Oligonucleotides. Medical search

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)

Short fragments of DNA or RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.

The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.

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.

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.

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.

Modified oligonucleotides in which one of the oxygens of the phosphate group is replaced with a sulfur atom.

Short fragments of DNA that are used to alter the function of target RNAs or DNAs to which they hybridize.

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 spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.

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.

Nucleotides in which the base moiety is substituted with one or more sulfur atoms.

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.

Short fragments of RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.

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)

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.

A ribonuclease that specifically cleaves the RNA moiety of RNA:DNA hybrids. It has been isolated from a wide variety of prokaryotic and eukaryotic organisms as well as RETROVIRUSES.

Organic compounds that contain phosphorus as an integral part of the molecule. Included under this heading is broad array of synthetic compounds that are used as PESTICIDES and DRUGS.

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)

A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.

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.

High molecular weight polymers containing a mixture of purine and pyrimidine nucleotides chained together by ribose or deoxyribose linkages.

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.

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.

DNA that is complementary to the sense strand. (The sense strand has the same sequence as the mRNA transcript. The antisense strand is the template for mRNA synthesis.) Synthetic antisense DNAs are used to hybridize to complementary sequences in target RNAs or DNAs to effect the functioning of specific genes for investigative or therapeutic purposes.

An enzyme catalyzing the endonucleolytic cleavage of RNA at the 3'-position of a guanylate residue. EC 3.1.27.3.

The parts of a macromolecule that directly participate in its specific combination with another molecule.

Substances used for the detection, identification, analysis, etc. of chemical, biological, or pathologic processes or conditions. Indicators are substances that change in physical appearance, e.g., color, at or approaching the endpoint of a chemical titration, e.g., on the passage between acidity and alkalinity. Reagents are substances used for the detection or determination of another substance by chemical or microscopical means, especially analysis. Types of reagents are precipitants, solvents, oxidizers, reducers, fluxes, and colorimetric reagents. (From Grant & Hackh's Chemical Dictionary, 5th ed, p301, p499)

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.

Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.

Agents that are capable of inserting themselves between the successive bases in DNA, thus kinking, uncoiling or otherwise deforming it and therefore preventing its proper functioning. They are used in the study of DNA.

The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.

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.

The rate dynamics in chemical or physical systems.

Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.

The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.

Established cell cultures that have the potential to propagate 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.

Linear furanocoumarins which are found in many PLANTS, especially UMBELLIFERAE and RUTACEAE, as well as PSORALEA from which they were originally discovered. They can intercalate DNA and, in an UV-initiated reaction of the furan portion, alkylate PYRIMIDINES, resulting in PHOTOSENSITIVITY DISORDERS.

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.

Biologically functional sequences of DNA chemically synthesized in vitro.

Inorganic derivatives of phosphoric acid (H3PO4). Note that organic derivatives of phosphoric acids are listed under ORGANOPHOSPHATES.

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.

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.

DNA analogs containing neutral amide backbone linkages composed of aminoethyl glycine units instead of the usual phosphodiester linkage of deoxyribose groups. Peptide nucleic acids have high biological stability and higher affinity for complementary DNA or RNA sequences than analogous DNA oligomers.

A group of 13 or more deoxyribonucleotides in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.

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.

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).

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.

Double-stranded nucleic acid molecules (DNA-DNA or DNA-RNA) which contain regions of nucleotide mismatches (non-complementary). In vivo, these heteroduplexes can result from mutation or genetic recombination; in vitro, they are formed by nucleic acid hybridization. Electron microscopic analysis of the resulting heteroduplexes facilitates the mapping of regions of base sequence homology of nucleic acids.

Nucleotide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.

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.

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.

Ribonucleic acid that makes up the genetic material of viruses.

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.

Synthetic analogs of NUCLEIC ACIDS composed of morpholine ring derivatives (MORPHOLINES) linked by phosphorodimidates. One standard DNA nucleic acid base (ADENINE; GUANINE; CYTOSINE; OR THYMINE) is bound to each morpholine ring.

A group of 13 or more ribonucleotides in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.

A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.

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 group of thymine nucleotides in which the phosphate residues of each thymine nucleotide act as bridges in forming diester linkages between the deoxyribose moieties.

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.

The integration of exogenous DNA into the genome of an organism at sites where its expression can be suitably controlled. This integration occurs as a result of homologous recombination.

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.

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.

Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.

A naturally occurring furocoumarin, found in PSORALEA. After photoactivation with UV radiation, it binds DNA via single and double-stranded cross-linking.

The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.

An exotic species of the family CYPRINIDAE, originally from Asia, that has been introduced in North America. They are used in embryological studies and to study the effects of certain chemicals on development.

