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.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
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)
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.
Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)
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.
The use of devices which use detector molecules to detect, investigate, or analyze other molecules, macromolecules, molecular aggregates, or organisms.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
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.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
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).
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Short fragments of DNA or RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.
3 beta,12 beta,14-Trihydroxy-5 beta-card-20(22)-enolide. A cardenolide which is the aglycon of digoxin. Can be obtained by hydrolysis of digoxin or from Digitalis orientalis L. and Digitalis lanata Ehrh.
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.
A group of atoms or molecules attached to other molecules or cellular structures and used in studying the properties of these molecules and structures. Radioactive DNA or RNA sequences are used in MOLECULAR GENETICS to detect the presence of a complementary sequence by NUCLEIC ACID HYBRIDIZATION.
Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)
The functional hereditary units of BACTERIA.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
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.
Agents that emit light after excitation by light. The wave length of the emitted light is usually longer than that of the incident light. Fluorochromes are substances that cause fluorescence in other substances, i.e., dyes used to mark or label other compounds with fluorescent tags.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
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.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.
The relationships of groups of organisms as reflected by their genetic makeup.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
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.
Refuse liquid or waste matter carried off by sewers.
Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.
Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
Community of tiny aquatic PLANTS and ANIMALS, and photosynthetic BACTERIA, that are either free-floating or suspended in the water, with little or no power of locomotion. They are divided into PHYTOPLANKTON and ZOOPLANKTON.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
Nucleic acid which complements a specific mRNA or DNA molecule, or fragment thereof; used for hybridization studies in order to identify microorganisms and for genetic studies.
The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.
A genus of gram-negative gliding bacteria found in SOIL; HUMUS; and FRESHWATER and marine habitats.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
A group of gram-negative, anaerobic bacteria that is able to oxidize acetate completely to carbon dioxide using elemental sulfur as the electron acceptor.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
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)
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.
The study of microorganisms living in a variety of environments (air, soil, water, etc.) and their pathogenic relationship to other organisms including man.
The discarding or destroying of liquid waste products or their transformation into something useful or innocuous.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
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.
A phthalic indicator dye that appears yellow-green in normal tear film and bright green in a more alkaline medium such as the aqueous humor.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
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.
Water containing no significant amounts of salts, such as water from RIVERS and LAKES.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
A class in the phylum PROTEOBACTERIA comprised of chemoheterotrophs and chemoautotrophs which derive nutrients from decomposition of organic material.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
Studies determining the effectiveness or value of processes, personnel, and equipment, or the material on conducting such studies. For drugs and devices, CLINICAL TRIALS AS TOPIC; DRUG EVALUATION; and DRUG EVALUATION, PRECLINICAL are available.
Modified oligonucleotides in which one of the oxygens of the phosphate group is replaced with a sulfur atom.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
Genotypic differences observed among individuals in a population.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Short fragments of DNA that are used to alter the function of target RNAs or DNAs to which they hybridize.
A functional system which includes the organisms of a natural community together with their environment. (McGraw Hill Dictionary of Scientific and Technical Terms, 4th ed)
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).
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).
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
Compounds that contain three methine groups. They are frequently used as cationic dyes used for differential staining of biological materials.
The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.
Proteins found in any species of bacterium.
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)
Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.
A genus of gram-negative, ellipsoidal or rod-shaped bacteria whose major source of energy and reducing power is from the oxidation of ammonia to nitrite. Its species occur in soils, oceans, lakes, rivers, and sewage disposal systems.
Established cell cultures that have the potential to propagate indefinitely.
Toxic substances formed in or elaborated by bacteria; they are usually proteins with high molecular weight and antigenicity; some are used as antibiotics and some to skin test for the presence of or susceptibility to certain diseases.
Any method used for determining the location of and relative distances between genes on a chromosome.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
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.
A genus of gram-negative aerobic bacteria that occurs free-living in the soil or associated with the roots of cereal crops or grasses (POACEAE).
Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.
A family of gram-negative, aerobic bacteria that do not form endospores or microcysts.
Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.
The sum of the weight of all the atoms in a molecule.
Excrement from the INTESTINES, containing unabsorbed solids, waste products, secretions, and BACTERIA of the DIGESTIVE SYSTEM.
Deoxyribonucleic acid that makes up the genetic material of fungi.
Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.
A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.
Two-dimensional separation and analysis of nucleotides.
A heat stable DNA-DIRECTED DNA POLYMERASE from the bacteria Thermus aquaticus. It is widely used for the amplification of genes through the process of POLYMERASE CHAIN REACTION. EC 2.7.7.-.
Deoxyribonucleic acid that makes up the genetic material of viruses.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
A mixture of solid hydrocarbons obtained from petroleum. It has a wide range of uses including as a stiffening agent in ointments, as a lubricant, and as a topical anti-inflammatory. It is also commonly used as an embedding material in histology.
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).
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.
Substances that are toxic to the intestinal tract causing vomiting, diarrhea, etc.; most common enterotoxins are produced by bacteria.
A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.
Electrophoresis in which agar or agarose gel is used as the diffusion medium.
Nucleotides in which the base moiety is substituted with one or more sulfur atoms.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
The rate dynamics in chemical or physical systems.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
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.
Coccus-shaped bacteria that retain the crystal violet stain when treated by Gram's method.
A group of hereditary hemolytic anemias in which there is decreased synthesis of one or more hemoglobin polypeptide chains. There are several genetic types with clinical pictures ranging from barely detectable hematologic abnormality to severe and fatal anemia.
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
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.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
Sequential operating programs and data which instruct the functioning of a digital computer.
A water-soluble, enzyme co-factor present in minute amounts in every living cell. It occurs mainly bound to proteins or polypeptides and is abundant in liver, kidney, pancreas, yeast, and milk.
A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).
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.
Phylum of green nonsulfur bacteria including the family Chloroflexaceae, among others.
Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.
The simplest saturated hydrocarbon. It is a colorless, flammable gas, slightly soluble in water. It is one of the chief constituents of natural gas and is formed in the decomposition of organic matter. (Grant & Hackh's Chemical Dictionary, 5th ed)
A genus of VIBRIONACEAE, made up of short, slightly curved, motile, gram-negative rods. Various species produce cholera and other gastrointestinal disorders as well as abortion in sheep and cattle.
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.
A large group of anaerobic bacteria which show up as pink (negative) when treated by the Gram-staining method.
A family of gram-negative, aerobic bacteria utilizing only one-carbon organic compounds and isolated from in soil and water.
The property of emitting radiation while being irradiated. The radiation emitted is usually of longer wavelength than that incident or absorbed, e.g., a substance can be irradiated with invisible radiation and emit visible light. X-ray fluorescence is used in diagnosis.
A genus of motile or nonmotile gram-positive bacteria of the family Clostridiaceae. Many species have been identified with some being pathogenic. They occur in water, soil, and in the intestinal tract of humans and lower animals.
Short fragments of RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.
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.
Proteins prepared by recombinant DNA technology.
A family of marine mollusks in the class BIVALVIA, commonly known as oysters. They have a rough irregular shell closed by a single adductor muscle.
