94 results about "Synthetic DNA" patented technology

The present invention provides DNA molecules that constitute fragments of the genome of a plant, and polypeptides encoded thereby. The DNA molecules are useful for specifying a gene product in cells, either as a promoter or as a protein coding sequence or as an UTR or as a 3′ termination sequence, and are also useful in controlling the behavior of a gene in the chromosome, in controlling the expression of a gene or as tools for genetic mapping, recognizing or isolating identical or related DNA fragments, or identification of a particular individual organism, or for clustering of a group of organisms with a common trait. One of ordinary skill in the art, having this data, can obtain cloned DNA fragments, synthetic DNA fragments or polypeptides constituting desired sequences by recombinant methodology known in the art or described herein

Methods and compositions for producing hRNA, e.g., shRNA, expression modules for specific target nucleic acids are provided. In the subject methods, an initial nucleic acid, e.g., dsDNA, synthetic DNA, etc., corresponding to the target nucleic acid of interest is converted to an intermediate nucleic acid. The resultant intermediate nucleic acid, following an optional size modification step, is then converted to a linear dsDNA that includes at least one copy of the hRNA expression module of interest, or a precursor (i.e., pro-shRNA expression module) thereof, where in certain embodiments conversion may include amplification. Also provided are reagents, systems and kits for use in practicing the subject methods. The subject methods and compositions find use in a variety of different applications.

The present invention relates to synthetic DNA sequences which encode one or more collections of homologous proteins/(poly)peptides, and methods for generating and applying libraries of these DNA sequences. In particular, the invention relates to the preparation of a library of human-derived antibody genes by the use of synthetic consensus sequences which cover the structural repertoire of antibodies encoded in the human genome. Furthermore, the invention relates to the use of a single consensus antibody gene as a universal framework for highly diverse antibody libraries.

A process for the production of humanized chimera antibody, wherein the chimera antibody is produced easily without changing any of the amino acids of its mouse antibody variable region, which comprises the steps of: (1) constructing a cassette vector by inserting a cDNA coding for a heavy chain constant region of human antibody into an expression vector for animal cell use and establishing a cloning site in the upstream region of the heavy chain constant region of said cassette vector for inserting a cDNA which encodes a heavy chain variable region of nonhuman animal antibody; (2) digesting a cDNA coding for the heavy chain variable region of nonhuman animal antibody with restriction enzymes; (3) inserting said cDNA coding for the heavy chain variable region of nonhuman animal antibody into the cassette vector, using a synthetic DNA which comprises a base sequence corresponding to the 5'-end side of said heavy chain constant region of human antibody and a base sequence corresponding to the 3'-end side of said heavy chain variable region of nonhuman animal antibody and is possessed of the restriction enzyme recognition sites on both of its ends, thereby constructing a humanized chimera antibody heavy chain expression vector in which said cDNA coding for the heavy chain constant region of human antibody and said cDNA coding for the heavy chain variable region of nonhuman animal antibody are linked together through said synthetic DNA; (4) constructing a cassette vector by inserting a cDNA coding for a light chain constant region of human antibody into an expression vector for animal cell use and establishing a cloning site in the upstream region of the light chain constant region of said cassette vector for inserting a cDNA which encodes a light chain variable region of nonhuman animal antibody; (5) digesting a cDNA coding for the light chain variable region of nonhuman animal antibody with restriction enzymes; (6) inserting said cDNA coding for a light chain variable region of nonhuman animal antibody into the cassette vector using a synthetic DNA which comprises a base sequence corresponding to the 5'-end side of said light chain constant region of human antibody and a base sequence corresponding to the 3'-end side of said light chain variable region of nonhuman animal antibody and is possessed of the restriction enzyme recognition sites on both of its ends, thereby constructing a humanized chimera antibody light chain expression vector in which said cDNA coding for the light chain constant region of human antibody and said cDNA coding for the light chain variable region of nonhuman animal antibody are linked together through said synthetic DNA; (7) introducing these expression vectors into host cells to obtain a transformant; and (8) culturing said transformant in an appropriate culture medium, thereby allowing the transformant to produce and accumulate a humanized chimera antibody, and collecting said humanized chimera antibody from the resulting culture broth.

