Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.
Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.
Nucleic Acid Hybridization
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Oligonucleotide Array Sequence Analysis
Molecular Probe Techniques
RNA, Ribosomal, 16S
Polymerase Chain Reaction
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Amino Acid Sequence
In Situ Hybridization, Fluorescence
Sequence Homology, Nucleic Acid
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
RNA, usually prepared by transcription from cloned DNA, which complements a specific mRNA or DNA and is generally used for studies of virus genes, distribution of specific RNA in tissues and cells, integration of viral DNA into genomes, transcription, etc. Whereas DNA PROBES are preferred for use at a more macroscopic level for detection of the presence of DNA/RNA from specific species or subspecies, RNA probes are preferred for genetic studies. Conventional labels for the RNA probe include radioisotope labels 32P and 125I and the chemical label biotin. RNA probes may be further divided by category into plus-sense RNA probes, minus-sense RNA probes, and antisense RNA probes.
Sensitivity and Specificity
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Sequence Analysis, DNA
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
RNA, Ribosomal, 18S
In Situ Hybridization
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
RNA, Ribosomal, 23S
Gene Expression Profiling
Nucleic Acid Probes
Nucleic Acid Conformation
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Colony Count, Microbial
Enumeration by direct count of viable, isolated bacterial, archaeal, or fungal CELLS or SPORES capable of growth on solid CULTURE MEDIA. The method is used routinely by environmental microbiologists for quantifying organisms in AIR; FOOD; and WATER; by clinicians for measuring patients' microbial load; and in antimicrobial drug testing.
Waste Disposal, Fluid
Nucleic Acid Denaturation
Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
DNA Restriction Enzymes
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Gene Expression Regulation
Evaluation Studies as Topic
Sequence Homology, Amino Acid
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
Base Pair Mismatch
The presence of an uncomplimentary base in double-stranded DNA caused by spontaneous deamination of cytosine or adenine, mismatching during homologous recombination, or errors in DNA replication. Multiple, sequential base pair mismatches lead to formation of heteroduplex DNA; (NUCLEIC ACID HETERODUPLEXES).
Promoter Regions, Genetic
A selective increase in the number of copies of a gene coding for a specific protein without a proportional increase in other genes. It occurs naturally via the excision of a copy of the repeating sequence from the chromosome and its extrachromosomal replication in a plasmid, or via the production of an RNA transcript of the entire repeating sequence of ribosomal RNA followed by the reverse transcription of the molecule to produce an additional copy of the original DNA sequence. Laboratory techniques have been introduced for inducing disproportional replication by unequal crossing over, uptake of DNA from lysed cells, or generation of extrachromosomal sequences from rolling circle replication.
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
Reproducibility of Results
The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.
Polymorphism, Restriction Fragment Length
Electrophoresis, Polyacrylamide Gel
Repetitive Sequences, Nucleic Acid
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
Reverse Transcriptase Polymerase Chain Reaction
Bacterial Typing Techniques
Electrophoresis, Agar Gel
Tools or devices for generating products using the synthetic or chemical conversion capacity of a biological system. They can be classical fermentors, cell culture perfusion systems, or enzyme bioreactors. For production of proteins or enzymes, recombinant microorganisms such as bacteria, mammalian cells, or insect or plant cells are usually chosen.
One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.
A genus of gram-positive, rod-shaped bacteria found in cavities of man and animals, animal and plant products, infections of soft tissue, and soil. Some species may be pathogenic. No endospores are produced. The genus Eubacterium should not be confused with EUBACTERIA, one of the three domains of life.
Nucleic Acid Amplification Techniques
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
Gram-Negative Anaerobic Bacteria
A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.
A mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)
RNA, Ribosomal, 28S
Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).
A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)
Tumor Cells, Cultured
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
Family of retrovirus-associated DNA sequences (ras) originally isolated from Harvey (H-ras, Ha-ras, rasH) and Kirsten (K-ras, Ki-ras, rasK) murine sarcoma viruses. Ras genes are widely conserved among animal species and sequences corresponding to both H-ras and K-ras genes have been detected in human, avian, murine, and non-vertebrate genomes. The closely related N-ras gene has been detected in human neuroblastoma and sarcoma cell lines. All genes of the family have a similar exon-intron structure and each encodes a p21 protein.
DNA, Ribosomal Spacer
A phylum of oxygenic photosynthetic bacteria comprised of unicellular to multicellular bacteria possessing CHLOROPHYLL a and carrying out oxygenic PHOTOSYNTHESIS. Cyanobacteria are the only known organisms capable of fixing both CARBON DIOXIDE (in the presence of light) and NITROGEN. Cell morphology can include nitrogen-fixing heterocysts and/or resting cells called akinetes. Formerly called blue-green algae, cyanobacteria were traditionally treated as ALGAE.
Shiga Toxin 1
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
Technique using an instrument system for making, processing, and displaying one or more measurements on individual cells obtained from a cell suspension. Cells are usually stained with one or more fluorescent dyes specific to cell components of interest, e.g., DNA, and fluorescence of each cell is measured as it rapidly transverses the excitation beam (laser or mercury arc lamp). Fluorescence provides a quantitative measure of various biochemical and biophysical properties of the cell, as well as a basis for cell sorting. Other measurable optical parameters include light absorption and light scattering, the latter being applicable to the measurement of cell size, shape, density, granularity, and stain uptake.
Chromatography, High Pressure Liquid
Any liquid or solid preparation made specifically for the growth, storage, or transport of microorganisms or other types of cells. The variety of media that exist allow for the culturing of specific microorganisms and cell types, such as differential media, selective media, test media, and defined media. Solid media consist of liquid media that have been solidified with an agent such as AGAR or GELATIN.
Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios.
Transcription factor AP-2 activity is modulated by protein kinase A-mediated phosphorylation. (1/5358)We recently reported that APOE promoter activity is stimulated by cAMP, this effect being mediated by factor AP-2 [Garcia et al. (1996) J. Neurosci. 16, 7550-7556]. Here, we study whether cAMP-induced phosphorylation modulates the activity of AP-2. Recombinant AP-2 was phosphorylated in vitro by protein kinase A (PKA) at Ser239. Mutation of Ser239 to Ala abolished in vitro phosphorylation of AP-2 by PKA, but not the DNA binding activity of AP-2. Cotransfection studies showed that PKA stimulated the effect of AP-2 on the APOE promoter, but not that of the S239A mutant. Therefore, cAMP may modulate AP-2 activity by PKA-induced phosphorylation of this factor. (+info)
A novel method for determining linkage between DNA sequences: hybridization to paired probe arrays. (2/5358)Cooperative hybridization has been used to establish physical linkage between two loci on a DNA strand. Linkage was detected by hybridization to a new type of high-density oligonucleotide array. Each synthesis location on the array contains a mixture of two different probe sequences. Each of the two probes can hybridize independently to a different target sequence, but if the two target sequences are physically linked there is a cooperative increase in hybridization yield. The ability to create and control non-linear effects raises a host of possibilities for applications of oligonucleotide array hybridization. The method has been used to assign linkage in 50:50 mixtures of DNA containing single nucleotide polymorphisms (SNPs) separated by 17, 693, 1350 and 2038 bp and to reconstruct haplotypes. Other potential uses include increasing the specificity of hybridization in mutation detection and gene expression monitoring applications, determining SNP haplotypes, characterizing repetitive sequences, such as short tandem repeats, and aiding contig assembly in sequen-cing by hybridization. (+info)
Localization and characterization of curved DNA in the human erythropoietin receptor gene by experimental and theoretical approaches. (3/5358)We report here the locations of curved DNA in the human erythropoietin receptor gene. A total of 13 DNA bend sites were mapped by circular permutation assays, appearing at an average interval of 651.2+/-214.6 (S.D.) in the 8-kb region. The bend centers in these 13 bend sites were confirmed by oligonucleotide-based assays where most of these centers had bend angles higher than that shown by (AAACCGGGCC) x (A)20 and lower than that shown by (AAACCGGGCC)2 x (A)10. DNA curvature mapping by TRIF software, which is based on the distribution of dinucleotides, primarily AA and TT, provided a highly accurate prediction for the locations of the bend sites. They showed approximately 20 degrees to 40 degrees of bend angles demonstrated by the oligonucleotide assays and by computer analysis. (+info)
Nitrate-dependent regulation of acetate biosynthesis and nitrate respiration by Clostridium thermoaceticum. (4/5358)Nitrate has been shown to shunt the electron flow in Clostridium thermoaceticum from CO2 to nitrate, but it did not influence the levels of enzymes involved in the Wood-Ljungdahl pathway (J. M. Frostl, C. Seifritz, and H. L. Drake, J. Bacteriol. 178:4597-4603, 1996). Here we show that under some growth conditions, nitrate does in fact repress proteins involved in the Wood-Ljungdahl pathway. The CO oxidation activity in crude extracts of nitrate (30 mM)-supplemented cultures was fivefold less than that of nitrate-free cultures, while the H2 oxidation activity was six- to sevenfold lower. The decrease in CO oxidation activity paralleled a decrease in CO dehydrogenase (CODH) protein level, as confirmed by Western blot analysis. Protein levels of CODH in nitrate-supplemented cultures were 50% lower than those in nitrate-free cultures. Western blots analyses showed that nitrate also decreased the levels of the corrinoid iron-sulfur protein (60%) and methyltransferase (70%). Surprisingly, the decrease in activity and protein levels upon nitrate supplementation was observed only when cultures were continuously sparged. Northern blot analysis indicates that the regulation of the proteins involved in the Wood-Ljungdahl pathway by nitrate is at the transcriptional level. At least a 10-fold decrease in levels of cytochrome b was observed with nitrate supplementation whether the cultures were sparged or stoppered. We also detected nitrate-inducible nitrate reductase activity (2 to 39 nmol min-1 mg-1) in crude extracts of C. thermoaceticum. Our results indicate that nitrate coordinately represses genes encoding enzymes and electron transport proteins in the Wood-Ljungdahl pathway and activates transcription of nitrate respiratory proteins. CO2 also appears to induce expression of the Wood-Ljungdahl pathway genes and repress nitrate reductase activity. (+info)
Morphological and compositional changes in a planktonic bacterial community in response to enhanced protozoan grazing. (5/5358)We analyzed changes in bacterioplankton morphology and composition during enhanced protozoan grazing by image analysis and fluorescent in situ hybridization with group-specific rRNA-targeted oligonucleotide probes. Enclosure experiments were conducted in a small, fishless freshwater pond which was dominated by the cladoceran Daphnia magna. The removal of metazooplankton enhanced protozoan grazing pressure and triggered a microbial succession from fast-growing small bacteria to larger grazing-resistant morphotypes. These were mainly different types of filamentous bacteria which correlated in biomass with the population development of heterotrophic nanoflagellates (HNF). Small bacterial rods and cocci, which showed increased proportion after removal of Daphnia and doubling times of 6 to 11 h, belonged nearly exclusively to the beta subdivision of the class Proteobacteria and the Cytophaga-Flavobacterium cluster. The majority of this newly produced bacterial biomass was rapidly consumed by HNF. In contrast, the proportion of bacteria belonging to the gamma and alpha subdivisions of the Proteobacteria increased throughout the experiment. The alpha subdivision consisted mainly of rods that were 3 to 6 microm in length, which probably exceeded the size range of bacteria edible by protozoa. Initially, these organisms accounted for less than 1% of total bacteria, but after 72 h they became the predominant group of the bacterial assemblage. Other types of grazing-resistant, filamentous bacteria were also found within the beta subdivision of Proteobacteria and the Cytophaga-Flavobacterium cluster. We conclude that the predation regimen is a major structuring force for the bacterial community composition in this system. Protozoan grazing resulted in shifts of the morphological as well as the taxonomic composition of the bacterial assemblage. Grazing-resistant filamentous bacteria can develop within different phylogenetic groups of bacteria, and formerly underepresented taxa might become a dominant group when protozoan predation is the major selective pressure. (+info)
Identification of a novel group of bacteria in sludge from a deteriorated biological phosphorus removal reactor. (6/5358)The microbial diversity of a deteriorated biological phosphorus removal reactor was investigated by methods not requiring direct cultivation. The reactor was fed with media containing acetate and high levels of phosphate (P/C weight ratio, 8:100) but failed to completely remove phosphate in the effluent and showed very limited biological phosphorus removal activity. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA was used to investigate the bacterial diversity. Up to 11 DGGE bands representing at least 11 different sequence types were observed; DNA from the 6 most dominant of these bands was further isolated and sequenced. Comparative phylogenetic analysis of the partial 16S rRNA sequences suggested that one sequence type was affiliated with the alpha subclass of the Proteobacteria, one was associated with the Legionella group of the gamma subclass of the Proteobacteria, and the remaining four formed a novel group of the gamma subclass of the Proteobacteria with no close relationship to any previously described species. The novel group represented approximately 75% of the PCR-amplified DNA, based on the DGGE band intensities. Two oligonucleotide rRNA probes for this novel group were designed and used in a whole-cell hybridization analysis to investigate the abundance of this novel group in situ. The bacteria were coccoid and 3 to 4 microm in diameter and represented approximately 35% of the total population, suggesting a relatively close agreement with the results obtained by the PCR-based DGGE method. Further, based on electron microscopy and standard staining microscopic analysis, this novel group was able to accumulate granule inclusions, possibly consisting of polyhydroxyalkanoate, inside the cells. (+info)
In situ identification of cyanobacteria with horseradish peroxidase-labeled, rRNA-targeted oligonucleotide probes. (7/5358)Individual cyanobacterial cells are normally identified in environmental samples only on the basis of their pigmentation and morphology. However, these criteria are often insufficient for the differentiation of species. Here, a whole-cell hybridization technique is presented that uses horseradish peroxidase (HRP)-labeled, rRNA-targeted oligonucleotides for in situ identification of cyanobacteria. This indirect method, in which the probe-conferred enzyme has to be visualized in an additional step, was necessary since fluorescently monolabeled oligonucleotides were insufficient to overstain the autofluorescence of the target cells. Initially, a nonfluorescent detection assay was developed and successfully applied to cyanobacterial mats. Later, it was demonstrated that tyramide signal amplification (TSA) resulted in fluorescent signals far above the level of autofluorescence. Furthermore, TSA-based detection of HRP was more sensitive than that based on nonfluorescent substrates. Critical points of the assay, such as cell fixation and permeabilization, specificity, and sensitivity, were systematically investigated by using four oligonucleotides newly designed to target groups of cyanobacteria. (+info)
Combination of fluorescent in situ hybridization and microautoradiography-a new tool for structure-function analyses in microbial ecology. (8/5358)A new microscopic method for simultaneously determining in situ the identities, activities, and specific substrate uptake profiles of individual bacterial cells within complex microbial communities was developed by combining fluorescent in situ hybridization (FISH) performed with rRNA-targeted oligonucleotide probes and microautoradiography. This method was evaluated by using defined artificial mixtures of Escherichia coli and Herpetosiphon aurantiacus under aerobic incubation conditions with added [3H]glucose. Subsequently, we were able to demonstrate the potential of this method by visualizing the uptake of organic and inorganic radiolabeled substrates ([14C]acetate, [14C]butyrate, [14C]bicarbonate, and 33Pi) in probe-defined populations from complex activated sludge microbial communities by using aerobic incubation conditions and anaerobic incubation conditions (with and without nitrate). For both defined cell mixtures and activated sludge, the method proved to be useful for simultaneous identification and analysis of the uptake of labeled substrates under the different experimental conditions used. Optimal results were obtained when fluorescently labeled oligonucleotides were applied prior to the microautoradiographic developing procedure. For single-cell resolution of FISH and microautoradiographic signals within activated sludge flocs, cryosectioned sample material was examined with a confocal laser scanning microscope. The combination of in situ rRNA hybridization techniques, cryosectioning, microautoradiography, and confocal laser scanning microscopy provides a unique opportunity for obtaining cultivation-independent insights into the structure and function of bacterial communities. (+info)
The effect of nucleobase-specific fluorescence quenching on in situ hybridization with rRNA-targeted oligonucleotide probes<...