The making of a radiograph of an object or tissue by recording on a photographic plate the radiation emitted by radioactive material within the object. (Dorland, 27th ed)
Disposal, processing, controlling, recycling, and reusing the solid, liquid, and gaseous wastes of plants, animals, humans, and other organisms. It includes control within a closed ecological system to maintain a habitable environment.
The use of computers for designing and/or manufacturing of anything, including drugs, surgical procedures, orthotics, and prosthetics.
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)
A group of the D-related HLA antigens found to differ from the DR antigens in genetic locus and therefore inheritance. These antigens are polymorphic glycoproteins comprising alpha and beta chains and are found on lymphoid and other cells, often associated with certain diseases.
A subclass of HLA-D antigens that consist of alpha and beta chains. The inheritance of HLA-DR antigens differs from that of the HLA-DQ ANTIGENS and HLA-DP ANTIGENS.
Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.
Biochemical identification of mutational changes in a nucleotide sequence.
Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
A family of spiro(isobenzofuran-1(3H),9'-(9H)xanthen)-3-one derivatives. These are used as dyes, as indicators for various metals, and as fluorescent labels in immunoassays.
A proposed family of bacteria belonging to the alpha-2 subgroup of PROTEOBACTERIA.
A genus of gram-negative, anaerobic, rod-shaped bacteria. Its organisms are normal inhabitants of the oral, respiratory, intestinal, and urogenital cavities of humans, animals, and insects. Some species may be pathogenic.
Ribonucleic acid that makes up the genetic material of viruses.
The discarding or destroying of garbage, sewage, or other waste matter or its transformation into something useful or innocuous.
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)
A class in the phylum PROTEOBACTERIA comprised mostly of two major phenotypes: purple non-sulfur bacteria and aerobic bacteriochlorophyll-containing bacteria.
Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.
Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.
A subtype of HLA-DRB beta chains that includes over one hundred allele variants. The HLA-DRB1 subtype is associated with several of the HLA-DR SEROLOGICAL SUBTYPES.
The presence of bacteria, viruses, and fungi in food and food products. This term is not restricted to pathogenic organisms: the presence of various non-pathogenic bacteria and fungi in cheeses and wines, for example, is included in this concept.
A phylum of ARCHAEA comprising at least seven classes: Methanobacteria, Methanococci, Halobacteria (extreme halophiles), Archaeoglobi (sulfate-reducing species), Methanopyri, and the thermophiles: Thermoplasmata, and Thermococci.
Measurement of the intensity and quality of fluorescence.
A group of PROTEOBACTERIA represented by morphologically diverse, anaerobic sulfidogens. Some members of this group are considered bacterial predators, having bacteriolytic properties.
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.
The study of the structure, growth, function, genetics, and reproduction of viruses, and VIRUS DISEASES.
The functional hereditary units of FUNGI.
A genus of microorganisms of the order SPIROCHAETALES, many of which are pathogenic and parasitic for man and animals.
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.
Techniques used in studying bacteria.
The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).
The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
Plasmids containing at least one cos (cohesive-end site) of PHAGE LAMBDA. They are used as cloning vehicles.
The complete absence, or (loosely) the paucity, of gaseous or dissolved elemental oxygen in a given place or environment. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Incorporation of biotinyl groups into molecules.
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.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.
Techniques used for determining the values of photometric parameters of light resulting from LUMINESCENCE.
A toxin produced by certain pathogenic strains of ESCHERICHIA COLI such as ESCHERICHIA COLI O157. It is closely related to SHIGA TOXIN produced by SHIGELLA DYSENTERIAE.
The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.
The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.
An enzyme that catalyzes the conversion of an orthophosphoric monoester and water to an alcohol and orthophosphate. EC
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
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.
A superfamily of proteins containing the globin fold which is composed of 6-8 alpha helices arranged in a characterstic HEME enclosing structure.
Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.
DNA present in neoplastic tissue.
Elements of limited time intervals, contributing to particular results or situations.
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.
Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.
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.
A genus of gram-negative, anaerobic, rod-shaped bacteria capable of reducing sulfur compounds to hydrogen sulfide. Organisms are isolated from anaerobic mud of fresh and salt water, animal intestines, manure, and feces.
The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.
Proteins obtained from ESCHERICHIA COLI.
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.
A genus of gram-positive, rod-shaped bacteria whose organisms are nonmotile. Filaments that may be present in certain species are either straight or wavy and may have swollen or clubbed heads.
Bacteria which lose crystal violet stain but are stained pink when treated by Gram's method.

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)

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 ...
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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 by amplification refractory mutation ...
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 ...
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, ...
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 are described, together with related arrays and oligonucleotide probes.
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Oligonucleotide quantification methods and units can vary between manufacturers. Be sure you accurately measure and dilute your DNA and RNA oligos.
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 E8/E9 and E9/E10 probes on a representative genomic DNA panel. There is no difficulty in distinguishing a
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. . ...
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 ...
হিস্টিরিয়া একটি নিউরোসিস রোগ। এ রোগটি শারীরিক সমস্যা বা মানসিক সমস্যা নিয়ে প্রকাশ পেতে পারে।যাদের হিস্টিরিয়া রয়েছে তারা সাধারণত কোনো না কোনো ফোবিয়ায় আক্রান্ত, অনিয়মতান্ত্রিক জীবন-যাপন ও মানসিক অবসাদগ্রস্ত থাকেন।
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%. ...
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 ...
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 ...
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
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 ...
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.
Imaging products of gene expression in live cells will provide unique insights into the biology of cells. Molecular beacons make attractive probes for imaging mRNA in live cells as they can report the presence of an RNA target by turning on the fluorescence of a quenched fluorophore. However, when oligonucleotide probes are introduced into cells, they are rapidly sequestered in the nucleus, making the detection of cytoplasmic mRNAs difficult. We have shown that if a molecular beacon is linked to a tRNA, it stays in the cytoplasm and permits detection of cytoplasmic mRNAs. Here we describe two methods of linking molecular beacons to tRNA and show how the joint molecules can be used for imaging an mRNA that is normally present in the cytoplasm in live cultured cells. This protocol should take a total of 4 d to complete.
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
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.
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.
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
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 ...
is also predominant in West Central and East African countries where other subtypes cocirculate.. We developed and validated a relatively simple oligonucleotide probe hybridization ...
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…
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 (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 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. ...
OligoProber are specific oligonucleotide probes for hybridization to its cognate species. These are specially designed 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 5OH 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. ...
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
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 ...
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. ...
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.
Latest issue of IDTs DECODED newsletter offers informative oligonucleotide selection guide Integrated DNA Technologies (IDT), the world leader in oligonucleotide synthesis, provides a guide to choosing the right oligonucleotide modification in this quarters edition of the companys DECODED newsletter. As IDT offers hundreds of useful modifications for oligonucleotides, choosing the appropriate one for your work can be confusing. The article provides insightful information to help when choosing the right modification, including a detailed list of the modification categories...
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 ...
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 ...
Locate Beacon App for iOS. Finds any nearby beacon with real-time distance estimates. Displays identifiers of each beacon discovered. Provides alerts when beacons are around. Allows you to calibrate beacons.