The present invention provides DNA molecules that constitute fragments of the genome of a plant, and polypeptides encoded thereby. The DNA molecules are useful for specifying a gene product in cells, either as a promoter or as a protein coding sequence or as an UTR or as a 3′ termination sequence, and are also useful in controlling the behavior of a gene in the chromosome, in controlling the expression of a gene or as tools for genetic mapping, recognizing or isolating identical or related DNA fragments, or identification of a particular individual organism, or for clustering of a group of organisms with a common trait. One of ordinary skill in the art, having this data, can obtain cloned DNA fragments, synthetic DNA fragments or polypeptides constituting desired sequences by recombinant methodology known in the art or described herein.

The present invention relates to a method for genomic DNA rearrangements, and more particularly, to a method for deletion, duplication, inversion, replacement, or rearrangement of genomic DNA using pairs of site-specific nucleases targeting two or more sites in the genome, a cell in which genomic DNA is deleted, duplicated, inverted, replaced, or rearranged by the same method, and a method for expressing the site-specific nucleases in cells. Further, the present invention relates to a method for inserting synthetic DNA molecules into the genome using site-specific nucleases targeting a pre-determined site in the genome, a cell in which DNA insertion occurs by the same method, and a method for expressing the site-specific nucleases in cells.

Synthetic DNA molecules encoding papillomavirus proteins are provided. The codons of the synthetic molecules are codons preferred by the projected host cell. The synthetic molecules may be used as a polynucleotide vaccine which provides effective immunoprophylaxis against papillomavirus infection through stimulation of neutralizing antibody and cell-mediated immunity.

The present invention relates to compositions and methods for the detection and characterization of nucleic acid sequences and variations in nucleic acid sequences. The present invention relates to methods for amplifying a synthetic DNA from a target nucleic acid, forming a nucleic acid cleavage structure on the synthetic DNA, and detecting cleavage of the nucleic acid cleavage structure as an indicator of the preset of the target nucleic acid.

A synthetic hCFTR DNA sequence has been developed that produces remarkably high levels of hCFTR mRNA and protein in dosed murine lungs and human cells in culture compared to the natural hCFTR cDNA. This synthetic DNA addresses problems inherent in some natural cDNAs, such as premature transcriptional truncation sites introduced during cDNA synthesis. Introns are initially present in mRNA until the mRNA is processed. cDNA made from processed mRNA is devoid of introns. Thus DNA sequences (exon junctions) are present in a cDNA molecule which are not present in cells in nature. These exon junctions may affect transcription. Methods for improving expression of CFTR are based on sequence changes in cDNA molecules. The improvement methods may be applied to other cDNA molecules which are refractory to in vivo expression efforts. Compositions embodying the sequence changes increase the production of both transgenic mRNA and protein from cDNA molecules.

The present invention relates to compositions and methods for the detection and characterization of nucleic acid sequences and variations in nucleic acid sequences. The present invention relates to methods for amplifying a synthetic DNA from a target nucleic acid, forming a nucleic acid cleavage structure on the synthetic DNA, and detecting cleavage of the nucleic acid cleavage structure as an indicator of the preset of the target nucleic acid.

The present invention provides DNA molecules that constitute fragments of the genome of a plant, and polypeptides encoded thereby. The DNA molecules are useful for specifying a gene product in cells, either as a promoter or as a protein coding sequence or as an UTR or as a 3′ termination sequence, and are also useful in controlling the behavior of a gene in the chromosome, in controlling the expression of a gene or as tools for genetic mapping, recognizing or isolating identical or related DNA fragments, or identification of a particular individual organism, or for clustering of a group of organisms with a common trait. One of ordinary skill in the art, having this data, can obtain cloned DNA fragments, synthetic DNA fragments or polypeptides constituting desired sequences by recombinant methodology known in the art or described herein.

