56 results about "Nucleotide substitution" patented technology

The present invention is directed to methods and compositions for the use of microsphere arrays to detect and quantify a number of nucleic acid reactions. The invention finds use in genotyping, i.e. the determination of the sequence of nucleic acids, particularly alterations such as nucleotide substitutions (mismatches) and single nucleotide polymorphisms (SNPs). Similarly, the invention finds use in the detection and quantification of a nucleic acid target using a variety of amplification techniques, including both signal amplification and target amplification. The methods and compositions of the invention can be used in nucleic acid sequencing reactions as well. All applications can include the use of adapter sequences to allow for universal arrays.

The present invention is directed to methods and compositions for the use of microsphere arrays to detect and quantify a number of nucleic acid reactions. The invention finds use in genotyping, i.e. the determination of the sequence of nucleic acids, particularly alterations such as nucleotide substitutions (mismatches) and single nucleotide polymorphisms (SNPs). Similarly, the invention finds use in the detection and quantification of a nucleic acid target using a variety of amplification techniques, including both signal amplification and target amplification. The methods and compositions of the invention can be used in nucleic acid sequencing reactions as well. All applications can include the use of adapter sequences to allow for universal arrays.

The invention discloses a DNA fragment with a promoter function and an application. The DNA fragment is any one of the following sequences: (a) a nucleotide sequence shown in SEQ ID NO: 1 or a complementary sequence of the nucleotide sequence; (b) a nucleotide sequence having a promoter function identical to SEQ ID NO: 1 or a complementary sequence of the nucleotide sequence obtained by substituting, deleting or adding one or more nucleotides on the nucleotide sequence shown in the SEQ ID NO: 1; and (c) sequences of one or more ribosome bind sites added in the nucleotide sequence shown in the SEQ ID NO: 1. The DNA has a promoter function and is high in expression activity, and high expression of exogenous genes can be realized under a condition that inducers are not needed, and the DNA fragment is applied to expression of heatproof beta-galactosidase and transglutaminase. An effective tool is particularly provided for expression of bacillus amyloliquefaciens.

The invention provides arrays and probes for resequencing a SARS virus using an array of probes that are complementary to a SARS reference sequence and to each possible single nucleotide substitution of the reference sequence. Methods of identifying mutations in viral sequences and methods of characterizing viral isolates are also provided. The invention also provides high throughput methods to monitor epidemics and pandemics caused by pathogens such as viruses.

The present invention relates to molecular biology, microbiology, and medicine and provides the method for detection of Mycobacterium tuberculosis complex with simultaneous evaluation of sensitivity of the strains to rifampicin and isoniazid in clinical sample on differentiating biochip. The method is based on two-stage multiplex PCR to obtain fluorescent DNA fragments followed by hybridization of these fragments on microarray containing the set of specific discriminating oligonucleotides. The determination of the resistance of Mycobacterium tuberculosis to rifampicin and isoniazid is carried out by evaluation of point nucleotide substitutions in DNA of microorganism. The present invention allows conduct analysis directly in clinical sample, to evaluate a number of mutations simultaneously, to decrease the cost price of analysis, and to reduce the time of its conducting. The present invention also relates to set of primers, biochip, and set of oligonucleotide probes used in realization of the method.

The invention discloses a signal peptide capable of effectively improving protein secretion efficiency and an application of the signal peptide. The amino acid sequence of the signal peptide is shownin SEQ ID NO.1. The nucleotide sequence for encoding the signal peptide is selected from any of the following sequences: (a) a nucleotide sequence shown in SEQ ID NO.2 or a complementary sequence of the nucleotide sequence; and (b) a nucleotide sequence which is obtained through substitution, deletion or addition of one or more nucleotides of the nucleotide sequence shown in SEQ ID NO.2, has a same function of being used a signal peptide with the nucleotide sequence shown in SEQ ID NO.2, or a complementary sequence of the obtained nucleotide sequence. According to the invention, an expressionvector with the combination of the signal peptide and beta-galactosidase encoding gene/transglutaminase zymogen encoding gene is constructed from a vacillus subtilis homologous protein signal peptidelibrary, the signal peptide capable of increasing the secretion of beta-galactosidase can be screened out, and the secretion expression of the transglutaminase zymogen is realized.

The invention discloses an aptamer capable of identifying a hepatitis C virus (HCV) nonstructural 5A (NS5A) protein, which is a DNA fragment represented by any of sequences from SEQ ID No.1 to SEQ ID No.5. The derivatives of the aptamer comprise nucleotide substituted RNA aptamers, skeleton-restructured derivatives, restructured peptide nucleic acid derivatives and radioactive molecule connected derivatives. The screening method of the aptamer comprises: preparing HCV NS5A protein with histidine marker, and preparing protein pET200/D/LacZ; immobilizing the proteins, and designing a random nucleic acid library; and finally, screening the aptamer by pretreating the DNA library, performing reverse screening, screening and repeated screening and other steps, wherein the obtained aptamer has high competition power and optimized sequence length. The aptamer and the derivatives thereof can be used in the preparation of detection kit or diagnosis reagent for the HCV NS5A protein and can also be used in preparation of reagents for inhibiting replication of hepatitis C virus in liver cells.

