31 results about "Codon pair" patented technology

The present invention relates to methods of optimization of a protein coding sequences for expression in a given host cell. The methods apply genetic algorithms to optimise single codon fitness and / or codon pair fitness sequences coding for a predetermined amino acid sequence. In the algorithm generation of new sequence variants and subsequent selection of fitter variants is reiterated until the variant coding sequences reach a minimum value for single codon fitness and / or codon pair fitness. The invention also relates to a computer comprising a processor and memory, the processor being arranged to read from and write into the memory, the memory comprising data and instructions arranged to provide the processor with the capacity to perform the genetic algorithms for optimisation of single codon fitness and / or codon pair fitness. The invention further relates to nucleic acids comprising a coding sequence for a predetermined amino acid sequence, the coding sequence being optimised with respect to single codon fitness and / or codon pair fitness for a given host in the methods of the invention, to host cells comprising such nucleic acids and to methods for producing polypeptides and other fermentation products in which these host cells are used.

Provided are methods for calculating codon pair translational kinetics values, creating a synthetic gene for expression in a host organism, and providing codon pair translational kinetic values. The methods typically are directed to refinement of statistical observed versus expected codon pair frequencies using one of several factors such as amino acid sequence homology, secondary or tertiary structural considerations, and empirical measurements. In some synthetic genes codon pairs are predicted not to cause a translational pause in the host organism, thereby providing a polynucleotide sequence encoding the desired polypeptide with desired translational kinetics properties. The methods can be performed using multiple parameter nucleotide sequence optimization methods, such as branch-and-bound methods for nucleotide sequence refinement.

The present provides attenuated influenza viruses comprising a modified viral genome containing a plurality of nucleotide substitutions. The nucleotide substitutions result in the rearrangement of preexisting codons of one or more protein encoding sequences and changes in codon pair bias. Substitutions of non-synonymous and synonymous codons may also be included. The attenuated influenza viruses enable production of improved vaccines and are used to elicit protective immune responses.

The invention discloses an optimized gene of ietalurus punetaus LEAP-2 mature peptide and a preparation method of recombinant protein of the optimized gene, and further provides a recombinant expression carrier and yeast host cell containing the optimized gene, application of the optimized gene to producing the ietalurus punetaus LEAP-2 mature peptide, and application of the recombinant protein to preparing antibacterial medicines. On the premise of not changing the amino acid sequence of the ietalurus punetaus LEAP-2 mature peptide, the amino acid sequence of the gene of the ietalurus punetaus LEAP-2 mature peptide is optimized according to pichia pastoris preferred codons, and the optimized sequence is SEQ ID NO:2. By expressing the optimized gene in a pichia pastoris host cell, the recombinant ietalurus punetaus LEAP-2 mature peptide is prepared. By means of the preparation method, the LEAP-2 mature peptide can be efficiently prepared, the applied culture conditions are simple, cost is low, and the obtained LEAP-2 mature peptide is good in antibacterial effect.

Graphical displays are provided of translational kinetics values of codon pairs in a host organism plotted as a function of polypeptide-encoding nucleotide sequence. Such translational kinetics values of codon pair frequencies correspond to the predicted translational pausing properties of a codon pair in a host organism. The graphical displays provided reflect the relative over-representation or under-representation of each codon pair in an organism, thereby facilitating analysis of translational kinetics of an mRNA into polypeptide by comparing graphical displays of different codon pairs in sequences encoding the polypeptide. The graphical displays of translational kinetics values also can display codon pair properties on comparable numerical scales, thereby facilitating analysis of translational kinetics of an mRNA into polypeptide in different organisms by comparing comparably scaled graphical displays of the same or different codon pairs in sequences encoding the polypeptide. Also contemplated herein is the use of the graphical displays described herein for tracking the entire process of creating a refined polypeptide-encoding nucleotide sequence. In particular, additional translational kinetics graphical displays can be created to illustrate differences and / or similarities of translational kinetics of a polypeptide-encoding nucleotide sequence in which one or more codon pairs have been modified. Additionally, numerous translational kinetics graphical displays can be created to illustrate differences and / or similarities of translational kinetics of a polypeptide-encoding nucleotide sequence when expressed in two or more different organisms.