Methods, systems, and computer program products for estimating the location of a probe cell in an image of a high-density microarray DNA chip interrogate a plurality of different closely spaced estimated locations to identify the most likely estimated location of the probe cell in the image.

Food distributed to consumers through a distribution chain may be traced by tagging the food with DNA tags that identify the origin of the food, such as the grower, packer and other points of distribution, and their attributes. This makes it much quicker and easier to trace the food in case of food contamination or adulteration. Preferably these attributes indicate the field, location, crew and machine used to grow and process the food, and the dates of the various steps of food harvesting, processing and distribution. Natural or synthetic DNA pieces may be used to tag items, including food items. Multidigit binary or other types of bar codes may be represented by multiple types of DNA. Each digit of the bar code may be represented by one, two or more unique DNA pieces.

A prerequisite of proteomics is the ability to quantify many selected proteins simultaneously. Fluorescent sandwich immunoassays on microarrays hold appeal for such studies, since equipment and antibodies are readily available, and assays are simple, scalable and reproducible. To attain adequate sensitivity and specificity, however, a general method of immunoassay amplification is required. Coupling of isothermal rolling circle amplification (RCA) to universal antibodies can be used for this purpose: RCA on a synthetic DNA circle is initiated by a complementary oligonucleotide attached to an anti-biotin antibody; single-stranded RCA product remains attached to the antibody, and is detected by hybridization of complementary, fluorescent oligonucleotides. 51 cytokines were measured simultaneously on microarrays with signal amplification by RCA with high specificity, femtomolar sensitivity and 4 log quantitative range. This cytokine microarray was used to measure secretion from human Dendritic cells (DCs) induced by lipopolysaccharide (LPS) or tumor necrosis factor-alpha (TNF-(alpha). Rapid secretion of inflammatory cytokines such as MIP-1beta, IL-8, and IP-10 was induced by LPS. Eotaxin-2 and I-309 were found to be induced by LPS, and MDC, TARC, sIL-6R, and sTNF-RI were found to be induced by TNF-alpha. Since microarrays can accommodate ~1000 sandwich immunoassays of this type, a relatively small number of RCA microarrays appears to offer a tractable approach for proteomic surveys.

Synthetic DNA molecules encoding the HPV58 L1 protein are provided. Specifically, the present invention provides polynucleotides encoding HPV58 L1 protein, wherein said polynucleotides are codon-optimized for high level expression in a yeast cell. The synthetic molecules may be used to produce HPV58 virus-like particles (VLPs), and to produce vaccines and pharmaceutical compositions comprising the HPV58 VLPs. The vaccines of the present invention provide effective imnunoprophylaxis against papillomavirus infection through neutralizing antibody and cell-mediated immunity and are also useful for treatment of existing HPV infections.

First generation adenoviral vectors and-recombinant adenovirus-based HIV vaccines which contain HIV-1 gag, HIV-1 pol and/or HIV-1 nef polynucleotide pharmaceutical products, and biologically relevant modifications thereof are described. The adenovirus vaccines, when directly introduced into living vertebrate tissue, express the relevant proteins, inducing a cellular immune response which specifically recognizes HIV-1. The exemplified polynucleotides of the present invention are synthetic DNA molecules encoding HIV-1 Gag, HIV-1 Pol, HIV-1 Nef, and derivatives thereof. The adenoviral vaccines of the present invention, alone or in combination, will offer a prophylactic advantage to previously uninfected individuals and/or provide a therapeutic effect by reducing viral load levels within an infected individual, thus prolonging the asymptomatic phase of HIV-1 infection.