TY - JOUR. T1 - The effect of nucleobase-specific fluorescence quenching on in situ hybridization with rRNA-targeted oligonucleotide probes. AU - Behrens, Sebastian. AU - Fuchs, Bernhard M.. AU - Amann, Rudolf. PY - 2004/9. Y1 - 2004/9. N2 - Oligonucleotide probes labeled with fluorescent dyes are used in a variety of in situ applications to detect specific DNA or RNA molecules. It has been described that probe fluorescence might be quenched upon hybridization in a sequence specific way. Here, a set of 17 oligonuleotides labeled with 6-carboxyfluorescein was used to examine the relevance of nucleotide specific quenching for fluorescence in situ hybridization (FISH) to whole fixed bacterial cells. Probes quenched upon hybridization to a guanine-rich region of purified RNA in solution were not quenched upon FISH. Among other factors the high protein concentration within cells may prevent quenching of probe fluorescence in situ.. AB - Oligonucleotide probes labeled with fluorescent dyes are used in ...
Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. |...
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Oligonucleotide Probes for Multiplex Genetic Analyses
Oligonucleotide probes are effective tools for the research of nucleic acids. This project discusses about Oligonucleotide Probes, Multiplex Genetic Analyses, Multiplex nucleic acid analyses, Genetic variation, Different Types of nucleic acid analyses, multiplex oligonucleotide design,
Accuracy of genotyping of single-nucleotide polymorphisms by PCR-ELISA allele-specific oligonucleotide hybridization typing and...
Accuracy of genotyping of single-nucleotide polymorphisms by PCR-ELISA allele-specific oligonucleotide hybridization typing and by amplification refractory mutation ...
Adenomatous polyposis Genetic Testing - Clinician - Ambry Genetics
APC coding exons 1-15 and well into the 5 and 3 ends of all the introns and untranslated regions are analyzed by sequencing. Gross deletion/duplication analysis determines gene copy number for coding exons 1-15. Additionally, all promoter 1B gross deletions as well as single nucleotide substitutions within the promoter 1B YY1 binding motif are analyzed and reported. Clinically significant intronic findings beyond 5 base pairs are always reported. Intronic variants of unknown or unlikely clinical significance are not reported beyond 5 base pairs from the splice junction. Genomic deoxyribonucleic acid (gDNA) is isolated from the patients specimen using standardized methodology and quantified. Sequence enrichment of the targeted coding exons and adjacent intronic nucleotides is carried out by a bait-capture methodology, using long biotinylated oligonucleotide probes followed by polymerase chain reaction (PCR) and next generation sequencing (NGS). Sanger sequencing is performed for any regions ...
Neurofibromatosis 2 Genetic Testing - Clinician - Ambry Genetics
NF2 coding exons and well into the 5 and 3 ends of all the introns and untranslated regions are analyzed by sequencing. Gross deletion/duplication analysis determines gene copy number for coding exons. Clinically significant intronic findings beyond 5 base pairs are always reported. Intronic variants of unknown or unlikely clinical significance are not reported beyond 5 base pairs from the splice junction. Genomic deoxyribonucleic acid (gDNA) is isolated from the patients specimen using standardized methodology and quantified. Sequence enrichment of the targeted coding exons and adjacent intronic nucleotides is carried out by a bait-capture methodology, using long biotinylated oligonucleotide probes followed by polymerase chain reaction (PCR) and next generation sequencing (NGS). Sanger sequencing is performed for any regions missing or with insufficient read depth coverage for reliable heterozygous variant detection. Reportable small insertions and deletions, potentially homozygous variants, ...
Jennifer Rebecca Arp , NC DOCKS (North Carolina Digital Online Collection of Knowledge and Scholarship)
Fluorescence in situ hybridization (FISH) with 16S rRNA-targeted oligonucleotide probes was used to examine the abundance and distribution of planktonic microorganisms within the Cape Fear River estuary in southeastern NC. This black water riverine s ...
BIOLOGICAL SAMPLE TARGET CLASSIFICATION, DETECTION AND SELECTION METHODS, AND RELATED ARRAYS AND OLIGONUCLEOTIDE PROBES -...
Biological sample target classification, detection and selection methods are described, together with related arrays and oligonucleotide probes.
Accuracy of genotyping of single-nucleotide polymorphisms by PCR-ELISA allele-specific oligonucleotide hybridization typing and...
Units of measurement for DNA and RNA oligonucleotide probes and primers
Oligonucleotide quantification methods and units can vary between manufacturers. Be sure you accurately measure and dilute your DNA and RNA oligos.
Surface Chemistry - HORIBA
The SPRi-Biochips™ are suitable for a range of surface chemistries and are not restricted to a single probe/target regime. The biochips are easily adapted for specific processes.
Results of molecular beacon end-point assays using the | Open-i
Results of molecular beacon end-point assays using the E8/E9 and E9/E10 probes on a representative genomic DNA panel. There is no difficulty in distinguishing a
DeCS Ingl s+escopo
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING. . ...
Help - Beacon
The GA4GH (Global Alliance for Genomics and & Health) Beacon Projectis a project to encourage international sites to share genetic data in the simplest of all technical contexts. The service is designed merely to accept a query of the form Do you have any genomes with an A at position 100,735 on chromosome 3 (or similar data) and responds with one of Yes or No.. The Beacon Network lists all the known beacons.. For programmatic access to the COSMIC beacon, the minimal URL for the request is ...
Application of a strain-specific rRNA oligonucleotide probe targeting Pseudomonas fluorescens Ag1 in a mesocosm study of...
Sequence analysis of domains 3 and 4 of 23S rRNA from Pseudomonas fluorescens Ag1 was carried out to allow the design of a strain-specific rRNA oligonucleotide probe targeting this strain. The specificity of the probe, Ps-Ag1, was assessed by dot blot analysis and whole-cell hybridization, and it was found to be specific for P. fluorescens Ag1. The correlation between the ribosomal content of P. fluorescens Ag1 and growth rate was determined during balanced growth conditions with generation times ranging from 1.2 to 31.8 h. Hybridization of the rRNA-targeting probes combined with charged coupled device-enhanced microscopy was used to determine the rRNA content. The total RNA content per cell was determined by staining with acridine orange and charged coupled device-enhanced microscopy. After 2 h under carbon starvation conditions, the rRNA content per cell decreased to 45% of the content of an exponentially growing cell. After 1 day of carbon starvation, the rRNA content had decreased to 20%. ...
Faculty Collaboration Database - Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays. ...
BACKGROUND: Long oligonucleotide microarrays are potentially more cost- and management-efficient than cDNA microarrays, but there is little information on the relative performance of these two probe types. The feasibility of using unmodified oligonucleotides to accurately measure changes in gene expression is also unclear.. RESULTS: Unmodified sense and antisense 70-mer oligonucleotides representing 75 known rat genes and 10 Arabidopsis control genes were synthesized, printed and UV cross-linked onto glass slides. Printed alongside were PCR-amplified cDNA clones corresponding to the same genes, enabling us to compare the two probe types simultaneously. Our study was designed to evaluate the mRNA profiles of heart and brain, along with Arabidopsis cRNA spiked into the labeling reaction at different relative copy number. Hybridization signal intensity did not correlate with probe type but depended on the extent of UV irradiation. To determine the effect of oligonucleotide concentration on ...
e-oligos Oligo Real Time Quantitative Detection Probes: Molecular Beacons*
Molecular beacons are oligonucleotide probes that can report the presence of specific nucleic acids in homogenous solutions (Tyagi S, Kramer FR. Molecular beacons: probes that fluoresce upon hybridization, Nature Biotechnology 1996; 14: 303-308.) They are useful in situations where it is either not possible or desirable to isolate the probe-target hybrids from an excess of the hybridization probes, such as in real time monitoring of polymerase chain reactions in sealed tubes or in detection of RNAs within living cells. Molecular beacons are hairpin shaped molecules with an internally quenched fluorophore whose fluorescence is restored when they bind to a target nucleic acid (Figure 1). They are designed in such a way that the loop portion of the molecule is a probe sequence complementary to a target nucleic acid molecule. The stem is formed by the annealing of complementary arm sequences on the ends of the probe sequence. A fluorescent moiety is attached to the end of one arm and a quenching ...
Spotted Cotton Oligonucleotide Microarrays for Gene Expression Analysi by Joshua A. Udall, Lex E. Flagel et al.
Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species. Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from |50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to target the diversity of the transcriptome and previously studied cotton genes, transcription factors, and genes with homology to Arabidopsis. A small portion of the oligonucleotides target unidentified protein coding sequences, thereby providing an element of gene discovery. Because many oligonucleotides were based on ESTs from
Quantification of Bacteria Adherent to Gastrointestinal Mucosa by Real-Time PCR | Journal of Clinical Microbiology
In this study an approach that combines the specificity of fluorescent oligonucleotide probes with the sensitivity of PCR was used. E. coli and B. vulgatus were used for evaluation of the 5′ nuclease PCR assay as a tool to identify and quantify intestinal bacteria. Both bacteria are prominent normal gut bacteria that play an important role in the maintenance of a healthy gut microflora.. Conventional PCR has several disadvantages. These include the sensitivity of the assay to inhibition by substances present in the sample to be analyzed, the limitation of a small sample input, and the possibility of nonspecific binding of the primers or the probe. Finally, the PCR assay is very susceptible to contamination. The 5′ nuclease PCR assay (real-time PCR) solves several of these problems. In real-time PCR two primers and one probe are used, and a fluorescent signal can be generated only when all three are bound to the DNA at the correct primer and probe locations, which greatly reduces the risk of ...
COMPOSITIONS AND METHODS FOR THE SIMULTANEOUS DETECTION AND QUANTIFICATION OF MULTIPLE SPECIFIC NUCLEIC ACID SEQUENCES - GEN...
The invention relates to methods for simultaneously or sequentially detecting multiple nucleic acid analytes in a single medium utilizing oligonucleotide hybridization probes coupled to different chemiluminescent labeling reagents. The methods may be used in a heterogeneous, homogeneous or non-homogeneous assay system. The invention also relates to specific combinations of chemiluminescent labeling reagents suitable, when coupled to an oligonucleotide probe, for use together in methods for the detection of multiple nucleic acid analytes. The invention also concerns kits useful in these methods.
Patent US6441152 - Methods, kits and compositions for the identification of nucleic acids ... - Google Patents
This invention pertains to methods, kits and compositions suitable for the detection, identification and/or quantitation of nucleic acids which are electrostatically immobilized to matrices using non-nucleotide probes which sequence specifically hybridize to one or more target sequences of the nucleic acid but do not otherwise substantially interact with the matrix. Once the nucleic acid is immobilized, the detectable non-nucleotide probe/target sequence complex, formed before or after the immobilization of the nucleic acid, can be detected, identified or quantitated under a wide range of assay conditions as a means to detect, identify or quantitate the target sequence in the sample. Because it is reversibly bound, the non-nucleotide probe/target sequence can optionally be removed from the matrix for detecting, identifying or quantitating the target sequence in the sample. Because the non-nucleotide probe/target sequence is protected against degradation, it is another advantage of this invention that
Patent EP0294098A1 - Synthetic DNA probes - Google Patents
A synthetic oligonucleotide hybridization probe comprising at least one sequence at least 12 nucleotides long, the probe forms duplexes in which at least 80% of the nucleotides are base paired with any nucleotide sequence that is either substantially of the form (Xl...Xi)n in which X is any nucleotide; i which designates the number of nucleotides in the sequence is at least 2 and n is at least 2, or substantially of the form [(Xl...Xi)mY]w in which X is any nucleotide, Y is any group of 1 or more nucleotides and is different from (Xl...Xi), m is at least 1, w is 2, and i is at least 2, the number of nucleotides in said probe being less than 3i when i is greater than 3.
Temas para TCC Detection of mRNA by in situ hybridisation and in northern blot analysis using oligodeoxynucleotide probes...
AIMS: To assess whether a reduction in intensity of signal observed using an alkaline phosphatase labelled oligodeoxynucleotide probe could be explained on the basis of procedural steps rather than reduced sensitivity. METHOD: Signal intensity was assessed on in situ hybridisation for pro-opiomelanocortin (POMC) mRNA in rat pituitary and for somatostatin mRNA in human pancreas and in northern blot analysis for POMC mRNA in the presence and absence of formamide. The direct effects of formamide on the alkaline phosphatase detection step were assessed using histochemical enzyme detection in rat kidney. RESULTS: All signals were reduced in systems containing formamide. CONCLUSIONS: In the absence of formamide clear, strong signals for specific mRNAs can be obtained by in situ hybridisation and northern blot analysis using oligodeoxynucleotide probes directly labelled with alkaline phosphatase. Formamide seems to inhibit the activity of alkaline phosphatase.
Graphical representation of ribosomal RNA probe accessibility data using ARB software package | BMC Bioinformatics | Full Text
Taxon specific hybridization probes in combination with a variety of commonly used hybridization formats nowadays are standard tools in microbial identification. A frequently applied technology, fluorescence in situ hybridization (FISH), besides single cell identification, allows the localization and functional studies of the microbial community composition. Careful in silico design and evaluation of potential oligonucleotide probe targets is therefore crucial for performing successful hybridization experiments. The PROBE Design tools of the ARB software package take into consideration several criteria such as number, position and quality of diagnostic sequence differences while designing oligonucleotide probes. Additionally, new visualization tools were developed to enable the user to easily examine further sequence associated criteria such as higher order structure, conservation, G+C content, transition-transversion profiles and in situ target accessibility patterns. The different types of sequence
A new usage of functionalized oligodeoxynucleotide probe for site-specific modification of a guanine base within RNA<...