The chemical and physical integrity of a pharmaceutical product.

Higher-order DNA and RNA structures formed from guanine-rich sequences. They are formed around a core of at least 2 stacked tetrads of hydrogen-bonded GUANINE bases. They can be formed from one two or four separate strands of DNA (or RNA) and can display a wide variety of topologies, which are a consequence of various combinations of strand direction, length, and sequence. (From Nucleic Acids Res. 2006;34(19):5402-15)

The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.

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.

A pyrimidine base that is a fundamental unit of nucleic acids.

The fission of a CELL. It includes CYTOKINESIS, when the CYTOPLASM of a cell is divided, and CELL NUCLEUS DIVISION.

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.

A purine nucleoside that has guanine linked by its N9 nitrogen to the C1 carbon of ribose. It is a component of ribonucleic acid and its nucleotides play important roles in metabolism. (From Dorland, 28th ed)

DNA or RNA bound to a substrate thereby having fixed positions.

RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.

Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.

A phosphoric diester hydrolase that removes 5'-nucleotides from the 3'-hydroxy termini of 3'-hydroxy-terminated OLIGONUCLEOTIDES. It has low activity towards POLYNUCLEOTIDES and the presence of 3'-phosphate terminus on the substrate may inhibit hydrolysis.

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.

Reagents with two reactive groups, usually at opposite ends of the molecule, that are capable of reacting with and thereby forming bridges between side chains of amino acids in proteins; the locations of naturally reactive areas within proteins can thereby be identified; may also be used for other macromolecules, like glycoproteins, nucleic acids, or other.

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.

Purine or pyrimidine bases attached to a ribose or deoxyribose. (From King & Stansfield, A Dictionary of Genetics, 4th ed)

A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.

Deoxyribonucleic acid that makes up the genetic material of viruses.

A series of heterocyclic compounds that are variously substituted in nature and are known also as purine bases. They include ADENINE and GUANINE, constituents of nucleic acids, as well as many alkaloids such as CAFFEINE and THEOPHYLLINE. Uric acid is the metabolic end product of purine metabolism.

Hard, amorphous, brittle, inorganic, usually transparent, polymerous silicate of basic oxides, usually potassium or sodium. It is used in the form of hard sheets, vessels, tubing, fibers, ceramics, beads, etc.

Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).

Enzymes that catalyze the release of mononucleotides by the hydrolysis of the terminal bond of deoxyribonucleotide or ribonucleotide chains.

A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.

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.

Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.

A negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.

Proteins obtained from the ZEBRAFISH. Many of the proteins in this species have been the subject of studies involving basic embryological development (EMBRYOLOGY).

2-Amino-1,5-dihydro-4,6-pteridinedione. Pigment first discovered in butterfly wings and widely distributed in plants and animals.

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.

The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.

Determination of the spectra of ultraviolet absorption by specific molecules in gases or liquids, for example Cl2, SO2, NO2, CS2, ozone, mercury vapor, and various unsaturated compounds. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

A cell line derived from cultured tumor cells.

2'-Deoxyuridine. An antimetabolite that is converted to deoxyuridine triphosphate during DNA synthesis. Laboratory suppression of deoxyuridine is used to diagnose megaloblastic anemias due to vitamin B12 and folate deficiencies.

The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.

An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.

A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)

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.

Forms to which substances are incorporated to improve the delivery and the effectiveness of drugs. Drug carriers are used in drug-delivery systems such as the controlled-release technology to prolong in vivo drug actions, decrease drug metabolism, and reduce drug toxicity. Carriers are also used in designs to increase the effectiveness of drug delivery to the target sites of pharmacological actions. Liposomes, albumin microspheres, soluble synthetic polymers, DNA complexes, protein-drug conjugates, and carrier erythrocytes among others have been employed as biodegradable drug carriers.

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).

Techniques and strategies which include the use of coding sequences and other conventional or radical means to transform or modify cells for the purpose of treating or reversing disease conditions.

A nucleoside consisting of the base guanine and the sugar deoxyribose.

That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.

A pattern recognition receptor that binds unmethylated CPG CLUSTERS. It mediates cellular responses to bacterial pathogens by distinguishing between self and bacterial DNA.

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.

The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.

Proteins prepared by recombinant DNA technology.

Compounds containing carbon-phosphorus bonds in which the phosphorus component is also bonded to one or more sulfur atoms. Many of these compounds function as CHOLINERGIC AGENTS and as INSECTICIDES.

Deoxyribonucleic acid that makes up the genetic material of bacteria.