The invention discloses a codon optimization method used for heterologous gene in-vitro expression. The method comprises the steps that a nucleotide sequence of a whole genome of a host cell and an amino acid sequence of a whole proteome of the host cell are acquired; codon pairs are taken as a statistical object, and statistics is conducted on the weight of each codon pair in the whole genome ofthe host cell; to-be-optimized protein is selected, and a single-direction graph model which takes codons as nodes and takes weight values of the upstream and downstream codon pairs as linear values is constructed; according to the single-direction graph model, a nucleotide sequence of an optimized gene is obtained. According to the codon optimization method used for heterologous gene in-vitro expression, the whole genome and whole proteome of the host cell are utilized as sequence libraries, the codon pairs are taken as the statistical object, and by constructing the single-direction graph model which takes the codons as the nodes and takes the weight values of the upstream and downstream codon pairs as linear values, the optimum codon combination sequence is obtained; the optimized genewith the optimum nucleotide sequence is obtained and can be efficiently expressed in vitro, and the expression amount is significantly improved.

The present invention relates to systems and methods for measuring the rate of translation of a target protein in cells, which are based on the detection of translation of one or more predetermined codon pairs during synthesis of the target protein. The detection is provided by a FRET signal emitted from labeled tRNA molecules which are juxtaposed during synthesis of the protein.

A novel and stable attenuated poliovirus is produced by engineering an indigenous replication element (cre), into the 5′ non-translated genomic region (with inactivation of the native ere element located in the coding region of 2C (mono-crePV), and replacing the nucleic acid sequence of all or part of the capsid coding region (PI) with a substitute PI coding region having reduced codon pair bias. The stably attenuated poliovirus is effective for vaccines and immunization.

The present invention is the use of designed recombinant viruses for the treatment of various forms of malignant tumors. The recombinant viruses of the invention are those in which one or more regionsof the wild type virus was exchanged with a synthetic recoded sequence that reduces the codon pair score relative to human codon pair bias, or that increase the number for CpG di-nucleotides, or thatincreases the number of UpA di-nucleotides. The method of the present invention is particularly useful for the treatment of malignant tumors in various organs, such as: breast, skin, colon, bronchialpassage, epithelial lining of the gastrointestinal, upper respiratory and genito-urinary tracts, liver, prostate and the brain. Astounding remissions in experimental animals have been demonstrated for the treatment of malignant glioblastoma multiforme, as well as for the treatment of breast cancer and melanoma as well.

The invention relates to a method for analyzing the codon usage pattern of multiple Rutaceae species, comprising: obtaining the codon sequence of each species through the genetic data of multiple Rutaceae species; extracting the first characteristic value of the codon sequence , verify the evolutionary relationship of the plurality of species with the relationship of the first eigenvalue; extract the second eigenvalue of the codon sequence, and draw a characteristic relationship diagram with the second eigenvalue to verify the evolutionary conservation of the plurality of species degree; extract the high-frequency codon / codon pair in the codon sequence, and verify the evolutionary conservation correlation of the multiple species with the relationship of the high-frequency codon / codon pair; the codon of the codon sequence The RSCU value was clustered with the codon RSCU value of the plant species, and the clustering results were used to verify the order of the multiple species; the Euclidean distance between the GC3 content of the codon sequence was obtained to verify the genetic relationship of the multiple species.

The present invention is the use of designed recombinant viruses for the treatment of various forms of malignant tumors. The recombinant viruses of the invention are those in which one or more regions of the wild type virus was exchanged with a synthetic recoded sequence that reduces the codon pair score relative to human codon pair bias, or that increase the number for CpG di-nucleotides, or that increases the number of UpA di-nucleotides. The method of the present invention is particularly useful for the treatment of malignant tumors in various organs, such as: breast, skin, colon, bronchial passage, epithelial lining of the gastrointestinal, upper respiratory and genito-urinary tracts, liver, prostate and the brain. Astounding remissions in experimental animals have been demonstrated for the treatment of malignant glioblastoma multiforme, as well as for the treatment of breast cancer and melanoma as well.

