This method is applicable to the identification of mixed male and female samples, the differentiation of kelp sporophytes from parthenogenesis and sexual reproduction, and the sex identification of gametophytes in other species of the Laminariales order, providing important support for the efficient management and research utilization of kelp gametophyte germplasm banks.

The present disclosure relates to an integrated system for generating optimized primer probe pair design for one or more quantitative polymerase chain reaction (qPCR) assays using a sequence alignment free design approach. The system includes a processor; and a computer- readable medium storing instructions which, when executed by the processor, cause the processor to: receive data including a genomic dataset; generate one or more k-mers from the genomic dataset; cluster the one or more k-mers to identify one or more targeted genomic regions; generate a plurality of primer-probe pair candidates corresponding to the one or more targeted genomic regions, wherein the one or more primer-probe pairs include degenerate primers; and perform one or more in silico operations using the one or more primers, wherein the one or more in silico operations comprise at least one of primer-probe pair optimization, specificity testing, secondary structure analysis, and in silico PCR simulation.