Systems for the delivery of drugs to target sites of pharmacological actions. Technologies employed include those concerning drug preparation, route of administration, site targeting, metabolism, and toxicity.

Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.

One of the mechanisms by which CELL DEATH occurs (compare with NECROSIS and AUTOPHAGOCYTOSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA; (DNA FRAGMENTATION); at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth.

The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.

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.

A group of condensed ring hydrocarbons.

A method of generating a large library of randomized nucleotides and selecting NUCLEOTIDE APTAMERS by iterative rounds of in vitro selection. A modified procedure substitutes AMINO ACIDS in place of NUCLEOTIDES to make PEPTIDE APTAMERS.

Enzymes which catalyze the hydrolases of ester bonds within DNA. EC 3.1.-.

Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.

Unstable isotopes of phosphorus that decay or disintegrate emitting radiation. P atoms with atomic weights 28-34 except 31 are radioactive phosphorus isotopes.

Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)

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.

The temperature at which a substance changes from one state or conformation of matter to another.

A photoactivable URIDINE analog that is used as an affinity label.

Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.

Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.

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.

Artificial, single or multilaminar vesicles (made from lecithins or other lipids) that are used for the delivery of a variety of biological molecules or molecular complexes to cells, for example, drug delivery and gene transfer. They are also used to study membranes and membrane proteins.

Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes.

Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.

Organic compounds containing the -CO-NH2 radical. Amides are derived from acids by replacement of -OH by -NH2 or from ammonia by the replacement of H by an acyl group. (From Grant & Hackh's Chemical Dictionary, 5th ed)

Measurement of the intensity and quality of fluorescence.

A technique which uses synthetic oligonucleotides to direct the cell's inherent DNA repair system to correct a mutation at a specific site in an episome or chromosome.

Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.

RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.

The covalent bonding of an alkyl group to an organic compound. It can occur by a simple addition reaction or by substitution of another functional group.

A class of enzymes that catalyze the hydrolysis of one of the two ester bonds in a phosphodiester compound. EC 3.1.4.

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.

A purine base and a fundamental unit of ADENINE NUCLEOTIDES.

Adenosine molecules which can be substituted in any position, but are lacking one hydroxyl group in the ribose part of the molecule.

Elements of limited time intervals, contributing to particular results or situations.

The molecular designing of drugs for specific purposes (such as DNA-binding, enzyme inhibition, anti-cancer efficacy, etc.) based on knowledge of molecular properties such as activity of functional groups, molecular geometry, and electronic structure, and also on information cataloged on analogous molecules. Drug design is generally computer-assisted molecular modeling and does not include pharmacokinetics, dosage analysis, or drug administration analysis.

The products of chemical reactions that result in the addition of extraneous chemical groups to DNA.

Molecules of DNA that possess enzymatic activity.

Positively charged atoms, radicals or groups of atoms which travel to the cathode or negative pole during electrolysis.

The functional hereditary units of VIRUSES.

A purine or pyrimidine base bonded to a DEOXYRIBOSE containing a bond to a phosphate group.

Fluorescent probe capable of being conjugated to tissue and proteins. It is used as a label in fluorescent antibody staining procedures as well as protein- and amino acid-binding techniques.

A yellow metallic element with the atomic symbol Au, atomic number 79, and atomic weight 197. It is used in jewelry, goldplating of other metals, as currency, and in dental restoration. Many of its clinical applications, such as ANTIRHEUMATIC AGENTS, are in the form of its salts.

The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)

The developmental entity of a fertilized egg (ZYGOTE) in animal species other than MAMMALS. For chickens, use CHICK EMBRYO.

Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)

The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.

The homogeneous mixtures formed by the mixing of a solid, liquid, or gaseous substance (solute) with a liquid (the solvent), from which the dissolved substances can be recovered by physical processes. (From Grant & Hackh's Chemical Dictionary, 5th ed)

Salts and derivatives of undecylenic acid.

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)

The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)

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 group of compounds which consist of a nucleotide molecule to which an additional nucleoside is attached through the phosphate molecule(s). The nucleotide can contain any number of phosphates.

Nucleic acids which hybridize to complementary sequences in other target nucleic acids causing the function of the latter to be affected.

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.

The relationship between the dose of an administered drug and the response of the organism to the drug.

A group of guanine ribonucleotides in which the phosphate residues of each guanine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.

A 60-kDa extracellular protein of Streptomyces avidinii with four high-affinity biotin binding sites. Unlike AVIDIN, streptavidin has a near neutral isoelectric point and is free of carbohydrate side chains.

DNA-dependent DNA polymerases found in bacteria, animal and plant cells. During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair.

Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION. These deviations may be caused by physical or chemical agents and occur by natural or unnatural, introduced circumstances. They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR). If the damage is extensive, it can induce APOPTOSIS.