Presented herein are live-attenuated viruses and methods of generating thereof from a parental virus through a plurality of nucleotide substitutions in the viral genome. The nucleotide substitutions result in a change in codon usage bias within codons of one or more protein encoding sequences and no change in amino acid sequences of the proteins. The live-attenuated viruses display unaltered replication in avian hosts for propagation, but attenuated replication in mammalian hosts, when compared to the replication of the parental virus. The live-attenuated viruses in a form of improved vaccines can be used to elicit protective immune responses.

The invention discloses a DNA fragment of bacillus subtilis with a promoter function and application thereof. The DNA fragment is any one of a, the nucleotide sequence as shown in SEQ ID NO.1 or a complementary sequence thereof; b, a nucleotide sequence obtained by substituting, deleting or adding one or more nucleotides of the nucleotide sequence as shown in SEQ ID NO.1 and having the promoter function the same as that of the nucleotide sequence as shown in SEQ ID NO.1, or a complementary sequence thereof; and c, a sequence obtained by adding one or more ribosome bind sites to the nucleotide sequence as shown in SEQ ID NO.1. The DNA fragment has the promoter function, and also has high expression activity. High expression of exogenous genes can be achieved without adding an inductor. The DNA fragment can be applied to expression of thermostable beta-galactosidase and transglutaminase, and particularly, an effective element is provided for a bacillus subtilis expression-secretion system.

The invention discloses a DNA fragment with a promoter function and a use thereof. The DNA fragment has a sequence selected from (a), a nucleotide sequence shown in the formula of SEQ ID NO. 1 or its complementary sequence, (b), a nucleotide sequence which is derived from the nucleotide sequence shown in the formula of SEQ ID NO. 1 through replacement, deletion or addition of one or multiple nucleotides and has a promoter function the same to that of the nucleotide sequence shown in the formula of SEQ ID NO. 1, or its complementary sequence, and (c), a sequence derived from the nucleotide sequence shown in the formula of SEQ ID NO. 1 through addition of one or more ribosome binding sites. The DNA fragment has a promoter function and strong specific expression activity, realizes high exogenous gene expression without an inducer and provides an effective element for bacillus subtilis expression of an exogenous gene.

The invention provides arrays and probes for resequencing gene sequences of HIV and HCV using an array of probes complementary to a set of reference sequences, and to each possible single nucleotide substitution of the reference sequences, and for identifying known mutations in HIV and HCV gene sequences associated with resistance to antiviral therapy. Methods of identifying mutations in HIV and HCV sequences, methods of characterizing HIV and HCV isolates, and methods of evaluating and optimizing a patient's antiviral therapy regimen are also provided.

The present invention relates to modified filamentous fungal organisms having improved activity profiles with respect to the conversion of complex carbohydrates into simple sugars from cellulosic materials, including fungal organisms belonging to a genus selected from the group consisting of: Chrysosporium, Thielavia, Talaromyces, Thermomyces, Thermoascus, Neurospora, Aureobasidium, Filibasidium, Piromyces, Corynascus, Cryplococcus, Acremonium, Tolypocladium, Scytalidium, Schizophyllum, Sporotrichum, Penicillium, Gibberella, Myceliophthora, Mucor, Aspergillus, Fusarium, Humicola, Trichoderma, and Talaromyces, plus anamorphs and teleomorphs thereof. Filamentous fungal organisms having improved activity profiles are obtained by modifying genes encoding enzymes involved in the production of cellobionolactone, cellobionic acid, gluconolactone, gluconic acid, and related products, by a variety of mutagenic methods, resulting in nucleotide substitutions, insertions, and deletions, increasing the level of saccharification in enzyme mixtures obtained from the modified organisms.

There is provided a computer-implemented method for identifying of nucleic acid variants between two cells, such as a normal cell vs. a pathological cell of a patient, or a cell at two different stages of development. The method is alignment-free, as it does not depend on the use of a reference genome, and is based on the generation and comparison of polymorphic k-mers derived from the nucleotide sequence reads of both biological states. The invention accurately identifies all sorts of genetic variants, ranging from single nucleotide substitutions (SNVs) to large structural variants with great sensitivity and specificity. As a major novelty, it also identifies non-human insertions, such as those derived from retroviruses. Altogether, this invention allows the integration with specific hardware architectures in order to speed up the executions to an unprecedented level.

This invention encompasses an isolated Bacillus phage AP50 that has one or more nucleotide substitutions in the phage genome, whereby the one or more nucleotide substitutions increase lytic activity of the phage. In addition, the invention encompasses proteins expressed by the phages, compositions containing the proteins and/or the phage as well as methods of using the Bacillus phage AP50 to test for the presence of B. anthracis.

The current invention concerns a computer-implemented method, a computer system and a tangible non-transitory computer-readable data carrier comprising a computer program product for aligning a query nucleic acid sequence against a reference nucleic acid sequence. An optimal alignment score of the query sequence against the reference sequence is determined by a dynamic programming algorithm. The algorithm is configured for locally optimizing a partial alignment score based on a nucleotide substitution cost, a gap insertion cost, an amino acid substitution cost, as well as a frameshift penalty.

This invention provides a modified protein encoding sequence containing nucleotide substitutions at multiple locations in the protein encoding sequence, wherein the substitutions introduce rare hexamers. These hexamers may be Frame Dependent, or depleted in only the reading frame, or Frame Independent, or depleted in all three frames. Modified protein encoding se quences of the present invention may include modified viruses useful for vaccines.