TY - JOUR. T1 - A new usage of functionalized oligodeoxynucleotide probe for site-specific modification of a guanine base within RNA. AU - Onizuka, Kazumitsu. AU - Taniguchi, Yosuke. AU - Sasaki, Shigeki. PY - 2010/1/29. Y1 - 2010/1/29. N2 - Site-specific modification of RNA is of great significance to investigate RNA structure, function and dynamics. Recently, we reported a new method for sequence-and cytosine-selective chemical modification of RNA based on the functional group transfer reaction of the 1-phenyl-2-methylydene-1,3-diketone unit of the 6-thioguanosine base incorporated in the oligodeoxynucleotide probe. In this study, we describe that the functionality transfer rate is greatly enhanced and the selectivity is shifted to the guanine base when the reaction is performed under alkaline conditions. Detailed investigation indicated that the 2-amino group of the enolate form of rG is the reactant of the functionality transfer reaction. As a potential application of this efficient ...
The biological importance of human immunodeficiency virus type 1 (HIV-1) circulating recombinant form (CRF) CRF02 AG | Vrije...
is also predominant in West Central and East African countries where other subtypes cocirculate.. We developed and validated a relatively simple oligonucleotide probe hybridization ...
SINGLE-USE TEST MODULE FOR DETECTION OF HYBRIDIZATION OF TARGETS WITH OLIGONUCLEOTIDE PROBES - diagram, schematic, and...
SINGLE-USE TEST MODULE FOR DETECTION OF HYBRIDIZATION OF TARGETS WITH OLIGONUCLEOTIDE PROBES - diagram, schematic, and image 93 ...
Label-free optical bifunctional oligonucleotide probe for homogeneous amplification detection of disease markers | Coffee and...
Label-free optical bifunctional oligonucleotide probe for homogeneous amplification detection of disease markers Kejun Feng, Li-Ping Qiu, Yifeng Yang, Zai-Sheng Wu, Guo-Li Shen and Ru-Qin Yu Biosensors and Bioelectronics Article in Press, Corrected Proof doi:10.1016/j.bios.2011.07.068Oligonucleotide-based detection schemes that avoid chemical modification possess significant advantages, including simplified design, intrinsic affinity for targets, low cost and ease to…
Protocols and Video Articles Authored by John Sousa
John Sousa is the author of this article in the Journal of Visualized Experiments: Rapid In Situ Hybridization using Oligonucleotide Probes on Paraformaldehyde-prefixed Brain of Rats with Serotonin Syndrome
ChiRP-Seq - Wikipedia
ChiRP-Seq (Chromatin Isolation by RNA purification) is a high-throughput sequencing method to discover regions of the genome which are bound by a specific RNA (or a by a ribonucleoprotein containing the RNA of interest). Recent studies have shown that a significant proportion of some genomes (including mouse and human genomes) synthesize RNA that apparently do not code for proteins. The function of most of these non-coding RNA still has to be ascertained. Various genomic methods are being developed to map the functional association of these novel RNA to distinct regions of the genome to gain a better understanding of their function. ChiRP-Seq is one of these new methods which uses the massively parallel sequencing capability of 2nd generation sequencers to catalog the binding sites of these novel RNA molecules on a genome. Overview of ChiRP-Seq method: Tens of oligonucleotide probes are designed to be complementary to the RNA of interest. These oligos are labeled with biotin. Cells are ...
OligoProber Rat beta-actin; 2 nmols from Gene Link
OligoProber are specific oligonucleotide probes for hybridization to its cognate species. These are specially suited for use in conjunction with Gene Link RT-PCRmers as the complementary target sequence is in the amplified sequence. The OligoProber can also be used for all northern blots. OligoProber are available for use as hybridization probes with either 5 OH for 32P labeling or with 3 biotin or digoxigenin for non-radioactive detection. The OligoProber is supplied as a lyophilized powder in aliquots of 2 nmoles. The 2 nmoles of probe when dissolved in 100uL sterile water or TE will give a solution of 20 uMolar i.e. 20 pmoles/uL. ...
World Oligonucleotide Pool Market to Cross USD 2.32 Bn by 2022, Predicts MRFR in Its In-Demand Study Available at...
LONDON - In the past year, the value of the worlds oligonucleotide pool exceeded USD 1.29 billion. It is expected to go beyond USD 2.32 billion, registering an 8.5% CAGR over 2017-2022. Robust growth is attributed to such factors as increasing Big PharmaCos investments in oligonucleotide drug development, constantly widening application area of oligonucleotides and also rising involvement of CMOs in therapeutic oligonucleotides manufacturing, amid others.. Still, there are certain barriers to the further growth in the oligonucleotide pool market, for instance, inaccuracy issues associated with specific oligonucleotides and complexity in the manufacturing technology.. At present, North America captures the major share of the global oligonucleotide pool market; as of 2016, the regions share was slightly over 42%.. Some of the prominent global market players include Creative Biogene, CustomArray, Agilent Technologies, TriLink BioTechnologies, MYcroarray, Integrated DNA Technologies, Twist ...
Molecular Beacons are hybridization probes that are used in a real time PCR assay for quantification of the target DNA. Molecular Beacons are single stranded and bind to the target when the target sequence is complementary
16S/18S Binding Sites?
I am a graduate student in Microbiology using extracted _S. cerevisae_ DNA as part of a series of standard controls in dot-blot hybridizations, and have one (seemingly trivial) question. One of the oligo probes which I am using is described as Universal, and it does indeed bind to yeast genomic DNA (as well as mitochondrial, I assume). In the literature the probes specificity is for the 16S rRNA coding region (E. coli numbering). I am assuming that this particular sequence is identical to a similar region in the 18S rRNA region of yeast...(?) In any case, does anyone know how many binding sites in a single yeast genome (approximately) would bind this probe assuming that it binds rRNA? ...or perhaps where I could discover this information? Thanks in advance. David Singleton University of Georgia - Microbiology dsingle at uga.cc.uga.edu ...
Nanonets for DNA detection
a- Biosensing: DNA probe/target recognition detected by field effect. DNA is naturally charged (phosphate ions) → negative charge Qext at the surface of the semi conductor. ...
Brevet US5853993 - Signal enhancement method and kit - Google Brevets
The invention discloses and claims a signal amplification method for detecting a target nucleic acid analyte having a homopolymeric region and a target sequence. The method comprises (a) contacting an analyte under hybridizing conditions with a multiplicity of reporter probes, each probe including a signal region and an oligonucleotide sequence which is complementary to, and capable of forming a stable hybrid with the analyte homopolymeric region, whereby the hybridization of multiple reporter probes to the homopolymeric region provides for signal amplification; and (b) forming an analyte:capture probe hybrid by contacting the analyte target sequence with a capture probe under hybridizing conditions.
Oligonucleotide Arrays for Expression Monitoring - Current Protocols
This unit provides protocols for the amplification and labeling of mRNA (and the necessary controls) for hybridization to oligonucleotide arrays
Inside PlexPCR® Technology. PlexZyme® technology offers high performance and reliable qPCR detection.. During PlexPCR®, primers amplify target nucleic acid sequences and produce amplicons, which serve as a template for PlexZyme® formation. Once the partzymes have assembled into PlexZyme® enzymes, universal probes bind and enzymatic cleavage of the probes between fluorophore and quencher dye pairs generates fluorescence. Changes in fluorescence allow detection and/or quantification of the target nucleic acid in real time ...
RISH Negative Control BIO Probe | Creative Bioarray
The Negative RNA is composed of oligonucleotide Probes; It is supplied as stable ready-to-use reagents labelled with biotin. It does not contain any sequences of human or viral origin. Therefore, the negative control probes should not yield any ...
Sequence diversity within the HA-1 gene as detected by melting...
Sequence diversity within the HA-1 gene as detected by melting temperature assay without oligonucleotide probes: 1471-2350-6-36.fm ral ss BioMed CentBMC Medical
ORMA (Oligonucleotide Retrieving for Molecular Applications) 1.0 Freeware Download - Tools, Development Tools - ORMA ...
Free Download ORMA (Oligonucleotide Retrieving for Molecular Applications) by Marco Severgnini - ORMA (Oligonucleotide Retrieving for Molecular Applications) is a series of integrated scripts in Matlab, which performs an accurate search of all the positions able to specifically discriminate...
Global Oligonucleotide Market Professional Survey Report Forecast 2017-2021
Global Oligonucleotide Market Professional Survey Report Forecast 2017-2021 Published by spinvestconsulting at researchbeam.com [Report Price $3400] 108 Pages
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Epidemiological studies have shown an inverse relationship between risk of CVD and intake of whole grain (WG)-rich food. Regular consumption of breakfast cereals can provide not only an increase in dietary WG but also improvements to cardiovascular health. Various mechanisms have been proposed, including prebiotic modulation of the colonic microbiota. In the present study, the prebiotic activity of a maize-derived WG cereal (WGM) was evaluated in a double-blind, placebo-controlled human feeding study (n 32). For a period of 21 d, healthy men and women, mean age 32 (sd 8) years and BMI 23·3 (sd 0·58) kg/m2, consumed either 48 g/d WG cereal (WGM) or 48 g placebo cereal (non-whole grain (NWG)) in a crossover fashion. Faecal samples were collected at five points during the study on days 0, 21, 42, 63 and 84 (representing at baseline, after both treatments and both wash-out periods). Faecal bacteriology was assessed using fluorescence in situ hybridisation with 16S rRNA oligonucleotide probes ...
Use of an oligonucleotide probe to detect Vibrio parahaemolyti...
Use of an oligonucleotide probe to detect Vibrio parahaemolyticus in artificially contaminated oysters.: A 26-mer oligonucleotide specific to Vibrio parahaemoly
Comparison of HLA class II genes in Caucasoid, Chinese, and Japanese patients with primary Sjögrens syndrome. | The Journal of...
To better define the genetic factors that predispose to primary Sjögrens syndrome (SS), we have used polymerase chain reaction in combination with oligonucleotide probe hybridization and DNA sequencing to analyze HLA-DRB1, -DQA1, -DQB1, and -DPB1 alleles in Caucasoid (California), Japanese (Tokyo), and Chinese (Shanghai and Beijing) SS patients. In comparison to local controls in each region, we found: 1) increased frequency of the predicted haplotype HLA-DRB1*0301-DRB3*0101-DQA1*0501-DQB1*0201 in Caucasoid patients (p , 0.001); 2) increased frequency of the predicted haplotype HLA-DRB1*0405-DRB4*0101-DQA1*0301-DQB1*0401 in Japanese patients (p , 0.05); 3) increased frequency of the predicted haplotype DRB1*0803-DQA1*0103-DQB1*0601 in Chinese patients (p , 0.05); and 4) no statistically significant association with DPB1 alleles in any group, although an increased number of Caucasoid and Japanese SS patients possessed DPB1*0301. Comparison of DNA sequences for the three disease-associated ...
Patent US20040081985 - Systems and method for examination of microarrays using scanning electron ... - Google Patents
The present invention provides methods to detect biomolecules on a microarray using a scanning electron microscope. In one embodiment of the invention, errors in oligonucleotide synthesis during manufacturing of microarrays are detected by monitoring synthesis of control probes on the chips. In another embodiment, misalignment of features on the chip is determined. In yet another embodiment, the size, shape and edge definition of features on the chip is determined. In further embodiments, methods are provided for analyzing interactions between an oligonucleotide target and an oligonucleotide probe on a microarray and methods for testing conditions in a microarray manufacturing process.
Southwestern blot - Wikipedia
Southwestern blotting, based along the lines of Southern blotting (which was created by Edwin Southern) and first described by B. Bowen, J. Steinberg and colleagues in 1980, is a lab technique which involves identifying and characterizing DNA-binding proteins (proteins that bind to DNA) by their ability to bind to specific oligonucleotide probes. The proteins are separated by gel electrophoresis and are subsequently transferred to nitrocellulose membranes similar to other types of blotting. The name southwestern blotting is based on the fact that this technique detects DNA-binding proteins, since DNA detection is by Southern blotting and protein detection is by western blotting. However, since the first southwestern blottings, many more have been proposed and discovered. The former protocols were hampered by the need for large amounts of proteins and their susceptibility to degradation while being isolated. Southwestern blot mapping is performed for rapid characterization of both DNA-binding ...
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Custom 60-mer Oligonucleotide Microarrays from Agilent Technologies,These extended-length microarrays are custom designed to meet your needs. Two probe density format configurations are available: 8,455 features per array (2 arrays/1 x 3 glass slide) or 22,575 features per array (1 array/slide).,biological,biology supply,biology supplies,biology product
Identification of genes differentially regulated by interferon α, β, or γ using oligonucleotide arrays | PNAS
We have used oligonucleotide arrays to study the changes in mRNA expression after stimulation of the human HT1080 cell line with different IFNs. The effectiveness of this approach was evident by the ability to successfully identify and quantify the mRNA levels for many known ISGs. Previous Northern blot analyses of HT1080 cells showed that while IFN-α induced 6-16 mRNA levels by more than 20-fold, there was no detectable induction by IFN-γ; also, 9-27 mRNA levels were induced by both IFN-α and IFN-γ, although the level of 9-27 induction by IFN-α was 3-fold higher than by IFN-γ (5). These characteristics were replicated with remarkable similarity by the oligonucleotide arrays: 6-16 was absent in untreated cells and induced at least 20- and 21-fold by IFN-α or IFN-β, respectively, but not by IFN-γ; 9-27 was induced 23- and 22-fold by IFN-α or IFN-β and 8-fold by IFN-γ (Fig. 1 and Table 2). The consistency between our data and previous studies regarding IFN-specific inducibility further ...
Digital Micrometer | Metrix Vibration
Model: 9060-010 The Metrix Digital Micrometer comes with the ability to change probe target material to match the material your proximity probe system is measuring. It comes standard with a 4140 steel target disk and four (4)...
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WO2016028843A2 - Rna-guided systems for probing and mapping of nucleic acids - Google Patents
Methods of detecting, probing, mapping and directed sequencing of target nucleic acids are provided using a guide RNA and a Cas9 protein. Methods for detecting the binding of the guide RNA/Cas9 complex to a target nucleic acid where the guide RNA includes a 3 tail sequence that can hybridize to a probe are provided. Methods for detecting the binding of the guide RNA/Cas9 complex to a target nucleic acid where the complex is physically detected are provided.
Oligonucleotide Array Sequence Analysis (Topic) - Rensselaer Libraries
div class=citation vocab=http://schema.org/,,i class=fa fa-external-link-square fa-fw,,/i, Data from ,span resource=http://link.lib.rpi.edu/resource/YFYOeLPGp9w/ typeof=Enumeration http://bibfra.me/vocab/lite/Topic,,span property=name http://bibfra.me/vocab/lite/label,,a href=http://link.lib.rpi.edu/resource/YFYOeLPGp9w/,Oligonucleotide Array Sequence Analysis,/a,,/span, - ,span property=offers typeOf=Offer,,span property=offeredBy typeof=Library ll:Library resource=http://link.lib.rpi.edu/,,span property=name http://bibfra.me/vocab/lite/label,,a property=url href=http://link.lib.rpi.edu/,Rensselaer Libraries,/a,,/span,,/span,,/span,,/span,,/div ...
tetramethylammonium chloride | Semantic Scholar
A set of broad-range PCR primers for the 16S rRNA gene in bacteria were tested, along with three series of oligonucleotide probes… Expand ...