Synthetic DNA molecules encoding the HPV 52 L1 protein are provided. Specifically, the present invention provides polynucleotides encoding HPV 52 L1 protein, wherein said polynucleotides are codon-optimized for high level expression in a yeast cell. In alternative embodiments of the invention, the nucleotide sequence of the synthetic molecule is altered to eliminate transcription termination signals that are recognized by yeast. The synthetic molecules may be used to produce HPV 52 virus-like particles (VLPs), and to produce vaccines and pharmaceutical compositions comprising the HPV 52 VLPs. The vaccines of the present invention provide effective immunoprophylaxis against papillomavirus infection through neutralizing antibody and cell-mediated immunity and may also be useful for treatment of existing HPV infections.

Methods for encoding data in synthetic DNA include, for an input data sequence, constructing a codebook of a number of unique codewords, of a nucleotide length, which are constructed such that, for each codeword, the codeword is formed from a selection of nucleotide pairs from a first predefined dictionary of nucleotide pairs, and, if the nucleotide length of the codeword is odd, an additional selection of a nucleotide from a second predefined dictionary of individual nucleotides. For each symbol from the input data sequence, at least one codeword is designated as associable therewith, and each symbol is coded as one codeword selected from the designated at least one codeword associable with that symbol. A code is formed from the codewords, arranged in corresponding order to that of their respective symbols in the input data sequence. A DNA sequence is synthetized with nucleotides ordered to match the code.

Provided herein is an internal standard method for determining copy number of a pathogen DNA in an unpurified nucleic acid sample by using a known copy number of synthetic DNA that shares a consensus region sequence with the pathogen. The sample is subject to two amplification steps using locus-specific primers and fluorescent primers respectively to obtain fluorescent amplicons for the pathogen and synthetic DNA. These are hybridized with immobilized pathogen-specific and synthetic DNA-specific nucleic acid probes and imaged to obtain fluorescent signals for pathogen-specific and synthetic DNA-specific amplicons. Signal intensities are correlated with the known copy number of synthetic DNA to determine copy number of pathogen DNA in the plant. Also described herein is a method to simultaneously quantitate using the above method, copy numbers of both pathogen and plant DNA in a sample.

Synthetic DNA molecules encoding the HPV31 L1 protein are provided. Specifically, the present invention provides polynucleotides encoding HPV31 L1 protein, wherein said polynucleotides are free from internal transcription termination signals that are recognized by yeast. Also provided are synthetic polynucleotides encoding HPV31 L1 wherein the polynucleotides have been codon-optimized for high level expression in a yeast cell. The synthetic molecules may be used to produce HPV31 virus-like particles (VLPs), and to produce vaccines and pharmaceutical compositions comprising the HPV31 VLPs. The vaccines of the present invention provide effective immunoprophylaxis against papillomavirus infection through neutralizing antibody and cell-mediated immunity.

The present invention relates to synthesis, purification and methods to obtain high purity novel 2′-arabino-O-methyl nucleosides and the corresponding phosphoramidites of various arabinonucleoside bases and introduction of such units into defined sequence synthetic DNA and RNA. Various synthetic oligonucleotides, such as HIV integrase inhibitor 14-mer and thrombin binding oligonucleotide, thrombin-1, bearing ara-2′-omethyl modification have been synthesized. It is anticipated the oligonucleotides incorporating these monomers will exhibit biological activities related to antisense approach approach, design of better SiRNA's, diagnostic agents. Similarly, it is anticipated that oligonucleotides incorporating such novel nucleosides will be useful to develop therapeutic candidates designing stable G-quadruplexes and Aptamers for oligonucleotide structure, folding topology, evaluation of biochemical properties and design and develop as therapeutic agents. It is further anticipated that the nucleosides, phosphates and triphosphates of this invention could develop as therapeutic agents.

A DNA sequence that functions as an origin in many different yeast species. From 1 to 17 mutations can be introduced into this sequence to improve its function across multiple yeasts. The resulting synthetic DNA sequence confers stable plasmid replication function in all yeast species tested, including but not limited to Saccharomyces cerevisiae, Lachancea kluyveri, Kluyveromyces lactis, Kluyveromyces wickerhammii, Hansenula polymorpha, and Pichia pastoris. Also provided are sequences that function as an optimal origin in the industrially useful Pichia pastoris.