Sequence diversity within the HA-1 gene as detected by melting temperature assay without oligonucleotide probes: ral ss BioMed CentBMC Medical
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 Published by spinvestconsulting at [Report Price $3400] 108 Pages
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"The oligonucleotide probe database". Applied and Environmental Microbiology. 62 (10): 3557-3559. Bibcode:1996ApEnM..62.3557A. ...
Here, traditional, linear oligonucleotide probes failed to yield results. Thus, padlock probes possess sufficient specificity ... If array-based approach is used, the probe may optionally contain a probe-specific tag that uniquely identifies the probe as ... similar to the probe-release site, is also a restriction site. Anneal probe to genomic target DNA Probes are added to the ... resulting in a fully circularized probe. Remove non-reacted probes Since gap filling is not performed for non-reacted probes, ...
Podyminogin, M. A.; Lukhtanov, E. A.; Reed, M. W. (2001). "Attachment of benzaldehyde-modified oligodeoxynucleotide probes to ... Oligonucleotide phosphorothioates (OPS) are modified oligonucleotides where one of the oxygen atoms in the phosphate moiety is ... Typically, synthetic oligonucleotides are single-stranded DNA or RNA molecules around 15-25 bases in length. Oligonucleotides ... 1) Most often, 5'-DMT group is removed at the end of the oligonucleotide chain assembly. The oligonucleotides are then released ...
Cell engineering methods including fluorogenic oligonucleotide signaling probes may be used to detect and isolate clonal cell ... May 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 ... 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 ...
"Prenatal diagnosis of neonatal alloimmune thrombocytopenia using allele-specific oligonucleotide probes". Blood. 78 (9): 2276- ...
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 ...
"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. 43 (5): ...
"Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays". Nucleic Acids Research. 30 (17): ...
March 2021). "Cell engineering method using fluorogenic oligonucleotide signaling probes and flow cytometry". Biotechnology ...
"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 ...
"Detection of target-probe oligonucleotide hybridization using synthetic nanopore resistive pulse sensing". Biosensors and ...
"Identification and classification of Oxalobacter formigenes strains by using oligonucleotide probes and primers". Journal of ... Interestingly, analysis with the DNA probes showed that group 2 may be further divided into two subgroups. Whole genome ... and DNA probes specific to the oxc (oxalyl-CoA decarboxylase) gene and frc (formyl-CoA transferase), O. formigenes has been ...
... 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- ...
"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 ...
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- ...
"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 Research. 30 (17): ...
This ncRNA was originally identified in E.coli using high-density oligonucleotide probe arrays (microarray). The function of ... "Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays". Nucleic Acids Res. 30 (17): 3732- ...
... this type of probe is known as an allele-specific oligonucleotide. One of the bead types will correspond to the methylated ... Both bead types are attached to single-stranded 50-mer DNA oligonucleotides that differ in sequence only at the free end; ... This assay is used for methylation probes on the Illumina Infinium HumanMethylation27 BeadChip (henceforth, 27k [methylation] ... and hybridized to the chip via allele-specific annealing to either the methylation-specific probe or the non-methylation probe ...
As another strategy for targeting RNA, antisense oligonucleotides were developed which have been pushed forward through the ... "Using Genome Sequence to Enable the Design of Medicines and Chemical Probes". Chemical Reviews. 118 (4): 1599-1663. doi:10.1021 ... While backbone modifications to antisense oligonucleotides in order to prevent nuclease degradation have been shown to work, ... one can identify an RNA involved in disease then the sequence can be used to design a complementary antisense oligonucleotide, ...
Each probe pair consists of two oligonucleotides, with sequence that recognizes adjacent sites of the target DNA, a PCR priming ... Pairs of probes are hybridized to the sample DNA, with each probe pair designed to query for the presence of a particular DNA ... The fragments obtained from digestion are recircularized and linked The probe design is quite similar. Each probe will be ... For example, probes may be designed to target various regions of chromosome 21 of a human cell. The signal strengths of the ...
... probes identify the cells based on the binding of fluorescent probes to individual cells through use of oligonucleotides that ... The use of multiple probes with different fluorescent dyes allows for the identification of different cell types in the same ...
Each probe for the detection of mRNA and lncRNA is composed of ~20-50 oligonucleotide pairs, each pair covering a space of 40- ... The mixture of probe sequences determines the type of feature the probe can detect. Probes that hybridize along an entire ... cellular placement of the probe Probe size is important because shorter probes hybridize less specifically than longer probes, ... In biology, a probe is a single strand of DNA or RNA that is complementary to a nucleotide sequence of interest. RNA probes can ...
... of the two different genomes are labeled with different fluorophores and co-hybridized to a microarray with probes specific to ... Representational oligonucleotide microarray analysis (ROMA) is a technique that was developed by Michael Wigler and Rob Lucito ... 2003) Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. ...
"Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and ... Quenching (fluorescence) Didenko, V. V. (November 2001). "DNA probes using fluorescence resonance energy transfer (FRET): ... Tyagi, Sanjay; Kramer, Fred Russell (March 1996). "Molecular Beacons: Probes that Fluoresce upon Hybridization". Nature ... "Evaluation of dual-labeled fluorescent DNA probe purity versus performance in real-time PCR". BioTechniques. 36 (2): 266-270, ...
Placement of a TINA molecule in the oligonucleotide is capable of improving the analytical sensitivity of the probe ... Para-TINA molecules decreases Tm in all positions especially when at the center of the oligonucleotide, while in the ortho-TINA ... Triple helixes are formed when a single-stranded triplex-forming oligonucleotide (TFO) binds to a purine-containing strand of ... Twisted intercalating nucleic acid (TINA) is a nucleic acid molecule that, when added to triplex-forming oligonucleotides (TFOs ...
Instead of probing for sequences of known or predicted genes that may be dispersed throughout the genome, tiling arrays probe ... Another study with Arabidopsis used high-density oligonucleotide arrays that cover the entire genome. More than 10 times more ... Overlapping probes or probes in very close proximity can be used. This gives an unbiased analysis with high resolution. Besides ... or the amount of known base pairs between probe sequences, as well as probe length. For smaller genomes such as Arabidopsis, ...
The probe types used for non-polymorphic arrays include cDNA, BAC clones (e.g., BlueGnome), and oligonucleotides (e.g., Agilent ... Knowing the address of each probe on the array and the address of each probe in the genome, the software lines up the probes in ... The arrays themselves can be genome-wide (probes distributed over the entire genome) or targeted (probes for genomic regions ... Further, arrays used for karyotyping may use non-polymorphic probes, polymorphic probes (i.e., SNP-containing), or a ...
... allele specific oligonucleotide (ASO) probes, and hybridization to DNA microarrays or beads. Genotyping is important in ...
... -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 ...
Secondly, a probe containing the complementary functional group is introduced to react and label the substrate. Although ... Its primary use has been in labeling DNA and RNA in automated oligonucleotide synthesizers, and polymer crosslinking in the ... Kinetics: The reaction must be rapid so that covalent ligation is achieved prior to probe metabolism and clearance. The ... BARAC has sufficient rate (and sensitivity) to the extent that washing away excess probe is unnecessary to reduce background. ...