Deborah A. Rusy, MD, MBA
Hogan KJ Burmester JK Caldwell MD Hogan QH Coursin DB Green DN Selzer RM Broderick TP Rusy DA Poroli M Lutz AL Sanders AM Oldenburg MC Koelbl JA de Arruda-Indig M Halsey JL Day SP Domanico MJ Perioperative genomic profiles using structure-specific oligonucleotide probes. Clin Med Res . 2009 Sep;7(3):69-84 ...
Ionis Pharmaceuticals | TIDES: Oligonucleotide and Peptide Therapeutics
KNect365s TIDES: Oligonucleotide and Peptide Therapeutics is the worlds largest meeting to accelerate oligonucleotide and peptide products from early discovery to late-stage development & commercialization.
Customer Care and Technical Services are available via phone and email at the numbers and addresses listed below. Use the Chat now button to reach us by web chat.. We service customers through direct sales and a network of distributors. Our staff includes experts in molecular biology, oligonucleotide design, sequencing, mutagenesis, PCR, and related research applications. We are available for consultation before or after an order is placed. ...
2014 01 30 azusa beacon by Beacon Media, Inc. - issuu
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Data::Beacon::Collection - search.cpan.org
Actually this class represents a hash that stores Beacon objects.. The current implementation is only a dummy.. See Data::Beacon::Collection::DBI and Data::Beacon::Collection::Files for implementation drafts.. ...
2017-2022 China Oligonucleotide Pool Library Market Report (Status and Outlook) : ReportsnReports
[123 Pages Report] Check for Discount on 2017-2022 China Oligonucleotide Pool Library Market Report (Status and Outlook) report by LP Information INC. ...
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"The oligonucleotide probe database". Applied and Environmental Microbiology. 62 (10): 3557-3559. doi:10.1128/aem.62.10.3557- ...
An array containing immobilized allele-specific oligonucleotide (ASO) probes.. *Fragmented nucleic acid sequences of target, ... Two probes must be used for each SNP position to detect both alleles; if only one probe were used, experimental failure would ... The ASO probes are often chosen based on sequencing of a representative panel of individuals: positions found to vary in the ... and Oligonucleotide Microarrays: A Platform Comparison based on Statistical Power Analysis". DNA Research. 14 (1): 1-11. doi: ...
Cystic fibrosis transmembrane conductance regulator
Cell engineering methods including fluorogenic oligonucleotide signaling probes may be used to detect and isolate clonal cell ... March 2021). "Cell engineering method using fluorogenic oligonucleotide signaling probes and flow cytometry". Biotechnology ...
Epithelial sodium channel
March 2021). "Cell engineering method using fluorogenic oligonucleotide signaling probes and flow cytometry". Biotechnology ... March 2021). "Cell engineering method using fluorogenic oligonucleotide signaling probes and flow cytometry". Biotechnology ... March 2021). "Cell engineering method using fluorogenic oligonucleotide signaling probes and flow cytometry". Biotechnology ... Chromovert technology enabled the production of a stable ENaC cell line using fluorogenic signaling probes and flow cytometry ...
Oligonucleotide design: primer design for polymerase chain reaction (PCR), probe design for fluorescence in situ hybridization ... Noguera DR, Wright ES, Camejo P, Yilmaz LS (2014). "Mathematical tools to optimize the design of oligonucleotide probes and ... "Automated Design of Probes for rRNA-Targeted Fluorescence In Situ Hybridization Reveals the Advantages of Using Dual Probes for ... "Modeling formamide denaturation of probe-target hybrids for improved microarray probe design in microbial diagnostics". PLOS ...
March 2021). "Cell engineering method using fluorogenic oligonucleotide signaling probes and flow cytometry". Biotechnology ... Fluorogenic signaling probes and flow cytometry have been used to create laboratory cells that comprise heteromultimetic Nav1.7 ...
Neonatal alloimmune thrombocytopenia
"Prenatal diagnosis of neonatal alloimmune thrombocytopenia using allele-specific oligonucleotide probes". Blood. 78 (9): 2276- ...
Biotechnology in pharmaceutical manufacturing
A unique oligonucleotide... homologous to Factor IX mRNA... was synthesized and labeled... The resultant probe was used to ... yielded sufficient amino acid sequence to construct oligonucleotide probes. The known sequence of Factor IX RNA was then used ... with a Factor IX cDNA probe. Hybridizing recombinant phage were isolated, plaque-purified, and the DNA isolated. Restriction ...
... s, or molecular beacon probes, are oligonucleotide hybridization probes that can report the presence of ... probes. Dual Hybridization (LightCycler®) probes Scorpions® Probes LUX (Light Upon Extension) Probes DNA binding dye assays (e. ... Fluorogenic signaling oligonucleotide probes were reported for use to detect and isolate cells expressing one or more desired ... March 2021). "Cell engineering method using fluorogenic oligonucleotide signaling probes and flow cytometry". Biotechnology ...
Autonomous detection system
"US5667972A - Method of sequencing of genoms by hybridization of oligonucleotide probes". Google Patents. 5 June 1995. Retrieved ...
"Cell engineering method using fluorogenic oligonucleotide signaling probes and flow cytometry". Biotechnology Letters. doi: ...
"Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays". Nucleic Acids Research. 30 (17): ...
"Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays". Nucleic Acids Res. 30 (17): 3732- ...
March 2021). "Cell engineering method using fluorogenic oligonucleotide signaling probes and flow cytometry". Biotechnology ...
Fluorogenic oligonucleotide signaling probes also known as molecular beacons may be used to track genetic modifications in ... March 2021). "Cell engineering method using fluorogenic oligonucleotide signaling probes and flow cytometry". Biotechnology ...
Circulating tumor cell
A target-specific probe set containing 20 oligonucleotide pairs hybridizes to the target RNA. An oligo pair hybridization event ... Therefore, a typical target-specific probe set (containing 20 oligo pairs) can generate 8,000-fold signal amplification at the ... The exceptional sensitivity and specificity is achieved by using proprietary probe design, simultaneous branched DNA (bDNA) ...
... fluorescently labeled oligonucleotide probes are more expensive than non-specific intercalating fluorescent dyes. For ... The probed sample is then observed by microscopy to identify where the mRNA or protein is. By replacing the gene with a new ... A single array or "chip" may contain probes to determine transcript levels for every known gene in the genome of one or more ... A sample of RNA is separated on an agarose gel and hybridized to a radioactively labeled RNA probe that is complementary to the ...
The most common oligonucleotide probe for Cytophaga-Flavobacteria is CF319a. However, CF319a does not recognize some Cytophaga- ...
Chimera (molecular biology)
"EST Assembly for the Creation of Oligonucleotide Probe Targets" (PDF). Agilent Technologies. Retrieved May 12, 2009. Birren, ...
Fluorescence in situ hybridization
FISH has also been successfully done on unfixed cells. A target-specific probe, composed of 20 oligonucleotide pairs, ... Probe size is important because longer probes hybridize less specifically than shorter probes, so that short strands of DNA or ... The mixture of probe sequences determines the type of feature the probe can detect. Probes that hybridize along an entire ... Targets can be reliably imaged through the application of multiple short singly labeled oligonucleotide probes. The binding ...
Restriction fragment length polymorphism
A limited version of the RFLP method that used oligonucleotide probes was reported in 1985. The results of the Human Genome ... the amplified segment can be analyzed by allele-specific oligonucleotide (ASO) probes, a process that can often be done by a ... In the first schematic, a small segment of the genome is being detected by a DNA probe (thicker line). In allele A, the genome ... In allele a, restriction site 2 has been lost by a mutation, so the probe now detects the larger fused fragment running from ...
"Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes". Nature ...
"Rapid HLA-DPB typing using enzymatically amplified DNA and nonradioactive sequence-specific oligonucleotide probes". ... 1991). "Positive correlation between oligonucleotide typing and T-cell recognition of HLA-DP molecules". Immunogenetics. 34 (1 ...
Williams F, Meenagh A, Maxwell AP, Middleton D (1999). "Allele resolution of HLA-A using oligonucleotide probes in a two-stage ...
U4 spliceosomal RNA
Blencowe BJ, Sproat BS, Ryder U, Barabino S, Lamond AI (November 1989). "Antisense probing of the human U4/U6 snRNP with ... biotinylated 2'-OMe RNA oligonucleotides". Cell. 59 (3): 531-9. doi:10.1016/0092-8674(89)90036-6. PMID 2478298. S2CID 45969803 ... Mougin A, Gottschalk A, Fabrizio P, Lührmann R, Branlant C (April 2002). "Direct probing of RNA structure and RNA-protein ... Several experiments involving X-ray crystallography, NMR, and chemical modification RNA structure probing indicate that U4 ...
Tens of oligonucleotide probes are designed to be complementary to the RNA of interest. These oligos are labeled with biotin. ... These chromatin fragments were hybridized to the biotinylated probe set. Complexes containing biotin-probe + RNA of interest + ...
This non-coding RNA was originally identified in E.coli using high-density oligonucleotide probe arrays (microarray.) The ... "Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays". Nucleic Acids Res. 30 (17): 3732- ...
... -labelled probes can be imaged using FISH, or targeted by antibodies using immunohistochemistry. The latter is a ... In oligonucleotide synthesis, several phosphoramidite reagents containing protected fluorescein, e.g. 6-FAM phosphoramidite 2,[ ... The use of fluorescein amidite, shown below right, allows one to synthesize labeled oligonucleotides for the same purpose. Yet ... Fluorescein can also be conjugated to nucleoside triphosphates and incorporated into a probe enzymatically for in situ ...
DNA-functionalized quantum dots
Amine-modified oligonucleotide probes attached to carboxyl groups on quantum dots show sequence-specific hybridization. These ... The increased solubility is necessary in order to allow quantum dots to be used as a DNA imaging probe in a biological system. ... Pinaud, Fabien; Clarke, Samuel; Sittner, Assa; Dahan, Maxime (30 March 2010). "Probing cellular events, one quantum dot at a ... probes can also detect low expressing genes. This potentially allows researchers to understand when and where certain proteins ...
Nuclear magnetic resonance spectroscopy of nucleic acids
It has been especially useful in probing the structure of natural RNA oligonucleotides, which tend to adopt complex ... Two dimensional NMR studies began to be reported in 1982 and then, with the advent of oligonucleotide synthesis and more ... NMR is also useful for probing the binding of nucleic acid molecules to other molecules, such as proteins or drugs. This can be ... Interactions between RNA and metal ions can be probed by a number of methods, including observing changes in chemical shift ...
Oligonucleotides are designed so that they are similar to the target sequence. The oligonucleotides are chemically synthesized ... A probe that hybridizes only to a single DNA segment that has not been cut by the restriction enzyme will produce a single band ... The probe DNA is labelled so that it can be detected, usually by incorporating radioactivity or tagging the molecule with a ... After hybridization, excess probe is washed from the membrane (typically using SSC buffer), and the pattern of hybridization is ...
Surface-enhanced Raman spectroscopy
Oligonucleotide targeting. SERS can be used to target specific DNA and RNA sequences using a combination of gold and ... New Probe Detects Trace Pollutants in Groundwater". Oak Ridge National Laboratory Review. 26 (2).. ... Nie, S; Emory, SR (1997). "Probing Single Molecules and Single Nanoparticles by Surface-Enhanced Raman Scattering". Science. ... which could lead to the development of non-overlapping probes for gene detection. ...
Fluorescence in situ hybridization (FISH) involves fluorescent labeling of probes that bind to specific DNA sequences, used for ... 200kb bacterial artificial chromosomes to small oligonucleotides) that represent unique regions of the genome. This method is ... Chromosome painting is a technique that uses fluorescent probes specific for each chromosome to differentially label each ... basic on detection of fragments of DNA separated by size through gel electrophoresis and detected using radiolabeled probes. ...
Zinc finger inhibitor
Saha, Mrinmoy (2017). "Probing Mercaptobenzamides as HIV Inactivators via Nucleocapsid Protein7". ChemMedChem. 12 (10): 714-721 ... "Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides". Nucleic Acids Research. 34 (2): 472-484. doi:10.1093 ...
... oligonucleotides), also called DNA probes, to reconstruct a target DNA sequence. Non-specific hybrids are removed by washing ... Use of oligonucleotides of defined sequence as primers in DNA sequence analysis". Biochem. Biophys. Res. Commun. 48 (5): 1295- ... Oligonucleotides are annealed and ligated; the preferential ligation by DNA ligase for matching sequences results in a signal ... Here, a pool of all possible oligonucleotides of a fixed length are labeled according to the sequenced position. ...
... s, also called DNA enzymes, DNAzymes, or catalytic DNA, are DNA oligonucleotides that are capable of performing a ... "A DNAzyme-gold nanoparticle probe for uranyl ion in living cells". Journal of the American Chemical Society. 135 (14): 5254-7 ... single-stranded oligonucleotides which contain a single ribonucleotide base to act as the cleavage site. Once sequenced, this ... which shows how oligonucleotides undergo competitive binding with the targets and how the evolutionary outcome can be improved ...
Oligonucleotide Synthesis. See also Oligonucleotide synthesis. Carbohydrate Synthesis. See also Carbohydrate synthesis. Small ... The study of organic reactions includes probing their scope through use in preparation of target compounds (e.g., natural ...
... a novel linker for oligonucleotide synthesis and hybridization properties of oligonucleotides synthesised in situ". Nucleic ... Svako DNK mesto sadrži nekoliko pikomola (10−12 mola) specifične DNK sekvence, poznate kao probe (ili reporteri ili oligoi). To ... Hibridizacija probe i cilja se obično detektuje i kvantitativno određuje detekcijom fluoroforom, srebrom, ili hemiluminescentno ...
Serial analysis of gene expression
However, SAGE sampling is based on sequencing mRNA output, not on hybridization of mRNA output to probes, so transcription ... the direct use of 26-base-pair transcript tags in oligonucleotide arrays". Nature Methods. 3 (6): 469-74. doi:10.1038/nmeth882 ... immobile cDNA fragments upstream from cleavage sites are divided in half and exposed to one of two adaptor oligonucleotides (A ...
Multiplex Ligation-dependent Probe Amplification (MLPA), and Quantitative Multiplex PCR of Short Fluorescent Fragments ( ... "High-resolution oligonucleotide array-CGH applied to the detection and characterization of large rearrangements in the ... by multi-capillary electrophoresis or also dedicated oligonucleotides array based on comparative genomic hybridization (array- ...