An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.

Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.

A group of compounds derived from ammonia by substituting organic radicals for the hydrogens. (From Grant & Hackh's Chemical Dictionary, 5th ed)

Pigmenting photosensitizing agent obtained from several plants, mainly Psoralea corylifolia. It is administered either topically or orally in conjunction with ultraviolet light in the treatment of vitiligo.

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).

An enzyme that catalyzes the transfer of a phosphate group to the 5'-terminal hydroxyl groups of DNA and RNA. EC 2.7.1.78.

A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.

Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.

Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.

A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.

A pyrimidine nucleoside that is composed of the base CYTOSINE linked to the five-carbon sugar D-RIBOSE.

A series of steps taken in order to conduct research.

Poly(deoxyribonucleotide):poly(deoxyribonucleotide)ligases. Enzymes that catalyze the joining of preformed deoxyribonucleotides in phosphodiester linkage during genetic processes during repair of a single-stranded break in duplex DNA. The class includes both EC 6.5.1.1 (ATP) and EC 6.5.1.2 (NAD).

The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.

A purine nucleoside that has hypoxanthine linked by the N9 nitrogen to the C1 carbon of ribose. It is an intermediate in the degradation of purines and purine nucleosides to uric acid and in pathways of purine salvage. It also occurs in the anticodon of certain transfer RNA molecules. (Dorland, 28th ed)

An enzyme that catalyzes the conversion of linear RNA to a circular form by the transfer of the 5'-phosphate to the 3'-hydroxyl terminus. It also catalyzes the covalent joining of two polyribonucleotides in phosphodiester linkage. EC 6.5.1.3.

The process of cleaving a chemical compound by the addition of a molecule of water.

A family of enzymes that catalyze the endonucleolytic cleavage of RNA. It includes EC 3.1.26.-, EC 3.1.27.-, EC 3.1.30.-, and EC 3.1.31.-.

Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 3.1.21.4.

DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.

The injection of very small amounts of fluid, often with the aid of a microscope and microsyringes.

Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.

Evidence on the conformation of HeLa-cell 5.8S ribosomal ribonucleic acid from the reaction of specific cytidine residues with sodium bisulphite. (1/6278)

The reaction of HeLa-cell 5.8S rRNA with NaHSO3 under conditions in which exposed cytidine residues are deaminated to uridine was studied. It was possible to estimate the reactivities of most of the 46 cytidine residues in the nucleotide sequence by comparing 'fingerprints' of the bisulphite-treated RNA with those of untreated RNA. The findings were consistent with the main features of the secondary-structure model for mammalian 5.85S rRNA proposed by Nazar, Sitz, & Busch [J. Biol. Chem (1975) 250, 8591--8597]. Five out of six regions that are depicted in the model as single-stranded loops contain cytidine residues that are reactive towards bisulphite at 25 degrees C (the other loop contains no cytidine). The cytidine residue nearest to the 3'-terminus is also reactive. Several cytidines residues that are internally located within proposed double-helical regions show little or no reactivity towards bisulphite, but the cytidine residues of several C.G pairs at the ends of helical regions show some reactivity, and one of the proposed loops appears to contain six nucleotides, rather than the minimum of four suggested by the primary structure. Two cytidine residues that are thought to be 'looped out' by small helix imperfections also show some reactivity. (+info)

Long-range oxidative damage to DNA: effects of distance and sequence. (2/6278)

INTRODUCTION: Oxidative damage to DNA in vivo can lead to mutations and cancer. DNA damage and repair studies have not yet revealed whether permanent oxidative lesions are generated by charges migrating over long distances. Both photoexcited *Rh(III) and ground-state Ru(III) intercalators were previously shown to oxidize guanine bases from a remote site in oligonucleotide duplexes by DNA-mediated electron transfer. Here we examine much longer charge-transport distances and explore the sensitivity of the reaction to intervening sequences. RESULTS: Oxidative damage was examined in a series of DNA duplexes containing a pendant intercalating photooxidant. These studies revealed a shallow dependence on distance and no dependence on the phasing orientation of the oxidant relative to the site of damage, 5'-GG-3'. The intervening DNA sequence has a significant effect on the yield of guanine oxidation, however. Oxidation through multiple 5'-TA-3' steps is substantially diminished compared to through other base steps. We observed intraduplex guanine oxidation by tethered *Rh(III) and Ru(III) over a distance of 200 A. The distribution of oxidized guanine varied as a function of temperature between 5 and 35 degrees C, with an increase in the proportion of long-range damage (> 100 A) occurring at higher temperatures. CONCLUSIONS: Guanines are oxidized as a result of DNA-mediated charge transport over significant distances (e.g. 200 A). Although long-range charge transfer is dependent on distance, it appears to be modulated by intervening sequence and sequence-dependent dynamics. These discoveries hold important implications with respect to DNA damage in vivo. (+info)