Antagomirs are single strand RNAs that are complementary, which have been chemically engineered oligonucleotides that silence ... Cyp2e1 mediated hydroxylation of its probe drug chlorzoxazone to its metabolite, 6-hydroxychlorzoxazone, correlated negatively ...
The oligonucleotide probe may also be blocked at the 3' end preventing equivalent extension of the probe, but this is not ... The oligonucleotides interact with each other in pairs; one oligonucleotide probe and one universal primer (containing ... Once hybridized, the universal primer can be extended, using the oligonucleotide probe as the template, to yield fully formed, ... The probe is not consumed; it is available to act as a template for the universal primer to be 'converted' into target specific ...
TaqMan probes TaqMan probes are oligonucleotides that have a fluorescent probe attached to the 5' end and a quencher to the 3' ... Molecular beacon probes Similar to the TaqMan probes, molecular beacons also make use of FRET detection with fluorescent probes ... Scorpion probes The scorpion probes, like molecular beacons, will not be fluorescent active in an unhybridized state, again, ... Multiplex probes TaqMan probes, molecular beacons, and scorpions allow the concurrent measurement of PCR products in a single ...
"Quantification of syntrophic fatty acid-β-oxidizing bacteria in a mesophilic biogas reactor by oligonucleotide probe ...
For the "in situ" detection of miRNA, LNA or Morpholino probes can be used. The locked conformation of LNA results in enhanced ... Biology portal Anti-miRNA oligonucleotides Gene expression List of miRNA gene prediction tools List of miRNA target prediction ... miRNAs can also be hybridized to microarrays, slides or chips with probes to hundreds or thousands of miRNA targets, so that ... You Y, Moreira BG, Behlke MA, Owczarzy R (May 2006). "Design of LNA probes that improve mismatch discrimination". Nucleic Acids ...
January 2009). "Customized oligonucleotide array-based comparative genomic hybridization as a clinical assay for genomic ... and the detection of genetic problems in the cells may require visualizing the DNA changes with fluorescent probes by FISH. CLL ...
FAM is used in the preparation of fluorescein-labeled oligonucleotide probes for the detection of the presence of the ... Oligonucleotides labeled with fluorescein at one of the termini and with a quencher at the other can serve as molecular beacons ... Fluorescein amidites, abbreviated as FAM, are important synthetic equivalents of fluorescein dye used in oligonucleotide ...
Then, the remaining unbound probes are washed out, the fluorescent signal from the bound probe is measured, and the bound probe ... 2 Base Encoding, also called SOLiD (sequencing by oligonucleotide ligation and detection), is a next-generation sequencing ... The ligation is performed using specific 8-mer probes: These probes are eight bases in length with a free hydroxyl group at the ... 9-mer probes which distinguished a different base according to the probes label and non degenerate base. This process was ...
The surface of the beads contains oligonucleotide probes with sequences that are complementary to the adaptors binding the DNA ... Non-ligated probes are washed away, followed by fluorescence imaging to determine the identity of the ligated probe. The cycle ... In its simplest form, a fluorescently labelled probe hybridizes to its complementary sequence adjacent to the primed template. ... is not carried out by polymerases but rather by DNA ligase and either one-base-encoded probes or two-base-encoded probes. ...
The Oligonucleotide Synthesis component of this facility makes conventional, long (up to 120 bases) and modified ... probe selection). It also provides cDNA library screening and quantitative PCR. The Genetic Analysis area includes capillary- ... oligonucleotides, and purifies these by desalting, cartridge or high-performance liquid chromatography (HPLC). The Microarray ...
The life science business unit specializes in genomics, and involves the development of oligonucleotides, DNA polymerases, Real ... qPCR Probes, assay services, and proteomics. The proteomics operations are primarily concerned with custom peptides and ... 2008: Eurogentec received ISO 13485 Certification for the production and sales of In Vitro Diagnostics (IVD) oligonucleotides ... Two years after EGT NA also received ISO 13485 certification for the Oligonucleotide diagnostics manufacturing. 2009 October, ...
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 ...
... the oligonucleotide probes of DNA microarrays. Annealing, in genetics, means for complementary sequences of single-stranded DNA ... The term annealing is often used to describe the binding of a DNA probe, or the binding of a primer to a DNA strand during a ... For DNA oligonucleotides, i.e. short sequences of DNA, the thermodynamics of hybridization can be accurately described as a two ... Oligonucleotides, DNA, or RNA will bind to their complement under normal conditions, so two perfectly complementary strands ...
To capture genomic regions of interest using in-solution capture, a pool of custom oligonucleotides (probes) is synthesized and ... The probes (labeled with beads) selectively hybridize to the genomic regions of interest after which the beads (now including ... Microarrays use hybridization probes to test the prevalence of known DNA sequences, thus they cannot be used to identify ... In solution capture (as opposed to hybrid capture) there is an excess of probes to target regions of interest over the amount ...
... paternity cases referred to seven different German laboratories for multilocus DNA fingerprinting with oligonucleotide probe ( ... Paternity testing with oligonucleotide multilocus probe (CAC)5/(GTG)5: a multicenter study Forensic Sci Int. 1993 May;59(2):101 ... paternity cases referred to seven different German laboratories for multilocus DNA fingerprinting with oligonucleotide probe ( ... confirms previous findings for other multilocus probes. A goodness-of-fit test on the normalized number of bands scored per ...
Here, we show that long-adapter single-strand oligonucleotide (LASSO) probes can capture and clone thousands of kilobase DNA ... A library of single-strand oligonucleotide probes with a common long-adapter sequence can clone, in a single reaction, ... LASSO probes could be used for the preparation of long-read sequencing libraries and for massively multiplexed cloning. ... We also show that LASSO probes can clone human ORFs from complementary DNA, and an ORF library from a human-microbiome sample. ...
US-5952201-A chemical patent summary.
Several probe background options,Unique probe within a group , Unique probe in a specific Unigene set , Unique probe based ... This probe design workflow is now upgraded to satisfy experiments that require a probe designing tool to take the increasing ... Probes designed by the UPS algorithm are suitable for generating microarrays, and the performance of UPS-designed probes has ... Parameters, such as salt concentration and the lower-bound Tm of probes, are available for users to optimize their probe design ...
We have designed an oligonucleotide probe for use in fluorescent in situ hybridization (FISH) and two pairs of PCR primers ... The FISH probe and one of the PCR primer pairs are suitable for quantification of C. testosteroni in mixed microbial ... The oligonucleotides presented here provide a useful tool to study C. testosteroni population dynamics in mixed microbial ... From: Design and evaluation of 16S rRNA sequence based oligonucleotide probes for the detection and quantification of Comamonas ...
... as well as 11,479 16S rRNA bacterial probes, 1,120 18S rRNA fungal probes, and 848 18S rRNA parasite probes. A total of 300 ... Fluorescently labeled synthetic oligonucleotides complementary to the control probes were included in all hybridizations. ... The 10 positive probes aligned with all 8 MARV gene motifs represented on the array (Figure 1B). Only 4 (17%) of 23 probes were ... GreeneChipPm version 1.0 contained 29,495 probes that included probes comprising GreeneChipVr version 1.0, ...