Antisense oligonucleotides (asONs) have been used in basic research and are being developed as possible medical treatments. CPP ... Quantum dots (QD) represent a relative new class of fluorescent probes that have superior optical properties than classical ... Eckstein, Fritz (2007). "The versatility of oligonucleotides as potential therapeutics". Expert Opinion on Biological Therapy. ... Morris, M. (1997). "A new peptide vector for efficient delivery of oligonucleotides into mammalian cells". Nucleic Acids ...
The oligonucleotide probe hybridizes with the repeat in the microsatellite, and the probe/microsatellite complex is then pulled ... However, which probes to use can be a trial and error process in itself. ... Once the potentially useful microsatellites are determined, the flanking sequences can be used to design oligonucleotide ... Colonies are then developed, and screened with fluorescently-labelled oligonucleotide sequences that will hybridize to a ...
Differential interaction of a fluorescent probe with the guanosine nucleotide complexes of bacterial elongation factor Tu". ... Oligonucleotide. *RNA. ReferencesEdit. *^ Crane, Laura J; Miller, David Lee (1974). "Guanosine triphosphate and guanosine ...
Gene Probes are Unpatentable Printed Matter. Fed. Cir. BJ, 20, p.527. "Archived copy" (PDF). Archived (PDF) from the original ... proven effective at anticipating prior art against oligonucleotide composition claims filed since his publication of the list ... Chin made the same algorithem-based obvious argument in DNA probes. ...
Oligonucleotide chips are microarrays of oligonucleotides. They can be used for detection of mutations and expression ... Michigan probes have been used in large-scale recordings and network analysis of neuronal assemblies , and the Utah electrode ... Bhatia, S.N.; Balis, U.J.; Yarmush, M.L.; Toner, M. (1998). "Probing heterotypic cell interactions: Hepatocyte function in ... Using inkjet technology, nucleotides are printed onto a surface drop by drop to form oligonucleotides cDNA microarrays are ...
Nuclear magnetic resonance spectroscopy
It has been especially useful in probing the structure of natural RNA oligonucleotides, which tend to adopt complex ... NMR is also useful for probing the binding of nucleic acid molecules to other molecules, such as proteins or drugs, by seeing ... a radio-frequency emitter and a receiver with a probe (an antenna assembly) that goes inside the magnet to surround the sample ...
Polymerase chain reaction
Multiplex ligation-dependent probe amplification (MLPA): permits amplifying multiple targets with a single primer pair, thus ... The oligonucleotides alternate between sense and antisense directions, and the overlapping segments determine the order of the ... This ability of PCR augments many methods, such as generating hybridization probes for Southern or northern blot hybridization ... This use of PCR augments many ways, such as generating hybridization probes for Southern or northern hybridization and DNA ...
Morpholino oligonucleotidesEdit. Main article: Morpholino. Morpholino oligos are used in both X. laevis and X. tropicalis to ... probe the function of a protein by observing the results of eliminating the protein's activity. For example, a set of X ... DNA oligonucleotides complementary to specific mRNA molecules are often chemically modified to improve their stability in vivo ... The expression of genes can be reduced by a variety of means, for example by using antisense oligonucleotides targeting ...
Also known as a genotypic assay, techniques include PCR, DNA fragment analysis, allele specific oligonucleotide (ASO) probes, ... "SoftGenetics Application Note - Software for Multiplex Ligation-dependent Probe Amplification (MLPA™)" (PDF). SoftGenetics. ... and multiplex ligation-dependent probe amplification (MLPA). ...
The adenine methyltransferase methylates the oligonucleotide making it a substrate for DpnI. Cutting of the oligonucleotide by ... Li J, Yan H, Wang K, Tan W, Zhou X (February 2007). "Hairpin fluorescence DNA probe for real-time monitoring of DNA methylation ... Methyl Sensitive Southern Blotting is similar to the HELP assay, although uses Southern blotting techniques to probe gene- ... This technique is used to evaluate local methylation near the binding site for the probe. ...
He was familiar with the use of DNA oligonucleotides as probes for binding to target DNA strands, as well as their use as ...
Allele-specific oligonucleotide. Main article: Allele-specific oligonucleotide. Allele-specific oligonucleotide (ASO) is ... Macromolecule blotting and probing. The terms northern, western and eastern blotting are derived from what initially was ... The membrane is then exposed to a labeled DNA probe that has a complement base sequence to the sequence on the DNA of interest. ... In this process RNA is separated based on size and is then transferred to a membrane that is then probed with a labeled ...
Dickins RA, Hemann MT, Zilfou JT, Simpson DR, Ibarra I, Hannon GJ, Lowe SW (Nov 2005). "Probing tumor phenotypes using stable ... either via expression in viruses or synthesis of oligonucleotides. Optimistically many studies indicate that small RNA- ...
... targets for detection by in situ hybridisation with oligonucleotide probes". Journal of Clinical Pathology. 45 (7): 616-20. doi ...
Method of sequencing by hybridization of oligonucleotide probes - Hyseq, Inc.
The conditions under which oligonucleotide probes hybridize preferentially with entirely complementary and homologous nucleic ... Oligonucleotide ONP Oligonucleotide probe ONS Oligonucleotide sequence PCR Polymerase chain reaction RE Restriction Enzyme RFLP ... further identifying a plurality of subsequent oligonucleotide probes of said set, beginning with a second oligonucleotide probe ... The oligonucleotide probes can comprise all known combinations of the four nucleotides of a given length, i.e. oligonucleotides ...
Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. - PubMed - NCBI
Operon detection using oligonucleotide probe intensities. Individual oligonucleotide probe intensities (PM - MM) from three ... Intensities for individual oligonucleotide probes interrogating ompA, the 356 bp intergenic region and sulA are shown. The ... Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays.. Tjaden B1, Saxena RM, Stolyar S, ... 5′-UTR detection upstream of ompA. Individual oligonucleotide probe intensities (PM - MM) from three conditions are shown to ...
Patent US5667972 - Method of sequencing of genoms by hybridization of oligonucleotide probes - Google Patents
The sequence of a given DNA fragment is read by the hybridization and assembly of positively hybridizing probes through ... with about 50,000 to 100,000 groups of probes, the main type of which is (A,T,C,G)(A,T,C,G)N8(A,T,C,G), information for ... The conditions under which oligonucleotides hybridize only with entirely homologous sequences are recognized. ... wherein a portion of the labeled oligonucleotide probe sequence at an end of the labeled oligonucleotide probe is the same as ...
Genomic DNA fingerprinting of clinical isolates of Helicobacter pylori using short oligonucleotide probes containing repetitive...
Five separate oligonucleotide probes were tested for hybridization sequentially to fingerprint the digested DNA from a panel of ... The ability of oligonucleotide probes containing short repetitive sequence motifs to differentiate between isolates of ... The results of this study demonstrate that oligonucleotide probes containing microsatellite sequences provide a new and ... Genomic DNA fingerprinting of clinical isolates of Helicobacter pylori using short oligonucleotide probes containing repetitive ...
OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes |...
Oligopaint Probe Synthesis.. OligoMiner settings used to design each Oligopaint FISH probe set are provided in Table S1. Probe ... 1992) Oligonucleotide probes for the analysis of specific repetitive DNA sequences by fluorescence in situ hybridization. Hum ... 2003) OligoArray 2.0: Design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res 31 ... OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes. ...
Biosensors | Free Full-Text | Thiol- and Biotin-Labeled Probes for Oligonucleotide Quartz Crystal Microbalance Biosensors of...
Grafting on a gold surface of 20-base thiol- or biotin-labeled probe, and selective hybridization with the complementary 20- ... Hybridization kinetic curves indicate that the biosensor designed with the thiol-labeled probe is more sensitive, and that the ... biosensor designed with the biotin-labeled probe has a shorter time response and a higher hybridization efficiency. ... Two quartz crystal microbalance oligonucleotide biosensors of a toxic microalga gene sequence (Alexandrium Minutum) have been ...
Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. ...
Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. ... Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. ... Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. ... Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. ...
Oligonucleotides, Primers, Probes & Genes | Thermo Fisher Scientific - US
Find oligonucleotides built to your specifications here. We offer options for virtually any application and delivery times to ... Oligos, Primers, Probes, & Genes. Review options for custom-synthesized oligos, primers, probes, and genes, for PCR, cloning, ... Select dual-labeled probes and unlabeled sequence detection primers for real-time PCR applications using TaqMan probe-based ...
Endonuclease V-assisted accurate cleavage of oligonucleotide probes controlled by deoxyinosine and deoxynucleoside...
Here, a novel kind of oligonucleotide probe that could be accurately cleaved at the given positio ... The ligated probes used in SBL should be accurately cleaved for a better ligation in the next cycle. ... oligonucleotide. probes in order to increase the cleavage accuracy of endonuclease V on double-stranded DNA templates. The ... oligonucleotide. probes controlled by deoxyinosine. and deoxynucleoside phosphorothioate for sequencing-by-ligation Y. Li, Z. ...
miChip: a microarray platform for expression profiling of microRNAs based on locked nucleic acid (LNA) oligonucleotide capture...
... oligonucleotide capture probes Methods. 2007 Oct;43(2):146-52. doi: 10.1016/j.ymeth.2007.04.009. ... Mixed LNA/DNA capture probes thus can be designed for equal T(m)s for all miRNAs, which naturally cover a range between 45 and ... The protocol focuses on the use of locked nucleic acid (LNA)-modified capture probes. LNAs are bicyclic nucleotide analogues ...
Evaluation of a nonisotopically labeled oligonucleotide probe to detect the heat-stable enterotoxin gene of Escherichia coli by...
The oligonucleotide probe was useful in specifically identifying the so-called STh gene. No deproteinization of sample was ... Evaluation of a nonisotopically labeled oligonucleotide probe to detect the heat-stable enterotoxin gene of Escherichia coli by ... Evaluation of a nonisotopically labeled oligonucleotide probe to detect the heat-stable enterotoxin gene of Escherichia coli by ... Evaluation of a nonisotopically labeled oligonucleotide probe to detect the heat-stable enterotoxin gene of Escherichia coli by ...
Internal labeling of oligonucleotide probes by Diels-Alder cycloaddition - Strathprints
Graham, D. and Grondin, A. and McHugh, C. and Fruk, L. and Smith, W.E. (2002) Internal labeling of oligonucleotide probes by ... dna, oligonucleotide probes, cycloaddition, Chemistry, Biochemistry, Organic Chemistry, Drug Discovery. Subjects:. Science , ... A new method of adding fluorescent labels to the middle of oligonucleotides is reported. Diets-Alder cycloaddition was used to ... This is a new approach to internal oligonucleotide chemistry that opens Lip a large range of possibilities for further ...
Efficient oligonucleotide probe selection for pan-genomic tiling arrays | BMC Bioinformatics | Full Text
PanArray is an oligonucleotide probe selection algorithm for tiling multiple genome sequences using a minimal number of probes ... To minimize the required number of probes, probes conserved across multiple strains in the pan-genome are selected first, and ... Instead, probes are evenly tiled across all sequences of the pan-genome at a consistent level of coverage. ... An unbiased tiling of probes across the entire length of the genome is the most flexible design approach. However, such a whole ...
Platinated DNA oligonucleotides: new probes forming ultrastable conjugates with graphene oxide
Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes
Synthesis of the LNA-modified oligonucleotide probes. The LNA-modified and DNA oligonucleotide probes (Table (Table1)1) were ... Comparison of LNA2- and LNA3-modified oligonucleotide probes with DNA probes in the detection of the low-abundant miR171 in A. ... Besides being highly efficient as northern probes, the same LNA-modified oligonucleotide probes would also be useful for miRNA ... Besides being highly efficient as northern probes, the same LNA3-modified oligonucleotide probes could also be useful for ...
Oligonucleotide Synthesis Market by Product & Services (Equipment, Reagent, Primer, Probe, Custom Oligos), End-User (Research,...
The global oligonucleotide synthesis market is expected to reach $1,712.1 million by 2019 from $1,070.7 million in 2014, ... Oligonucleotide Synthesis Market by Product & Services (Equipment, Reagent, Primer, Probe, Custom Oligos), End-User (Research, ... Original Article: Oligonucleotide Synthesis Market by Product & Services (Equipment, Reagent, Primer, Probe, Custom Oligos), ... More From BioPortfolio on "Oligonucleotide Synthesis Market by Product & Services (Equipment, Reagent, Primer, Probe, Custom ...
Detection of Plasmodium sporozoites in mosquitoes by polymerase chain reaction and oligonucleotide rDNA probe, without...
Oligonucleotide Probes That Detect Quantitatively Significant Groups of Butyrate-Producing Bacteria in Human Feces | Applied...
... and named according to the nomenclature suggested by the Oligonucleotide Probe Database (OPD) (1). The probe sequences have ... Oligonucleotide Probes That Detect Quantitatively Significant Groups of Butyrate-Producing Bacteria in Human Feces. Georgina L ... 16S rRNA-targeted oligonucleotide probes were designed for butyrate-producing bacteria from human feces. Three new cluster- ... in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 66:375-382. ...
Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. |...
Fluorescent oligonucleotide hybridization probes were used to label bacterial cells for analysis by flow cytometry. The probes ... Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations.. R I ... Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. ... Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. ...
Oligonucleotide Synthesis Market by Product (Primer, Probe, Linker, Adaptor, Custom, Reagent, Equipment), Application (PCR, DNA...
The Global Oligonucleotide Synthesis Market is Expected to Reach USD 2.46 Billion by 2022 from USD 1.47 Billion in 2017 at a ... 126.96.36.199 Probes. 188.8.131.52 Large-Scale Synthesis Oligonucleotides. 184.108.40.206 Intermediate-Scale Synthesis Oligonucleotides. 220.127.116.11 ... 18.104.22.168 Custom Oligonucleotides. 22.214.171.124 Pre-Designed Oligonucleotides. 6.3 Reagents. 6.4 Equipment. 7 Oligonucleotide ... 4.2 Oligonucleotides Synthesis Market, By Synthesized Oligonucleotides Products. 4.3 Market, By Synthesized Oligonucleotides ...
Genomic Analysis Using High-Density Single Nucleotide Polymorphism-Based Oligonucleotide Arrays and Multiplex Ligation...
Molecular Probes). Probes for the Ewings sarcoma region in 22q12 were used simultaneously with the probe for INI1 as an ... 8 This kit contains 2 probes for each of the 9 exons of INI1, probes for 9 other genes on chromosome 22, and 14 control probes ... High-density SNP-based oligonucleotide array analysis. The high-density oligonucleotide array analysis was done using an ... The probes were applied to slides of the tumor cells and codenatured at 75°C on an Isotemp 125D heat block (Fisher Scientific ...
Kinetics and thermodynamics of biotinylated oligonucleotide probe binding to particle-immobilized avidin and implications for...