The present invention provides for modified Flavivirus such as a modified Zika virus. The modification according to various aspects of the invention results in reduced viral proteins compared to a parent virus, wherein the reduction in expression is the result of recoding one or more regions of the virus. For example, the prM, or envelope (E) region, or the nonstructural protein 3 (NS3) region or both the E and NS3 regions can be recoded. In various embodiments one or more regions are recoded by reducing the codon pair bias or codon usage bias of the protein-encoding sequence. These modified Flavivirus are used as vaccine compositions to provide a protective immune response.

The invention discloses a gene synthesis of Alpha-interferon of wild boars and vector construction thereof as well as a production method of a product. A number of problems of low expression capacity, products expressed in a fusion state, products with purification tags or no fermentation technology with high density exist in the domestic recombinant strains. The invention includes a method that a codon and codon pairs, preferred by Escherichia coli, are used for synthesizing an Alpha-interferon gene of the wild boar, establishing a high-efficiency expression vector and transforming a high-efficiency expression strain as well as methods of high-density fermentation of engineering bacteria, separation and purification of inclusion bodies, the modification, the renaturation and the purification of target protein and the determination of biological activity of the expressed product. The gene synthesis, the vector construction and the production method pertain to the technical field of the production of polypeptide drugs by genetic engineering in biopharmaceuticals.

The invention discloses a codon optimization method for in vitro expression of heterologous genes. The method comprises: obtaining the nucleotide sequence of the whole genome of the host cell and the amino acid sequence of the whole protein group; taking the codon pair as the statistical object, and counting The weight of each codon pair in the whole genome of the host cell; select the protein to be optimized, and construct a one-way graph model with codons as nodes and the weight values ​​between upstream and downstream codon pairs as line values; according to the one-way graph Model to obtain the nucleotide sequence of the optimized gene. The present invention uses the whole genome and whole protein group of the host cell as the sequence library, takes codon pairs as statistical objects, and constructs a one-way graph model with codons as nodes and the weight values ​​between upstream and downstream codon pairs as line values, To obtain the optimal codon combination sequence, an optimized gene with an optimized nucleotide sequence can be obtained, and the optimized gene can be highly expressed in vitro, and the expression level is significantly increased.

The invention discloses an optimized gene of recombinant glucose oxidase and an expression vector and application of the optimized gene. On the premise that the amino acid sequence of the glucose oxidase is not changed, the gene sequence of the glucose oxidase is optimized according to pichia pastoris preferred codons by comprehensively considering the influencing factors such as use frequency ofthe codons, adjustment of GC content, deletion of instable sequences, secondary mRNA structure and the like; and the nucleotide sequence of the optimized glucose oxidase gene is shown as SEQ ID NO.1.The invention further provides the expression vector and a recombinant host strain containing the optimized gene of the glucose oxidase. The optimized gene is transferred to the pichia pastoris for expression, and the test results show that: compared with the gene before optimization, the secreting expression quantity of the optimized gene in the pichia pastoris is remarkably improved. The application effect tests of the glucose oxidase show that the expressed recombinant glucose oxidase has the same using effect as a commercial enzyme preparation.

The present invention provides a modified flavivirus, such as a modified type 1, type 2, type 3, type 4 dengue virus, a combination of these viruses, or a tetravalent combination of these viruses. The modifications according to various aspects of the invention result in reduced expression of the viral protein as compared to the parent virus, where the expression reduction is the result of recoding one or more regions of the virus. For example, a prM or envelope (E) region may be recoded. In various embodiments, the one or more regions are recoded by reducing the codon pair preference or codon use preference of the protein coding sequence. These modified flaviviruses are useful as vaccine compositions to provide protective immune responses.

The embodiment of the present application provides a gene sequence optimization method, device and data processing terminal, by obtaining the amino acid sequence corresponding to the codon sequence to be optimized, and importing the amino acid sequence into a pre-established optimization model for optimization to obtain the codon box sequence. Wherein, each group of codon boxes contained in the codon box sequence corresponds to at least one group of codons, and the codons corresponding to the same group of codon boxes contain the same code elements. Then for each codon box, obtain the codon corresponding to the codon box, and the codon corresponding to the amino acid corresponding to the codon box, obtain an optimized codon according to the codons corresponding to the two, and use the optimized codon Optimize the codon sequence to be optimized. In this way, by optimizing the way to obtain the codon box, the complexity of the optimization process is simplified, and the method of combining amino acids and codons corresponding to the codon box to obtain the optimized codon improves the accuracy of the optimized codon.