BNA-oligonucleotide probes were designed to specifically bind to telomere repeats. Researchers at the UTSW Medical Center, ... Compared with commercially available DIG-labeled telomere probes, probes generated using this new approach significantly ... containing oligonucleotides (ONTs). Using our method, we were able to generate probes to detect both C- and G-rich telomeric ... Oligonucleotides , Peptides , Bioconjugation , Organic Synthesis , Molecular Biology , Protein Services , Bioanalytical , ...
We deliver oligonucleotides in various grades for research, diagnostic or commercial applications. ... We produce custom qPCR probes and labeled oligonucleotides with the original BHQ® molecules. ... By purchasing your BHQ® labeled oligonucleotides and qPCR Probes from Eurogentec you can use them for diagnostic and commercial ... Diagnostic Grade Oligonucleotides Research Grade Oligonucleotides. Research grade Oligonucleotides can be easily ordered via ...
Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection. BMC ...
Custom LNA-enhanced oligonucleotides for a range of applications ... On the right, LNA substitutions allow shortening of the probe, ... Custom LNA Oligonucleotides. Custom LNA Oligonucleotides. Custom LNA Oligonucleotides. For experiments requiring custom- ... For Custom LNA Oligonucleotide Large Scale and Custom LNA Oligonucleotide Manual Design, please contact us for ordering and for ... This is important when the oligonucleotide is used to detect small or highly similar targets. Since LNA oligonucleotides ...
This qualitative in-vitro diagnostics test uses oligonucleotide probes labeled with four different fluorescent dyes. The ...
Polymorphism of murine endogenous proviruses revealed by using virus class-specific oligonucleotide probes. J Virol. 1988;62: ... Furthermore, our probe does not hybridize to some of the genes shown to be regulated by elements of MER41 subfamilies (e.g., ... Our strategy to probe TE interaction frequency across the genome, consists of using 4C-Seq with primers that hybridize to the ... c Hi-C and Capture-4Tran using the MER41 probe. Boxes in the top panels show zoomed in views from the bottom panels. Data from ...
Oligonucleotide Synthesis Market Size - USD 3.98 billion in 2019, Market Growth - CAGR of 12.8 %, Market Trends - The rise in ... Oligonucleotide Synthesis Market Future development, Key Business Strategies and Deep Exploration Till 2027. Emergen Research ... The report offers a complete analysis of the global Oligonucleotide Synthesis market on a global and regional scale and offers ... VANCOUVER, BC, CANADA, August 10, 2022 / -- The global Oligonucleotide Synthesis Market1 is forecasted to be ...
All probes synthesized with FAM (fluorescein) and black hole quencher 1 (BHQ1) from Biosearch Technologies. ... Quantitative PCR primer and probes used to target specific genes and organisms in tubewell water samples ... temperature) Oligonucleotide sequences. a. Reference. E. coli 23S rRNA. (fluorogenic probe, ... Quantitative PCR primer and probes used to target specific genes and organisms in tubewell water samples ...
Incorporate locked nucleic acid monomers to increase PCR probe Tm, heighten target specificity, impart nuclease resistance, ... When incorporated into an oligonucleotide probe, locked nucleic acid monomers impart heightened structural stability, resulting ... locked nucleic acid qPCR probes can be designed with shorter lengths than standard probes. Shorter probes are more effectively ... Affinity Plus qPCR Probes. Use Affinity Plus qPCR Probes for SNP genotyping, transcript variant identification, and sensitive ...
The assay relies on the hybridization of the target DNA with the silver nanoparticle-oligonucleotide DNA probe, followed by the ... using silver nanoparticles as the oligonucleotide labeling tag, is described. ... oligonucleotide. DNA probe, followed by the release of the silver metal atoms anchored on the hybrids by oxidative metal ... oligonucleotide. labeling tag, is described. The assay relies on the hybridization of the target DNA with the silver ...
The development of specific rRNA-derived oligonucleotide probes for Haemophilus ducreyi, the causative agent of chancroid Rudi ... ducreyi strains revealed that all eight oligonucleotide probes were highly reliable and completely specific for H. ducreyi ... From the nucleotide sequence, eight oligonucleotides complementary to different regions in the 16S and 23S rRNA molecules were ... selected, chemically synthesized, and used as hybridization probes. Hybridization experiments with at least 41 H. ducreyi ...
A typing system for neisseria gonorrhoeae based on biotinylated oligonucleotide probes to pib gene variable regions. J Infect ... Bash MC, Zhu P, Gulati S, McKnew D, Rice PA, Lynn F. por Variable-region typing by DNA probe hybridization is broadly ...
Custom double dye probes with a wide range of fluorophores and quenchers. Free primers offered. Our offer covers all qPCR ... Double-Dye probes Principle. Double-Dye Oligonucleotides have a fluorescent reporter dye and a quencher at their 5 and 3 ends ... We provide Classical and LNA® Double-Dye probes.. Compared to DNA Double-Dye probes, LNA® Double-Dye probes exhibit higher ... Probe Design: Available on request. *Larger scales are available on request. ***Higher scales from 2.5 µmol may be delivered in ...
Using the probe design feature of the ARB software, an oligonucleotide probe, PricSym652 (5′-TATCCCCTT CTGTTCTCT-3′, spanning E ... Stoecker, K., Dorninger, C., Daims, H., and Wagner, M. (2009). Double labeling of oligonucleotide probes for Fluorescence In ... a web tool that uses thermodynamics-based mathematical models for In Silico evalulation of oligonucleotide probes for ... a central resource for evaluating oligonucleotide probe coverage and specificity. Environ. Microbiol. 10, 2894-2896. doi: ...
Order QPCR Probes. Want to order custom qPCR probes and primers? We offer many different probe formats including BHQ and ... Supports and reagents for therapeutic oligonucleotides * Marker-assisted selection (MAS) and Marker-assisted breeding (MAB) * ... GMP and commercial oligonucleotides. LGC Biosearch Technologies provides comprehensive, cost-effective nucleic acid services. ... An online account also provides you free access to various design software such as RealTimeDesign™ Software, Stellaris® Probe ...
on Adhered Bacteria in Percolated Columns Monitored by In Situ Hybridization with Fluorescent Oligonucleotide Probes. Appl. ... Haig, S.J.; Schirmer, M.; DAmore, R.; Gibbs, J.; Davies, R.L.; Collins, G.; Quince, C. Stable-isotope probing and metagenomics ...
Solid phase synthesis of oligonucleotides and analogues. *oligonucleotide synthesis, modification and conjugation including DNA ... construction or reactive probes incorporating caged reactive functionalities for nucleic acid target identification ...
in reduction buffer for RNA Sequential Probing of Targets (SPOTs) imaging. *for the reduction of oligonucleotides ...
Oligonucleotide probes were 3′ end-labeled with (γ33P)dATP and terminal transferase (NEN, Hounslow, UK). Pretreatment of ... Using appropriate oligonucleotide probes (see Materials and Methods), we found α1- and α2-chimaerin mRNA expression to differ ... In situ hybridization. Oligonucleotide probes used forin situ hybridization were: sequences complementary to α2-chimaerin- ... and oligonucleotide probe diluted to 2× 107 cpm/ml. Glass coverslips were removed in 2× SSC at room temperature (RT). Washes, ( ...