Kinetics and thermodynamics of biotinylated oligonucleotide probe binding to particle-immobilized avidin and implications for ... Kinetics and thermodynamics of biotinylated oligonucleotide probe binding to particle-immobilized avidin and implications for ... Kinetics and thermodynamics of biotinylated oligonucleotide probe binding to particle-immobilized avidin and implications for ... Kinetics and thermodynamics of biotinylated oligonucleotide probe binding to particle-immobilized avidin and implications for ...
Radiolabeling of Subtracted cDNA Probes by Random Oligonucleotide Extension
Synthesis of cDNA Probes from mRNA Using Random Oligonucleotide Primers *Protocol 7: Radiolabeling of Subtracted cDNA Probes by ... Radiolabeling of Subtracted cDNA Probes by Random Oligonucleotide Extension. (Protocol summary only for purposes of this ... Protocol 18: Hybridization of Oligonucleotide Probes in Aqueous Solutions: Washing in Buffers Containing Quaternary Ammonium ... Protocol 3: Labeling of DNA Probes by Nick Translation *Protocol 4: Labeling of DNA Probes by Polymerase Chain Reaction * ...
BIOLOGICAL SAMPLE TARGET CLASSIFICATION, DETECTION AND SELECTION METHODS, AND RELATED ARRAYS AND OLIGONUCLEOTIDE PROBES -...
BIOLOGICAL SAMPLE TARGET CLASSIFICATION, DETECTION AND SELECTION METHODS, AND RELATED ARRAYS AND OLIGONUCLEOTIDE PROBES. United ... together with related arrays and oligonucleotide probes.. Inventors:. Gardner, Shea N. (Oakland, CA), Jaing, Crystal J. ( ... together with related arrays and oligonucleotide probes. ...
Oligonucleotide Synthesis Market by Product & Services (Primer, Probe, Custom, Predesigned, Reagent Equipment), Application ...
Probe, Custom, Predesigned, Reagent Equipment), Application (Research, PCR, Gene, DNA, NGS, Diagnostic, RNAI), End user ( ... Oligonucleotide Synthesis Market by Product & Services (Primer, Probe, Custom, Predesigned, Reagent Equipment), Application ( ... Oligonucleotide Synthesis Market by Product & Services (Primer, Probe, Custom, Predesigned, Reagent Equipment), Application ( ... Oligonucleotide Synthesis Market by Product & Services (Primer, Probe, Custom, Predesigned, Reagent Equipment), Application ( ...
Oligonucleotide Probes for Multiplex Genetic Analyses
This project discusses about Oligonucleotide Probes, Multiplex Genetic Analyses, Multiplex nucleic acid analyses, Genetic ... Oligonucleotide probes are effective tools for the research of nucleic acids. ... variation, Different Types of nucleic acid analyses, multiplex oligonucleotide design, ... In fact techniques utilizing oligonucleotide probes are effective tools for the research of nucleic acids. In the past few ...
Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays |...
Based on this transcript-level annotation, a new probe set definition was created in which every probe in a probe set maps to a ... In addition, using artificial data sets we identified that a minimal probe set size of 4 is necessary for reliable statistical ... Redefinitions introduce probe sets whose sizes may not support reliable statistical summarization; therefore, we advocate using ... For convenience, we have created custom chip-description-files (CDFs) and annotation files for our new probe set definitions ...
A comparison of alternative 60-mer probe designs in an in-situ synthesized oligonucleotide microarray | BMC Genomics | Full Text
We report here an analysis of alternative 60mer probe designs for an in-situ synthesized oligonucleotide array for the GC rich ... Next, we determined that the variance of replicate probes (1178 total probes examined) of identical sequence was 3.8% whereas ... We also determined that several different measures commonly utilized in probe design were not predictive of outlier probes. ... of alternative probes produced outlier conclusions. Finally, we determined none of the probe design subscores (GC content, ...
Exploration, normalization, and summaries of high density oligonucleotide array probe level data. - ScienceOpen
Exploration, normalization, and summaries of high density oligonucleotide array probe level data.. ... and examine the variance-mean relationship with probe-level data from probes believed to be defective, and so delivering noise ... Keywords: Statistics, Nonparametric, Algorithms, Reproducibility of Results, methods, Oligonucleotide Array Sequence Analysis, ... We explain why we need to normalize the arrays to one another using probe level intensities. We then examine the behavior of ...
MicroarraysAbstractGlobal oligonucleotide synthesis marketSynthesis marketAssayDetection using oligonuclOligosArraysGenomicSequencesFluorescence in situ hybrCleavage of oligonucleotide probesHigh-density oligonucleotide arrayPrimers and ProbesSituMarket for oligonucleotide synthesisMRNANonisotopically labeled oligonucleotideAssaysPolymeraseDetectMethodsGenesMoleculesSpecificityGenomeMolecular ProbesMultiplexDesign2019Microarray probeTargetsGene expressionIntensitiesDual-labeledPrimerComplementaryFluorescently labelledAmplificationTherapeuticsIndividual probesTarget nucleic acidMicroRNAs
- As the density of DNA microarrays increased in recent years, it has become possible to probe the entire genome of an organism in addition to only specific genes. (biomedcentral.com)
- Besides being highly efficient as northern probes, the same LNA-modified oligonucleotide probes would also be useful for miRNA in situ hybridization and miRNA expression profiling by LNA oligonucleotide microarrays. (pubmedcentralcanada.ca)
- Using this method, we found that probes containing multiple guanines in a row (G-stacks) have abnormal binding behavior compared with other probes, both in gene expression assays and genotyping assays using Affymetrix microarrays. (ucf.edu)
- Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays. (mcw.edu)
- BACKGROUND: Long oligonucleotide microarrays are potentially more cost- and management-efficient than cDNA microarrays, but there is little information on the relative performance of these two probe types. (mcw.edu)
- CONCLUSIONS: Microarrays of UV cross-linked unmodified oligonucleotides provided sensitive and specific measurements for most of the genes studied. (mcw.edu)
- To overcome the drawbacks associated with conventional 2-D flat microarrays, such as long hybridization times and large sample consumption, oligonucleotide arrays were constructed into the microfluidic channels hot embossed into PMMA substrate. (lsu.edu)
- Against the backdrop of this past experience, oligo-based microarrays hold the potential of enhanced design flexibility and eventual full-genome representation of probes capable of accurately reporting single-copy number changes. (aacrjournals.org)
- Oligonudeotide-based microarrays involving various probe preparations have been compared by a number of researchers. (dasmaninstitute.org)
- Limited data are available, however, regarding the concordances and efficacies of various probe preparations on long oligonucleotide-based microarrays. (dasmaninstitute.org)
- 2003). Aldape KD: A model of molecular interactions on short oligonucleotide microarrays. (core.ac.uk)
- It will also reduce the costs of microarrays, improve the application efficiency of microarrays, and promote both the research and development (R&D) and commercialization of high-performance probe design software . (bvsalud.org)
Global oligonucleotide synthesis market5
- The global oligonucleotide synthesis market is expected to reach $1,712.1 million by 2019 from $1,070.7 million in 2014, growing at a CAGR of 9.8% from 2014 to 2019. (bioportfolio.com)
- The global oligonucleotide synthesis market is categorized on the basis of products and s. (bioportfolio.com)
- The global oligonucleotide synthesis market is expected to reach USD 8.2 billion by 2024 from USD 4.31 billion in 2019, at a CAGR of 13.7% during the forecast period. (yahoo.com)
- This report provides a detailed picture of the global oligonucleotide synthesis market. (yahoo.com)
- According to the report, the global oligonucleotide synthesis market was valued at approximately USD 1,508 million in 2017 and is expected to generate around USD 3,697 million by 2026, at a CAGR of around 10.6% between 2019 and 2026. (digitaljournal.com)
- Based on end-user, the oligonucleotide synthesis market is segmented into academic research institutes, pharmaceutical and biotechnology companies, diagnostic laboratories, and hospitals. (yahoo.com)
- The oligonucleotides synthesis market is likely to benefit from the constant growth of gene editing and genomics markets, as there are a large number of advancements related to genetic tools for simplifying the synthesis of oligonucleotide process. (digitaljournal.com)
- By offering, the oligonucleotide synthesis market is segmented into equipment, reagents and consumables, and synthesized oligonucleotides. (digitaljournal.com)
- North America is anticipated to dominate the market for oligonucleotide synthesis and hold a major share of the oligonucleotide synthesis market over the forecast timeline. (digitaljournal.com)
- The Asia Pacific oligonucleotide synthesis market is projected to be driven by the strong presence of innumerable companies offering consumables and reagents for oligonucleotide synthesis and the increased need for better health outcomes, the rising prevalence of infectious and chronic diseases, and the availability of improved healthcare infrastructure in the region. (digitaljournal.com)
- We also developed a comprehensive set of assays, including a new multiplex ligation-dependent probe amplification assay, to interrogate the INI1 locus in 22q11.2. (aacrjournals.org)
- We have developed a rapid, immobilized probe-based assay for the detection of sequence variation in the hypervariable segment II (HVII) of the mitochondrial DNA (mtDNA) control region. (diva-portal.org)
- We then set up a novel melting temperature (Tm) assay that may help identification of HA-1 alleles without oligonucleotide probes. (biomedcentral.com)
- Our assay for the success of probe hybridization and detection was the demonstration of β‐actin mRNA highly localized in the lamellipodia of single cells (Lawrence and Singer, Cell 45:407, 1986) as well as the expression of α‐cardiac actin mRNA and the repression of β‐actin mRNA in differentiating myoblasts and in myotubes. (elsevier.com)
- In this study, we describe the use of an oligonucleotide-based microarray platform and development of requisite assay conditions and bioinformatic mining tools that permits high-resolution genome-wide array-comparative genome hybridization profiling of human and mouse tumors. (aacrjournals.org)
- Probes that labelled those species well in the FISH format were then incorporated into a sandwich hybridization assay (SHA). (edu.au)
- Multiplex analysis Although each probe examines one specific genomic locus, multiple probes can be combined into a single tube for multiplexed assay that simultaneously examines multiple loci. (wikipedia.org)
Detection using oligonucl3
- The recent development of FISH methods employing probes composed of synthetic DNA oligonucleotides (oligos) allows researchers to tightly control aspects of probe design such as binding energy and genomic specificity. (pnas.org)
- Oligonucleotide (oligo)-based FISH has emerged as an important tool for the study of chromosome organization and gene expression and has been empowered by the commercial availability of highly complex pools of oligos. (pnas.org)
- Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. (nih.gov)
- We explain why we need to normalize the arrays to one another using probe level intensities. (nih.gov)
- Unlike arrays built on clustered gene families, PanArray uses an unbiased, probe-centric approach that does not rely on annotations, gene clustering, or multi-alignments. (biomedcentral.com)
- However, these earlier, low-density arrays did not contain enough probes to target the entire genome of the bacterium, and were forced to probe only a small subset of the known genes. (biomedcentral.com)
- A multiplatform approach using Illumina single nucleotide polymorphism-based oligonucleotide arrays, multiplex ligation-dependent probe amplification, fluorescence in situ hybridization, and coding sequence analysis was used to characterize genome-wide copy number changes, LOH, and genomic alterations of INI1/SMARCB1 in a series of pediatric rhabdoid tumors. (aacrjournals.org)
- Extracting biological information from high-density Affymetrix arrays is a multi-step process that begins with the accurate annotation of microarray probes. (biomedcentral.com)
- Arrays of HLA Class I oligonucleotide probes on a solid support are provided, wherein the probes are sufficient to represent at least 80% of the known polymorphisms in exons 2 and 3 of the HLA Class I locus. (freepatentsonline.com)
- This invention relates to arrays of oligonucleotides that are useful for HLA typing. (freepatentsonline.com)
- Purpose: The goal of this work was to test the ability of oligonucleotide-based arrays to reproduce the results of focused bacterial artificial chromosome (BAC)-based arrays used clinically in comparative genomic hybridization experiments to detect constitutional copy number changes in genomic DNA. (nature.com)
- Methods: Custom oligonucleotide (oligo) arrays were designed using the Agilent Technologies platform to give high-resolution coverage of regions within the genome sequence coordinates of BAC/P1 artificial chromosome (PAC) clones that had already been validated for use in previous versions of clone arrays used in clinical practice. (nature.com)
- Because of the technical limitations of array production and establishment of rigorous quality control standards for spotted clone-based arrays, it seemed likely that this approach would be only a temporary solution to detect genomic copy number changes and would most likely be supplanted by oligonucleotide arrays. (nature.com)
- Citation Query Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. (psu.edu)
- Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. (psu.edu)
- The surface modification of polymer substrates for covalent attachment of oligonucleotide probes, the construction of fluidic channels/arrays, and hybridization kinetics will be covered. (lsu.edu)
- There was a similar increase in signal when these multiply labelled oligonucleotides were used as probes to oligonucleotide arrays. (ox.ac.uk)
- 1999). DJ: High density synthetic oligonucleotide arrays. (core.ac.uk)
- 2002). Head SR: Analysis of results variability from highdensity oligonucleotide arrays comparing same-species and cross-species hybridisations. (core.ac.uk)
- 2004). S: A method for cross-species gene expression analysis with high-density oligonucleotide arrays. (core.ac.uk)
- ST: Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species. (core.ac.uk)
- 2003). TA: Probe selection for high-density oligonucleotide arrays. (core.ac.uk)
- 2001). Wong WH: Model-based analysis of oligonucleotide arrays: design issues and standard error application. (core.ac.uk)
- This thesis talks about new enhancements to get over the difficulties of multiplex amplification of genomic sequences and design of sets of oligonucleotide probes for multiplex genetic analyses . (projectsparadise.com)
- Initially developed to improve sequencing efforts in the Human Genome Project, the oligonucleotide array technology has been successfully applied to many fields of molecular biology, including large scale gene discovery, monitoring the expression of thousands of genes, mutation and polymorphism detection, as well as mapping of genomic clones. (freepatentsonline.com)
- Using a commercially available 60-mer oligonucleotide microarray, we demonstrate that this platform provides sufficient sensitivity to detect single-copy difference in gene dosage of full complexity genomic DNA while offering high resolution. (aacrjournals.org)
- Genomic DNA probes. (slideshare.net)
- We\ud have previously developed a technique to study the transcriptomes of heterologous species based\ud on hybridising genomic DNA (gDNA) to a GeneChip array designed for a different species, and subsequently using only those probes with good homology. (core.ac.uk)
- Molecular Inversion Probe (MIP) belongs to the class of Capture by Circularization molecular techniques for performing genomic partitioning, a process through which one captures and enriches specific regions of the genome. (wikipedia.org)
- these probes hybridize to and capture the genomic target. (wikipedia.org)
- MIP stands unique from other genomic partitioning strategies in that MIP probes share the common design of two genomic target complementary segments separated by a linker region. (wikipedia.org)
- If the identification of the captured genomic target is performed using array-based hybridization approaches, the internal region may optionally contain a probe-specific tag sequence that uniquely identifies the given probe as well as a tag-release site, which, similar to the probe-release site, is also a restriction site. (wikipedia.org)
- Anneal probe to genomic target DNA Probes are added to the genomic DNA sample. (wikipedia.org)