Associates said this week that it will supply Applied Biosystems with a reagent required to make oligonucleotide probes for the ... Associates to Supply ABI with Oligo Probe Component for SOLiD Berry & ... Berry & Associates said this week that it will supply Applied Biosystems with a reagent required to make oligonucleotide probes ... affinity products for oligonucleotide purification and BlackBerry quenchers for use in fluorogenic oligonucleotide probes. ...
OligoMiner: A rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes ... Oligonucleotide (oligo)-based fluorescence in situ hybridization (FISH) has emerged as an important tool for the study of… ...
  • High-density oligonucleotide arrays (HDONAs) are a powerful tool for assessing differential mRNA expression levels. (
  • Figure 1: Synthesis of the DNA LASSO probe components. (
  • Oligonucleotide Synthesis Market Size - USD 3.98 billion in 2019, Market Growth - CAGR of 12.8 %, Market Trends - The rise in the synthesized oligonucleotides applications. (
  • VANCOUVER, BC, CANADA, August 10, 2022 / / -- The global Oligonucleotide Synthesis Market 1 is forecasted to be worth USD 9.91 Billion by 2027, according to a current analysis by Emergen Research. (
  • The rising need for sophisticated treatment techniques can be linked to the swift expansion of the worldwide oligonucleotide synthesis industry. (
  • The report offers a complete analysis of the global Oligonucleotide Synthesis market on a global and regional scale and offers a forecast for the market for 8 years. (
  • Under the five-year agreement, the company, which is based in Dexter, Mich., will provide ABI with a custom nucleoside phosphoramidite that meets purity standards required for the synthesis of the oligonucleotide probes. (
  • Our wide range of reagents with unrivaled quality provides a single source for your oligonucleotide synthesis reagents-simplifying your supply chain so you can focus on your science and accelerate your path forward. (
  • Synthesise oligonucleotides containing a 5' or 3'-phosphate group with our phosphoramidites, CPGs and synthesis columns. (
  • This probe design workflow is now upgraded to satisfy experiments that require a probe designing tool to take the increasing volume of sequence datasets. (
  • Algorithms and probe parameters applied in UPS 2.0 include GC content, the secondary structure, melting temperature (Tm), the stability of the probe-target duplex estimated by the thermodynamic model, sequence complexity, similarity of probes to non-target sequences, and other empirical parameters used in the laboratory. (
  • Several methods have been derived based on this principle to detect targets using sequence-specific probes ( e.g. , northern blot, southern blot, and in situ hybridization). (
  • Usually, in dual-labeled qPCR Probes, Black Hole Quenchers are conjugated to the 3'end of the nucleic acid sequence. (
  • When locked nucleic acid modified bases are incorporated into a DNA sequence (such as a qPCR probe), its duplex melting characteristics are changed, resulting in increased T m . (
  • Locked nucleic acid oligonucleotides are useful in template switching oligo designs and for strengthening target oligo binding in challenges sequence regions, such as AT-rich areas. (
  • a) In Spotted microarrays, the probes are synthesized prior to deposition on the array surface and are then 'spotted' onto glass while in oligonucleotide microarrays, the probes are short sequences designed to match parts of the sequence of known or predicted open reading frames. (
  • b) A probe is a single-stranded sequence of DNA or RNA used to search for its complementary sequence in a sample genome. (
  • The probe is placed into contact with the sample under conditions that allow the probe sequence to hybridize with its complementary sequence. (
  • The coverage of these probes in relation to the present sequence database is discussed. (
  • We have been synthesizing custom oligonucleotides and qPCR probes labeled with the original BHQ® quencher dyes for decades. (
  • By purchasing your BHQ® labeled oligonucleotides and qPCR Probes from Eurogentec you can use them for diagnostic and commercial applications without license fees. (
  • BHQ® quenchers are the most popular and used quenchers for fluorescence quenched qPCR probes as they absorb a wide range of wavelengths from 480 nm to 730 nm. (
  • Because of the afforded increase in T m , locked nucleic acid qPCR probes can be designed with shorter lengths than standard probes. (
  • These probes also show greater mismatch discrimination compared to traditional qPCR probes. (
  • As with locked nucleic acid qPCR probes, hybridization T m can be manipulated by the number of locked nucleic acid bases incorporated. (
  • IDT provides 2 types of locked nucleic acid products: Custom Affinity Plus DNA & RNA Oligonucleotides, and Affinity Plus qPCR Probes. (
  • While Affinity Plus modified sequences provide identical performance to traditional LNA ® sequences, PrimeTime Affinity Plus qPCR Probes and custom Affinity Plus DNA & RNA Oligonucleotides are a better value. (
  • Use Affinity Plus qPCR Probes for SNP genotyping, transcript variant identification, and sensitive target detection in challenging samples (FFPE tissue, biofluids). (
  • Want to order custom qPCR probes and primers? (
  • We provide Classical and LNA ® Double-Dye probes. (
  • Compared to DNA Double-Dye probes, LNA ® Double-Dye probes exhibit higher thermal stabilities, specificity and reproducibility . (
  • Furthermore, LNA ® offers the possibility to adjust Tm values of primers and probes in multiplex assays. (
  • Oligonucleotide primers and probes are key diagnostic agents of today's molecular diagnostic methods. (
  • Two new algorithms have been developed which help to improve the search and evaluation step of suitable binding sites of primers and probes on genetic material. (
  • Padlock probes: circularizing oligonucleotides for localized DNA detection. (
  • Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping. (
  • Here we present a generalized version of the RNA -mediated oligonucleotide Annealing Selection and Ligation with next generation DNA sequencing (RASL-seq) assay, called "capture RASL-seq" (cRASL-seq), which enables highly sensitive (down to ~1-100 pfu/ml or cfu/ml) and highly multiplexed (up to ~10,000 target sequences) detection of pathogens. (
  • A novel, sensitive electrochemical DNA hybridization detection assay, using silver nanoparticles as the oligonucleotide labeling tag, is described. (
  • The combination of the remarkable sensitivity of the stripping metal analysis at the microelectrode with the large number of silver( I ) ions released from each DNA hybrid allows detection at levels as low as 0.5 pmol L −1 of the target oligonucleotides . (
  • Real-time multiplex assays utilizing PCR amplification have been demonstrated with TaqMan dual-labeled linear probes and the 5′ nuclease detection process and, alternatively, with PCR amplification and molecular beacon probes, Tyagi. (
  • Detection and typing of NDV, IBV, or AIV using oligonucleotide microarrays. (
  • With our extensive library of reagents, you can synthesise oligos with your modification of choice-from conjugation chemistry to cell delivery to probe detection, we've got you covered. (
  • The CDC Influenza SARS-CoV-2 (Flu SC2) Multiplex ValuPanel Reagents - which are for research use only and not for use in diagnostic procedures - consists of probes and primers for multiplex RT-PCR detection and allows discrimination of SARS-CoV-2, influenza A, and influenza B from a single patient sample. (
  • It has previously provided detection solutions for viruses including seasonal influenza, H1N1 (swine flu), Chikungunya, Zika, and Ebola and also has CDC-qualified lots of SARS-CoV-2 probe and primer kits available for sale. (
  • The lab protocol for probe hybridization is further optimized and miniaturized into microarray format to detect transcriptional activity of thousands of genes simultaneously [ 1 ]. (
  • The selection of suitable oligonucleotide probes remains a bottleneck in the microarray workflow [ 2 ]. (
  • Thus, to address the challenge of more highly multiplexed differential diagnoses, we established an oligonucleotide microarray platform. (
  • Reference and validation studies were performed on different microarray platforms with different probe sets and probe content. (
  • A supervised pathway-based analysis enhances the understanding of the biological context of the results, the comparability of results across different microarray studies, and reduces multiple testing problems by focusing on a limited number of pathways of interest instead of analyzing the large number of probes available on the microarray. (
  • The UPS 2.0 evaluates probe-to-target hybridization under a user-defined condition to ensure high-performance hybridization with minimal chance of non-specific binding at the pangenomic and genomic levels. (
  • Perioperative genomic profiles using structure-specific oligonucleotide probes. (
  • Nucleic acid hybridization is an extensively adopted principle in biomedical research, in which the performance of any hybridization-based method depends on the specificity of probes to their targets. (
  • The performance of these widely adopted methods depends on the specificity of probes to their targets. (
  • Kits for highly multiplexed homogeneous in vitro screening assays for numerous possible nucleic acid targets, any of which might be present in a sample, that utilize fluorescent hybridization probes that are combinatorially coded from a panel of fluorophores by subdividing each probe into portions and differently labeling each portion such that, when portions are combined, each probe has a unique code. (
  • 2'-O-Methyl oligoribonucleotide probes bind to RNA targets faster and with much higher melting temperatures at various probe length. (
  • The increased melt, faster kinetics of hybridization, ability to bind to structured targets and increased specificity of 2'-O-methyl oligoribonucleotide probes render them superior to corresponding 2'-deoxy oligoribonucleotides for use in assays that detect RNA targets. (
  • An in situ hybridization approach to labeling DNA and RNA targets in the specimen using oligonucleotide-based fluorescent probes. (
  • Prepare electrochemical oligo probes for nucleic acid analysis using ferrocene or methylene blue as the signaling redox moiety. (
  • Fluorescent probes are a kind of fluorescent molecules with characteristic fluorescence in the UV-visible-near infrared region, and their fluorescence properties (emission and excitation wavelength, intensity, polarization, lifetime) could be sensitively changed with the properties of the environment, such as polarity, refractive index, viscosity and so on. (
  • In the fluorescent molecular probe, the fluorophore reflects the molecular recognition function of the micro world by giving information such as the enhancement and weakening of fluorescence intensity and the shift of fluorescence peak wavelength. (
  • In inorganic analysis, the elements to be measured in inorganic compounds interact with organic reagents, and the complexes combined with fluorescent probes can emit fluorescence of different wavelengths under ultraviolet light, so as to determine the content of elements to be measured. (
  • The UPS 2.0 website has had more than 1,300 visits and 360,000 sequences performed the probe designing task in the last 30 months. (
  • Custom LNA Oligonucleotides are ideal for studies involving short or very similar sequences. (
  • The ValuPanel Reagents were designed to match the sequences and performance of the probes and primers from the CDC's Flu SC2 Multiplex Assay, which was granted EUA in July 2020. (
  • 4, 5 Complex cDNA probes can cross-hybridize to related sequences, and low-intensity hybridization indicators are challenging to interpret. (
  • Nucleic acids, either DNA or RNA, in a sample may be probed directly. (
  • In biochemical research, fluorescent probes can label antigens, antibodies and nucleic acids, detect the active sites of proteins, study the damage and repair of DNA base pairs and the chemical reaction activity of drug molecules, and complete the qualitative, quantitative and structural research of biological compounds. (
  • The company's first software platform, OMP™ (Oligonucleotide Modeling Platform™), models in silico the folding and hybridization of single-stranded nucleic acids with great accuracy. (
  • 2'-O-methylnucleotides offer advantages in kinetic and melting properties oligoribonucleotide probes. (
  • Because of their greatly enhanced Tm when bound to RNA, 2'-O-methyl oligoribonucleotide probes can efficiently bind to double-stranded regions of structured RNA molecules. (
  • Berry & Associates said this week that it will supply Applied Biosystems with a reagent required to make oligonucleotide probes for the SOLiD system. (
  • Fluorescent probes are also a kind of fluorescent chemical sensors. (
  • In industry, fluorescent probes can be used to determine the content of impurities in castings, so as to control the quality of products. (
  • In agriculture, fluorescent probes can be used to check the purity of agricultural products, identify the viability of seeds, detect the deterioration of agricultural products as soon as possible, judge the maturity of fruits and diagnose crop diseases and pests. (
  • In addition, fluorescent probes can also be used to detect the content of pesticides. (
  • BOC Sciences provides high-quality Fluorescent Probes and Fluorescent Dyes products for global customers. (
  • Use Affinity Plus DNA & RNA Oligonucleotides for increased hybridization T m , stability, and nuclease resistance over standard oligonucleotides. (
  • Amplification assays may be monitored in real time utilizing intercalating dyes, for example SYBR green, or fluorescently labeled probes, such as 5′ nuclease probes Livak, K. J. et al. (
  • Modifications at the 2′ position of the ribose ring are commonly used to help increase oligonucleotide stability and improve resistance to nuclease activity in vivo . (
  • RNA oligonucleotides synthesized using 2′-MOE modifications phosphoramidites have shown to be more nuclease resistant, with lower toxicity, and slightly increased hybridization affinities, making them well suited for therapeutic in vivo applications, such as ASO, siRNA, and aptamers. (
  • and 4) the designed primers, 5´-nuclease probes, and amplicons displayed no considerable homology to other viruses, including human CoV OC43 and 229E in BLAST searches (available from ). (
  • Assays may include oligonucleotide probes bearing detectable labels, for example, P 32 or fluorophores. (
  • Generate reliable hapten labelled probes with our biotinylation and DNP reagents. (
  • Each line of ValuPanel Reagents consists of separately delivered probes and primers, which allow assay flexibility and sizes that can help facilitate scale-up. (
  • By ordering your BHQ® probes from us, you will benefit from our know-how, our experience and the quality of the original BHQ® quenchers. (
  • Recently, it added fluorous affinity products for oligonucleotide purification and BlackBerry quenchers for use in fluorogenic oligonucleotide probes. (
  • LGC, Biosearch Technologies offers 1000+ phosphoramidites, nucleosides, solid supports and expert knowledge to ensure you can find exactly what you need to synthesise the ideal oligonucleotide and achieve your project goals faster. (
  • The assay relies on the hybridization of the target DNA with the silver nanoparticle - oligonucleotide DNA probe, followed by the release of the silver metal atoms anchored on the hybrids by oxidative metal dissolution and the indirect determination of the solubilized Ag I ions by anodic stripping voltammetry ( ASV ) at a carbon fiber ultramicroelectrode. (
  • This qualitative in-vitro diagnostics test uses oligonucleotide probes labeled with four different fluorescent dyes. (