- In this linearized probe the universal PCR primer sequences are located at the 5' and 3' ends and the captured genomic target becomes part of the internal segment of the probe. (wikipedia.org)
- If array-based approach is used, the probe may optionally contain a probe-specific tag that uniquely identifies the probe as well as the genomic region targeted by it. (wikipedia.org)
- Detection of subpicogram quantities of specific DNA sequences on blot hybridization with biotinylated probes," Nucleic Acids Research, 23:8083-8091 (1985). (freepatentsonline.com)
- The conditions under which oligonucleotides hybridize only with entirely homologous sequences are recognized. (google.com)
- 2. The method of claim 1, wherein step (b) is repeated with other labeled second oligonucleotide probes which are exactly complementary to other possible sequences at said ambiguous locus. (google.com)
- However, a dedicated bioinformatic design utility has yet to be created specifically for the purpose of identifying optimal oligo FISH probe sequences on the genome-wide scale. (pnas.org)
- On the basis of partial 16S rRNA sequences of six Fibrobacter strains, four hybridization probes were designed to discriminate between the species Fibrobacter succinogenes and Fibrobacter intestinalis and to identify F. succinogenes subsp. (asm.org)
- Single-mismatch discrimination between certain probe and nontarget sequences was demonstrated, and fluorescent intensity was shown to be enhanced by hybridization to multiple probes of the same specificity. (asm.org)
- Instead, probes are evenly tiled across all sequences of the pan-genome at a consistent level of coverage. (biomedcentral.com)
- PanArray is an oligonucleotide probe selection algorithm for tiling multiple genome sequences using a minimal number of probes. (biomedcentral.com)
- The probe sequences have also been deposited in the ProbeBase data bank ( 15 ). (asm.org)
- We performed DNA sequence analysis of 129 samples to characterize the sequences associated with "blanks" (absence of probe signals) and weak probe signals. (diva-portal.org)
- By matching probe sequences to an up-to-date Reference Sequence (RefSeq) database [ 20 , 21 ], Gautier et al [ 22 ] investigated an "alternative mapping" approach, wherein probes were grouped together if they matched a common RefSeq transcript and were excluded from a probe set if they matched 2 or more RefSeq entries. (biomedcentral.com)
- YODA is an application primarily for selecting microarray probe sequences for measuring gene expression. (vt.edu)
- Although the vast majority of primers and probes employed in qPCR applications today are synthesized using unmodified DNA bases, selective use of chemically modified bases and non-base modifying groups can prevent primer dimer artefacts, improve specificity, and allow for selective amplification of sequences that differ by as little as a single base. (owczarzy.net)
- Two LC hybridization probes specific for two adjacent sequences in the target DNA are used for quantitative Real-Time PCR. (biozyme.ro)
- Two LC hybridisation probes labelled with a single fluorescent molecule specifically recognise two adjacent sequences in the target DNA. (biozyme.ro)
- Abs - probes to recognize specific protein sequences. (slideshare.net)
Fluorescence in situ hybr2
- Faecal microbiota of conventional mouse strains and specific pathogen-free mice from different breeding colonies were analysed by fluorescence in situ hybridization using these five probes. (semanticscholar.org)
- Oligonucleotide probes and the non-denaturing fluorescence in situ hybridization (ND-FISH) technique are widely used to analyze plant chromosomes because they are convenient tools. (mdpi.com)
Cleavage of oligonucleotide probes1
- Using structure-specific cleavage of oligonucleotide probes (Invader, Third Wave Technologies, Inc., Madison, WI), 96-well plates were configured so that each well contained reagents for detection of both the wild type and mutant alleles at each locus. (cdc.gov)
High-density oligonucleotide array3
- Exploration, normalization, and summaries of high density oligonucleotide array probe level data. (nih.gov)
- In this paper we report exploratory analyses of high-density oligonucleotide array data from the Affymetrix GeneChip system with the objective of improving upon currently used measures of gene expression. (nih.gov)
- In the case of high density oligonucleotide array, the probes are assumed to have been normalized to produce an expression summary, represented here as ygi, for each gene on each array as in Li and Wong (2001) or Irizarry et al (2003). (psu.edu)
Primers and Probes6
- Gene Link's proprietary synthesis and processing methods for fluorescent dyes yield primers and probes of superior quality. (genelink.com)
- Gene Link offers synthesis of various forms of molecular primers and probes. (genelink.com)
- T m -enhancing modifications allows both primers and probes to be shorter, improving the differential T m (Δ T m = T m match - T m mismatch ) between perfect match and mismatch hybridization. (owczarzy.net)
- Universal bases permit use of primers and probes in polymorphic loci when it is desirable to detect all sequence variants and minimize mismatch discrimination. (owczarzy.net)
- OEM by QIAGEN provides customized primers and probes. (qiagen.com)
- We have ramped up and prioritized our production of primers and probes that specifically support the detection of the SARS-CoV-2 virus, allowing for pre-manufacturing that ensures quick supply to meet the high demands. (qiagen.com)
- Grafting on a gold surface of 20-base thiol- or biotin-labeled probe, and selective hybridization with the complementary 20-base target, have been monitored in situ with a 27 MHz quartz crystal microbalance under controlled hydrodynamic conditions. (mdpi.com)
- After in situ hybridization to whole cells of the six sequenced strains, epifluorescence microscopy confirmed probe specificity. (asm.org)
- The specificity of the newly designed probes was tested by whole-cell in situ hybridization against a panel of 120 reference strains derived from the human and animal gastrointestinal tract as described by Schwiertz et al. (asm.org)
- 1. The developed TFO-probes could be exploited for cytogenetic quantitative detection of valuable TISH-technology (third strand in situ hybridization). (jbsdonline.com)
- We have designed an oligonucleotide probe for use in fluorescent in situ hybridization (FISH) and two pairs of PCR primers targeting a C. testosteroni subgroup. (biomedcentral.com)
- The following study reports on the development of 16S rRNA sequence based oligonucleotide probes which are suitable for detection and quantification of Comamonas testosteroni in mixed cultures using PCR and/or fluorescent in situ hybridization (FISH). (biomedcentral.com)
- To overcome this obstacle, we screened soybean repetitive DNA to develop a cocktail of fluorescent in situ hybridization (FISH) probes that could differentially label mitotic chromosomes in root tip preparations. (genetics.org)
- To resolve these potential problems and to provide a useful resource for correlating physical soybean chromosomes to the other available soybean mapping resources, we undertook efforts to generate a soybean karyotype map using fluorescent in situ hybridization (FISH) with chromosome-specific, pseudomolecule- and repeat-derived DNA probes. (genetics.org)
- Oligonucleotide probes labeled with fluorescent dyes are used in a variety of in situ applications to detect specific DNA or RNA molecules. (umn.edu)
- Among other factors the high protein concentration within cells may prevent quenching of probe fluorescence in situ. (umn.edu)
- Behrens, S , Fuchs, BM & Amann, R 2004, ' The effect of nucleobase-specific fluorescence quenching on in situ hybridization with rRNA-targeted oligonucleotide probes ', Systematic and Applied Microbiology , vol. 27, no. 5, pp. 565-572. (umn.edu)
- We have developed in situ hybridization methodology for nonisotopically labeled oligonucleotide probes to detect cellular mRNA with improved speed, convenience, and resolution over previous techniques. (elsevier.com)
- Previous work using isotopically labeled oligonucleotide probes characterized important parameters for in situ hybridization (Anal Biochem 166:389, 1987). (elsevier.com)
- Taneja, KL & Singer, RH 1990, ' Detection and localization of actin mRNA isoforms in chicken muscle cells by in situ hybridization using biotinated oligonucleotide probes ', Journal of Cellular Biochemistry , vol. 44, no. 4, pp. 241-252. (elsevier.com)
- Oligonucleotides directed toward H. akashiwo and F. japonica were evaluated using fluorescent in situ hybridization (FISH). (edu.au)
Market for oligonucleotide synthesis2
- The probe hybridizes with a specific mRNA, if present. (uchicago.edu)
- Eleven oligonucleotide probes were made to coding and noncoding regions of chick β‐actin mRNA and one oligonucleotide probe to chick α‐cardiac actin mRNA. (elsevier.com)
- With the α‐cardiac probe, we found that this mRNA was distributed all over the cytoplasm of myotubes and differentiated (bipolar) single cells and negative in undifferentiated single cells and at the ends of myotubes. (elsevier.com)
- When β‐actin probes were used, two of 11 probes were highly sensitive, and, in pooling them together, the localization of β‐actin mRNA in fibroblastic single cells was evident at the leading edge of the motile cells, the lamellipodium. (elsevier.com)
- Mouse cDNA clones for a putative Ah receptor have been isolated from a cDNA library of mRNA from Hepa-1 cells by an oligonucleotide probe produced by PCR with a pair of primers which was synthesized according to the reported N-terminal sequence of 26 amino acids. (nih.gov)
- We have identified quencher-free molecular beacons that allow the sensitive probing of CAG repeat oligonucleotides, including mRNA fragments of trinucleotide repeat diseases, with significant increases in fluorescence intensity mediated by disruption of the stacking of their PyU units. (edu.au)
Nonisotopically labeled oligonucleotide1
- Evaluation of a nonisotopically labeled oligonucleotide probe to detect the heat-stable enterotoxin gene of Escherichia coli by the DNA colony hybridization test. (asm.org)
- These findings are critical for the design of multiplexed assays where probe molecules are immobilized to biosensors via the avidin?biotin interaction. (soton.ac.uk)
- Here, an individual dye-modified component (universal reporter) can be used for many different assays, whereby only the primers and an unlabelled probe (mediator probe) have to be individually designed for the respective detection. (biomers.net)
- With the mediator probe PCR the universal reporter can be used in different assays. (biomers.net)
- Marras, S.A., Tyagi, S. and Kramer, F.R. (2006) Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes. (scirp.org)
- At OEM by QIAGEN, we know that high-quality, pure oligonucleotides can make a difference, helping our customers' success in creating reliable commercial assays. (qiagen.com)
- Detection of Plasmodium sporozoites in mosquitoes by polymerase chain reaction and oligonucleotide rDNA probe, without dissection of the salivary glands. (wur.nl)
- The hybridised specific 3´-part of the mediator probe is digested subsequently, while the polymerase synthesises the complementary strand. (biomers.net)
- Techniques used to define human MHC antigens: polymerase chain reaction and oligonucleotide probes. (ox.ac.uk)
- Sequence-specific oligonucleotides (SSO) can be used to detect individual alleles with a high degree of accuracy by probing dot-blotted DNA, amplified to high copy number by the polymerase chain reaction (PCR). (ox.ac.uk)
- A 3' phosphate group is also added to prevent extension of the reporter probe by Taq DNA polymerase during the PCR cycles. (biozyme.ro)
- Gap filling The gap is filled by DNA polymerase using free nucleotides and the ends of the probe are ligated by ligase, resulting in a fully circularized probe. (wikipedia.org)
- We further demonstrate that applying the new probe set definition can detect specific transcript variants contributing to differential expression and it also improves cross-platform concordance. (biomedcentral.com)
- Oligonucleotide probes can be labeled with fluorophores which emit at different wavelengths, this means different probes can be used to detect multiple targets within a single reaction tube. (europeanmedical.info)
- Use of an oligonucleotide probe to detect Vibrio parahaemolyti. (mysciencework.com)
- Use of an oligonucleotide probe to detect Vibrio parahaemolyticus in artificially contaminated oysters. (mysciencework.com)
- These studies have demonstrated that commercially available cDNA array-CGH platforms are sufficiently robust to detect regional single-copy changes (13) , providing that high background probes are eliminated by empirical and bioinformatic means. (aacrjournals.org)
- In this study, five new oligonucleotide probes were designed and applied to detect these clostridial groups that are essential for the normalization of germfree mice. (semanticscholar.org)
- These five new probes for mouse clostridia were able to detect the difference in clostridial diversity in each mouse group. (semanticscholar.org)
- Examples of the use of these probes to detect different class I gene transcripts in cloned murine T cells, T cells transformed with Radiation Leukemia Virus, chemically induced thymoma cell lines and embryonic tissues are described. (elsevier.com)
- Although oligo FISH probes are central to many recently developed massively multiplexed and superresolution imaging methods, no dedicated computational utility exists to facilitate the design of such probes on the genome-wide scale. (pnas.org)
- Different immobilization methods showed little variation in complex stability but differed in total binding and nonspecific biotin-modified oligonucleotide binding. (soton.ac.uk)
- The present invention features compositions and methods that are useful for storing labeled detection probes and detecting whether a target nucleic acid sequence is present in a sample. (google.com)
- Methods of using a subject probe to assess target polynucleotides, e.g., small RNAs, in a sample are provided, as are kits for use in practicing the subject methods. (google.com.au)
- Kofiadi, I.A. and Rebrikov, D.V. (2006) Methods for detecting single nucleotide polymorphisms: Allele-specific PCR and hybridization with oligonucleotide probe. (scirp.org)
- Our oligonucleotides are produced using AIE-HPLC and RP-HPLC methods, resulting in a very high purity level. (qiagen.com)
- Using AceView, a comprehensive human transcript database, we have reannotated the probes by matching them to RNA transcripts instead of genes. (biomedcentral.com)
- Probes within a probe set can be both ambiguous (non-specific, i.e. targeting multiple genes) and heterogeneous (target different transcript variants from one gene). (biomedcentral.com)
- These probes are less likely to covary with other probes that interrogate the same genes. (ucf.edu)
- RESULTS: Unmodified sense and antisense 70-mer oligonucleotides representing 75 known rat genes and 10 Arabidopsis control genes were synthesized, printed and UV cross-linked onto glass slides. (mcw.edu)
- Printed alongside were PCR-amplified cDNA clones corresponding to the same genes, enabling us to compare the two probe types simultaneously. (mcw.edu)
- Approximately 8% of the genes showed discordant results with the two probe types, and in each case the cDNA results were more accurate, as determined by real-time PCR. (mcw.edu)
- Consequently, it is difficult to distinguish between RNA transcripts of individual class I genes solely on the basis of nucleic acid hybridization analysis using DNA probes over 50 base pairs long. (elsevier.com)
- To avoid this problem, I have designed and synthesized a set of oligonucleotide probes capable of detecting transcripts of single class I genes in the MHC of C57BL/10 mice or sets of allelic class I genes at the same genetic locus in MHC disparate mouse strains. (elsevier.com)
- Oligonucleotide probes with the potential to discriminate closely related species were designed taking into account the genetic polymorphisms found in target genes. (mdpi.com)
- Probe selection based on gDNA hybridisation\ud intensity increased the number of genes identified as significantly differentially expressed in two\ud published studies of Arabidopsis development, and optimised the analysis of technical replicates obtained from pooled samples of RNA from rice. (core.ac.uk)
- In order to exploit the improved hybridization properties of LNA with their target RNA molecules, we designed several LNA-modified oligonucleotide probes for detection of different microRNAs in animals and plants. (pubmedcentralcanada.ca)
- Deep UV patterning using a through-hole mask indicated that more oligonucleotide molecules were immobilized on the UV-exposed areas than the non-exposed area in the presence of EDC conjugating reagent. (lsu.edu)
- Similar to MIP, padlock probes are single stranded DNA molecules with two 20-nucleotide long segments complementary to the target connected by a 40-nucleotide long linker sequence. (wikipedia.org)