  • 1995), Oligonucleotides with fluorescent Dyes at Opposite Ends Provide a Quenched Probe System Useful for Detecting PCR Product and Nucleic Acid Hybridization, PCR Meth. (
  • We are ISO 9001 and ISO 13485 certified for the development, production and sales of synthetic oligonucleotides in support of research, in vitro diagnostics and related applications. (
  • Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g. (
  • Prepare primer-probe mix containing a final concentration of 20 uM each primer and 10 uM each probe listed above. (
  • These factors subsequently impact the representation of low-abundance transcripts in the ultimate cDNA probe. (
  • The Santa Clara-based company currently has around 700 people in Weld County, where it makes therapeutic oligonucleotides, also known as "oligos. (
  • They show better mismatch discrimination which allows the use of shorter probes. (
  • Both the perfect-match (PM) probes and the differentials between PM and single-mismatch (MM) probes are considered as raw intensities. (
  • Background intensity was corrected as the difference between the perfect match (PM) and mismatch (MM) pair of each probe set. (
  • Use these probes in methods that use differential hybridization to distinguish polymorphisms. (
  • During the amplification process, the 5'>3' exonuclease activity of the Taq DNA polymerase cleaves the fluorophore from the probe. (
  • Especially in diseases with genetic causes, oligonucleotide chains offer a promising therapy approach - often the first ever. (
  • IMSEAR at SEARO: Diagnostic value of gene probes and its correlation with clinical profile of leprosy in children. (
  • Dayal R, Agarwal PK, Kalra K, Bharadwaj VP, Katoch VM, Katoch K. Diagnostic value of gene probes and its correlation with clinical profile of leprosy in children. (
  • Several probe background options, Unique probe within a group , Unique probe in a specific Unigene set , Unique probe based onthe pangenomic level , and Unique Probe in the user-defined genome/transcriptome , are available to meet the scenarios that the experiments will be conducted. (
  • Mark Dearden, Managing Director, Genomics, LGC, said, "LGC was one of the first companies to support the initial US public health response to COVID-19, partnering with the CDC to provide oligonucleotides used to support the CDC 2019-nCoV Real-Time PCR Diagnostic Panel. (
  • c) A probeset is the set of probes relating to a gene while a probeset summarization is a program for doing background subtraction, normalization and summarizing probe sets from Affymetrix expression microarrays. (
  • Therefore, translating the measured probe intensities into a global gene-intensity or ratio score requires a composite scoring function. (
  • These probes have the same or similar physiological and biochemical characteristics as the natural metabolites in the human body, so as to understand the changes in the functions, physiology and biochemistry, metabolism and gene expression of human organs. (
  • Two M. leprae specific gene probes were applied in 42 cases to assess their diagnostic value. (
  • This study highlights the immense potential of gene probes in diagnosing leprosy in children. (
  • When incorporated into an oligonucleotide probe, locked nucleic acid monomers impart heightened structural stability, resulting in increased hybridization melting temperature (T m ), both in vitro and in vivo (Figure 2). (
  • The formula for the melting temperature depends on the oligonucleotide concentration, the enthalpy ( δh ) and the entropy ( δs ) of the duplex. (
  • Another spatial-segregation probe technique is the use of multiplex probe arrays, including arrays on DNA chips. (
  • The parameters used in UPS include GC content, GC clamps, the duplex stability estimated by thermodynamic theory model, the secondary structure of probes, a low-complexity mask, and other empirical preferences of wet-lab researchers. (
  • Parameters, such as salt concentration and the lower-bound Tm of probes, are available for users to optimize their probe design query. (
  • Using oligonucleotide probes from the egr-1 responsive region of the VEGF promoter in EMSA, we demonstrated that SLS treatment resulted in the appearance of nuclear complexes that bound the VEGF promoter derived EMSA probe. (
  • Shorter probes are more effectively quenched and have a higher signal-to-noise ratio. (
  • To find the best, unique probe(s) for detecting target(s) from a sample cocktail, we developed an algorithm and implemented this algorithm in a probe design web platform, the Unique Probe Selector (UPS) [ 3 ]. (
  • Thus, this probe design tool is able to overcome the problem of background noise during hybridization. (
  • Several tools are available for probe design. (
  • OligoWiz2 [ 12 ] is a java-based server-client solution for probe design in a graphical user interface. (
  • Researchers can set up an SOL and refine the parameters when working on probe design tasks for other species. (
  • An online account also provides you free access to various design software such as RealTimeDesign™ Software, Stellaris® Probe Designer, and ChIRP Designer. (
  • Ann Arbor, Mich. - April 12, 2003 -The National Institute of Health ( NIH ) grant to develop PCR software has awarded DNA Software a Small Business Innovation Research Program (SBIR) Phase II Grant to enhance its existing Oligonucleotide Modeling Platform™ ( OMP ™) to develop advanced, high-throughput PCR design software . (
  • Molecular tools for a molecular medicine: analyzing genes, transcripts and proteins using padlock and proximity probes. (
  • Custom LNA Oligonucleotides are intended for molecular biology applications. (
  • We offer many different probe formats including BHQ and BHQplus probes, Molecular Beacons and Scorpions Primers. (
  • Single photon emission computed tomography (SPECT), one of the molecular imaging methods in nuclear medicine, involves the use of radioisotope-labelling probes. (
  • The recognition group in the fluorescent probe, also known as the receptor part, is the main part of the molecular recognition function of the probes. (
  • Probes designed by the UPS algorithm are suitable for generating microarrays, and the performance of UPS-designed probes has been validated by experiments. (
  • The evolution of the medicinal chemistry of oligonucleotides has been critical to the steadily improving performance of ASOs in the clinic. (
  • Using our method, we were able to generate probes to detect both C- and G-rich telomeric DNA strands. (
  • Research grade Oligonucleotides can be easily ordered via one of our configurators online. (
  • The statistical analysis is reported of 256 paternity cases referred to seven different German laboratories for multilocus DNA fingerprinting with oligonucleotide probe (CAC)5/(GTG)5 and restriction enzyme HinfI. (
  • Figure 2: Single ORF target capture with LASSO probes. (
  • To determine the optimal probe(s) for detecting target(s) from a sample cocktail, we developed a novel algorithm, which has been implemented into a web platform for probe designing. (
  • Thus, microbes can be detected when melting temperatures are high enough to allow hybridization, despite a lack of precise complementarity between probe and target. (
  • The influence of the relevant experimental variables, including the surface coverage of the target oligonucleotide , the duration of the silver dissolution steps and the parameters of the electrochemical stripping measurement of the silver( I ) ions, is examined and optimized. (
  • Nuclear medicine imaging is to introduce a small amount of imaging drugs called "probes" into the body and use emission computed tomography equipment to explore the dynamic and/or static distribution of "probes" in the human body or target organs. (
  • Currently there are two main approaches used to target RNA: double stranded RNA-mediated interference (RNAi) and antisense oligonucleotides (ASO). (