- Our streamlined method uses standard bioinformatic file formats, allowing users to seamlessly integrate new and existing utilities into the pipeline as desired, and introduces a method for evaluating the specificity of each probe molecule that connects simulated hybridization energetics to rapidly generated sequence alignments using supervised machine learning. (pnas.org)
- Four broad-specificity probes were designed to target the small subunit rRNA of bacteria related to Eubacterium hallii , the recently reclassified Faecalibacterium prausnitzii (formerly Fusobacterium prausnitzii ) ( 9 ), Coprococcus eutactus , and Roseburia intestinalis clusters (Table 1 and Fig. 1 and 2 ). (asm.org)
- Here, we introduce a streamlined pipeline for the rapid, genome-scale design of oligo FISH probes and validate our approach by using conventional and superresolution imaging. (pnas.org)
- Here, we introduce OligoMiner, a rapid and robust computational pipeline for the genome-scale design of oligo FISH probes that affords the scientist exact control over the parameters of each probe. (pnas.org)
- We demonstrate the scalability of our approach by performing genome-scale probe discovery in numerous model organism genomes and showcase the performance of the resulting probes with diffraction-limited and single-molecule superresolution imaging of chromosomal and RNA targets. (pnas.org)
- An unbiased tiling of probes across the entire length of the genome is the most flexible design approach. (biomedcentral.com)
- To minimize the required number of probes, probes conserved across multiple strains in the pan-genome are selected first, and additional probes are used only where necessary to span polymorphic regions of the genome. (biomedcentral.com)
- An array providing unbiased coverage of probes across a genome is commonly referred to as a whole-genome tiling array . (biomedcentral.com)
- Current designs select suitable probes through in silico scanning of transcriptome/genome based on first principles. (ucf.edu)
- 3. The method of claim 2, wherein selecting probes from the ranked group-specific candidate probes comprises, for each target, selecting the most conserved or least conserved probes representing that target until each target genome is represented by a predetermined number of probes. (patentsencyclopedia.com)
- 2004). Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. (core.ac.uk)
- Molecular probes kashmeera n.a. (slideshare.net)
- Intragenic deletions could be detected using the Illumina 550K Beadchip, whereas single exon deletions could be detected using multiplex ligation-dependent probe amplification. (aacrjournals.org)
- Second, probes facilitate multiplex reactions. (europeanmedical.info)
- These results suggest that probes containing G-stacks tend to have increased cross hybridization signals and reduced target- specific hybridization signals, presumably due to multiplex binding forming G-quartet structures. (ucf.edu)
- We anticipate that this pipeline will make the FISH probe design process much more accessible and will more broadly facilitate the design of pools of hybridization probes for a variety of applications. (pnas.org)
- of probe/target hybridization, allowing rational probe design. (caltech.edu)
- The viability of the algorithm is demonstrated by array designs for seven different bacterial pan-genomes and, in particular, the design of a 385,000 probe array that fully tiles the genomes of 20 different Listeria monocytogenes strains with overlapping probes at greater than twofold coverage. (biomedcentral.com)
- By modifying DNA oligonucleotides with LNAs using a design, in which every third nucleotide position was substituted by LNA, we could use the probes in northern blot analysis employing standard end-labelling techniques and hybridization conditions. (pubmedcentralcanada.ca)
- The purpose of the present study was, therefore, to design 16S rRNA-targeted oligonucleotide probes for butyrate-producing bacteria, including recent isolates from the human gut, many of which represent new species ( 8 , 9 , 21 ). (asm.org)
- We have offered a software tool for the design of sequence-tagged oligonucleotide probes. (projectsparadise.com)
- The ProbeMaker software program is a framework for design of sets of probes consisting of independent functional elements, and makes use of an extension mechanism to add support for new probe types as required. (projectsparadise.com)
- We have also introduced a technique to a unified system for oligonucleotide design. (projectsparadise.com)
- This system assists to lower development times for new oligonucleotide design applications by permitting substantial code reuse. (projectsparadise.com)
- We conclude that our transcript-level reannotation and redefinition of probe sets complement the original Affymetrix design. (biomedcentral.com)
- Knowing which specific transcripts are differentially expressed is important to properly design probe/primer pairs for validation purposes. (biomedcentral.com)
- Comprehensive viral oligonucleotide probe design using conserved protein regions. (uchicago.edu)
- We provide technical service in the design of novel probes and synthesize numerous combinations of dyes, quenchers, RNA, phosphorothioate, 2′-O-methyl and chimeric probes. (genelink.com)
- Design oligonucleotide probes by looking for an area of the sequence that matches the order for the selected allele but for no other group. (barnardhealth.us)
- Motivation: In microarray experiments, probe design is critical to the specific and accurate measurement of target concentrations. (ucf.edu)
- Design and application of group-specific oligonucleotide probes for detecting and monitoring mouse clostridia. (semanticscholar.org)
- There are two types of selectivity that are critical for the rational design of highly specific oligonucleotides probes. (scirp.org)
- The results allowed us to postulate points of principle to rationally design the most selective probes on the basis of oli- gonucleotides or their derivatives. (scirp.org)
- The design and selection of oligonucleotide probes are critical for preparing gene chips with high quality . (bvsalud.org)
- Several sets of probe design software have been developed and are available to perform this work now. (bvsalud.org)
- This review will be helpful for users to choose an appropriate probe -design software . (bvsalud.org)
- With this design, when the probe hybridizes to the target, it undergoes an inversion in configuration (as suggested by the name of the technique) and circularizes. (wikipedia.org)
- The design of the molecular inversion probes (MIP) originated from padlock probes, a molecular biology technique first reported by Nilsson et al. (wikipedia.org)
- Chemical modification of PS-ASO therapeutics reduces cellular protein-binding and improves the therapeutic index ," published in Nature Biotechnology , is the 2019 recipient of the OTS Paper of the Year Award , recognizing the most impactful paper in the field of oligonucleotide therapeutics. (yahoo.com)
- At the time of its development, none of the existing programs for this task satisfied the best-known requirements for microarray probe selection. (vt.edu)
- The question of what makes a good microarray probe was a research area at the time, and YODA was developed to incorporate the latest understanding of these requirements, drawn from the research literature, into a tool that can be used by a research biologist. (vt.edu)
- The conditions under which oligonucleotide probes hybridize preferentially with entirely complementary and homologous nucleic acid targets are described. (freepatentsonline.com)
- We will demonstrate RNA pull-down using surface-immobilized SC probes, exploiting covalent target capture to remove unwanted material using stringent washes, and then reversing the crosslinks to recover the targets. (caltech.edu)
- It should be noted that grouping probes that map to different targets may create divergent signals that will significantly influence expression measurements from stochastic-model-based summarization approaches ( e.g . (biomedcentral.com)
- Result: In this study, we describe a probe performance assessment method based on the concordance of the observed signals from probes that share common targets. (ucf.edu)
- and selecting probes from the ranked group-specific candidate probes, thus obtaining the plurality of oligonucleotide probes for detection of targets of a target group, wherein a target is represented if a candidate probe matches with at least 85% sequence similarity over the total candidate probe length and has a perfectly matching subsequence of at least 29 contiguous bases spanning the middle of the probe. (patentsencyclopedia.com)
- thus obtaining the plurality of oligonucleotide probes for detection of targets of a target group, wherein a target is represented if a candidate probe matches an at least 85% sequence identity to the target over the length of the probe and a detection probability of at least 85% derived from an alignment score, a predicted T m , and the start position of the match on the probe. (patentsencyclopedia.com)
- The first type is the real selectivity of hybridization (f a ) that is the ratio of association degrees of targets with an oligonucleotide probe upon the perfect and imperfect complex formation. (scirp.org)
- The level of gene expression is typically summarized from a probe set composed of several 25 mer probes designed to span a target region based on a UniGene cluster. (biomedcentral.com)
- The feasibility of using unmodified oligonucleotides to accurately measure changes in gene expression is also unclear. (mcw.edu)
- Individual oligonucleotide probe intensities (PM - MM) from three conditions are shown to validate the microarray-predicted hnr - galU operon. (nih.gov)
- Intensities for individual probes interrogating hnr , the 200 bp intergenic region and galU are shown. (nih.gov)
- Individual oligonucleotide probe intensities (PM - MM) from three conditions are shown to validate the microarray-detected 5′-UTR upstream of ompA . (nih.gov)
- Intensities for individual oligonucleotide probes interrogating ompA , the 356 bp intergenic region and sulA are shown. (nih.gov)
- The heat shock and pre-heat shock signal intensities for this probe are lower than the majority, however the ratio is the same. (biomedcentral.com)
- Signal intensities across probe-pairs within a probe-set vary in part due to different physical hybridisation characteristics of individual probes with their target labelled transcripts. (core.ac.uk)
- Select dual-labeled probes and unlabeled sequence detection primers for real-time PCR applications using TaqMan probe-based chemistry. (thermofisher.com)
- The FISH probe and one of the PCR primer pairs are suitable for quantification of C. testosteroni in mixed microbial communities using FISH followed by quantitative image analysis or real-time quantitative PCR, respectively. (biomedcentral.com)
- This combination of primer/probe binding makes it less likely to generate a signal from a nonspecific product or from misannealing. (europeanmedical.info)
- Common to all is the measurement of fluorescence increase over time, as well as the need for an individual fluorescently labelled probe (single or in combination with a primer) for each detection. (biomers.net)
- Prepare primer-probe mix containing a final concentration of 20 uM each primer and 10 uM each probe listed above. (cdc.gov)
- A dendrimeric oligonucleotide was used successfully as a primer in the PCR. (ox.ac.uk)
- The internal region contains two universal PCR primer sites that are common to all MIPs as well as a probe-release site, which is usually a restriction site. (wikipedia.org)
- 3. The method of claim 1, further comprising the step of forming a covalent link between the complementary sequence and the unlabeled first probe that is hybridized to the complementary sequence in the nucleic acid fragment. (google.com)
- 4. The method of claim 3, wherein the covalent link is formed by exposing the unlabeled first probe hybridized to the complementary sequence in the nucleic acid fragment to psoralen in the presence of ultraviolet radiation. (google.com)
- The probes, complementary to short sequence elements within the 16S rRNA common to phylogenetically coherent assemblages of microorganisms, were labeled with tetramethylrhodamine and hybridized to suspensions of fixed cells. (asm.org)
- The intensity of fluorescence was increased additively by the combined use of two or three fluorescent probes complementary to different regions of the same 16S rRNA. (asm.org)
- 3. The composition of claim 2 , wherein said hybridization complex formed between said detection probe and said protection probe has a Tm at least about 4 C. lower in a solution containing 0.05 M lithium succinate, pH 5.0, 0.6 M LiCl, 1% w/v LLS, 10 mM EDTA, and 10 mM EGTA, than said hybridization complex formed between said detection probe and said fully complementary target nucleic acid. (google.com)
- 4. The composition of claim 3 , wherein said hybridization complex formed between said detection probe and said protection probe has a Tm at least 5 C. lower in said solution than said hybridization complex formed between said detection probe and said fully complementary target nucleic acid. (google.com)
- The probe may further include a nucleotide clamp, a stem-complementary. (google.com.au)
- The probe may further include a nucleotide clamp, a stem-complementary region and/or a linker moiety. (google.com.au)
- 3 . The probe of claim 1 , further comprising a nucleotide clamp region bound to the target complementary region and to the stem-complementary region, wherein the stem-complementary region is bound to the target complementary region via said nucleotide clamp. (google.com.au)
- 5 . The probe of claim 3 , wherein the target complementary region is from 10 to 25 nucleotides long. (google.com.au)
- 6 . The probe of claim 1 , wherein said RNA hairpin extension domain includes a portion that base-pairs to the stem-complementary region to form a stem-duplex, wherein the stem-duplex stabilizes the probe/target duplex. (google.com.au)
- Specifically, the two target complementary regions at the 5' and 3' ends of the probe become adjacent to one another while the internal linker region forms a free hanging loop. (wikipedia.org)
- After a denaturation followed by an annealing step, the target-complementary ends of the probe are hybridized to the target DNA. (wikipedia.org)
- An enormous advantage over classic real-time PCR applications is the absence of a target-specific fluorescently labelled probe. (biomers.net)
- Mixed LNA/DNA capture probes thus can be designed for equal T(m)s for all miRNAs, which naturally cover a range between 45 and 74 degrees C. The protocols established are easy to apply, as they do not require RNA size selection and/or amplification of miRNAs. (nih.gov)
- In addition, fine resolution of specificities such as the subtypes of DR4 is possible using a combination of SSO probes and group-specific amplification in which PCR primers designed to amplify only DR4 alleles are employed. (ox.ac.uk)
- Preferred compositions are made up of a detection probe containing a label susceptible to a chemical or enzymatic alteration and a protection probe that protects the label from alteration and/or decreases the ability of the detection probe to inhibit nucleic acid amplification. (google.com)
- Captured target enrichment If the probe is linearized, traditional PCR amplification is performed to enrich the captured target using the universal primers of the probe. (wikipedia.org)
- Otherwise, rolling circle amplification is performed for the circular probe. (wikipedia.org)
- The Young Investigator Award recognizes the outstanding achievements and contributions by a professional scientist in the field of oligonucleotide therapeutics who has recently received his or her doctoral degree. (yahoo.com)
- The growing applications of ready-to-use synthesized oligonucleotides in therapeutics and a large number of manufacturers offering various customizations is likely to drive the synthesized oligonucleotides segment in the years ahead. (digitaljournal.com)
- However, due to lack of tools, the observed microarray data have not been used to assess the performance of individual probes to provide feedback to improve future designs. (ucf.edu)
Target nucleic acid2
- Using these hybridization conditions, overlapping oligonucleotide probes associate with a target nucleic acid. (freepatentsonline.com)
- Such compositions can be used, for example, to stabilize a detection probe label and to prevent a detection probe from hybridizing prematurely to amplified or target nucleic acid. (google.com)
- We describe here a new method for highly efficient detection of microRNAs by northern blot analysis using LNA (locked nucleic acid)-modified oligonucleotides. (pubmedcentralcanada.ca)
- The sensitivity in detecting mature microRNAs by northern blots was increased by at least 10-fold compared to DNA probes, while simultaneously being highly specific, as demonstrated by the use of different single and double mismatched LNA probes. (pubmedcentralcanada.ca)