B-MYB transactivates its own promoter through SP1-binding sites. (3/6278)

B-MYB is an ubiquitous protein required for mammalian cell growth. In this report we show that B-MYB transactivates its own promoter through a 120 bp segment proximal to the transcription start site. The B-MYB-responsive element does not contain myb-binding sites and gel-shift analysis shows that SP1, but not B-MYB, protein contained in SAOS2 cell extracts binds to the 120 bp B-myb promoter fragment. B-MYB-dependent transactivation is cooperatively increased in the presence of SP1, but not SP3 overexpression. When the SP1 elements of the B-myb promoter are transferred in front of a heterologous promoter, an increased response to B-MYB results. In contrast, c-MYB, the prototype member of the Myb family, is not able to activate the luciferase construct containing the SP1 elements. With the use of an SP1-GAL4 fusion protein, we have determined that the cooperative activation occurs through the domain A of SP1. These observations suggest that B-MYB functions as a coactivator of SP1, and that diverse combinations of myb and SP1 sites may dictate the responsiveness of myb-target genes to the various members of the myb family. (+info)

The Jun kinase 2 isoform is preferentially required for epidermal growth factor-induced transformation of human A549 lung carcinoma cells. (4/6278)

We have previously found that epidermal growth factor (EGF) mediates growth through the Jun N-terminal kinase/stress-activated kinase (JNK/SAPK) pathway in A549 human lung carcinoma cells. As observed here, EGF treatment also greatly enhances the tumorigenicity of A549 cells, suggesting an important role for JNK in cancer cell growth (F. Bost, R. McKay, N. Dean, and D. Mercola, J. Biol. Chem. 272:33422-33429, 1997). Several isoforms families of JNK, JNK1, JNK2, and JNK3, have been isolated; they arise from alternative splicing of three different genes and have distinct substrate binding properties. Here we have used specific phosphorothioate oligonucleotides targeted against the two major isoforms, JNK1 and JNK2, to discriminate their roles in EGF-induced transformation. Multiple antisense sequences have been screened, and two high-affinity and specific candidates have been identified. Antisense JNK1 eliminated steady-state mRNA and JNK1 protein expression with a 50% effective concentration (EC50) of <0.1 microM but did not alter JNK2 mRNA or protein levels. Conversely, antisense JNK2 specifically eliminated JNK2 steady-state mRNA and protein expression with an EC50 of 0.1 microM. Antisense JNK1 and antisense JNK2 inhibited by 40 and 70%, respectively, EGF-induced total JNK activity, whereas sense and scrambled-sequence control oligonucleotides had no effect. The elimination of mRNA, protein, and JNK activities lasted 48 and 72 h following a single Lipofectin treatment with antisense JNK1 and JNK2, respectively, indicating sufficient duration for examining the impact of specific elimination on the phenotype. Direct proliferation assays demonstrated that antisense JNK2 inhibited EGF-induced doubling of growth as well as the combination of active antisense oligonucleotides did. EGF treatment also induced colony formation in soft agar. This effect was completely inhibited by antisense JNK2 and combined-antisense treatment but not altered by antisense JNK1 alone. These results show that EGF doubles the proliferation (growth in soft agar as well as tumorigenicity in athymic mice) of A549 lung carcinoma cells and that the JNK2 isoform but not JNK1 is utilized for mediating the effects of EGF. This study represents the first demonstration of a cellular phenotype regulated by a JNK isoform family, JNK2. (+info)

Transcriptional regulation of cell type-specific expression of the TATA-less A subunit gene for human coagulation factor XIII. (5/6278)

To study the mechanism of gene regulation for coagulation factor XIII A subunit (FXIIIA), we characterized its 5'-flanking region using a monocytoid (U937), a megakaryocytoid (MEG-01), and other cells. Our results confirmed that U937 and MEG-01 contained FXIIIA mRNA. A tentative transcription start site was determined to be 76 bases upstream from the first exon/intron boundary. Reporter gene assays revealed that a 5'-fragment (-2331 to +75) was sufficient to support basal expression in U937 and MEG-01 but not in the other cells. Deletion analysis confined a minimal promoter sequence from -114 to +75. DNase footprinting, electrophoretic mobility shift, and reporter gene assays demonstrated that promoter elements for a myeloid-enriched transcription factor (MZF-1-like protein) and two ubiquitous transcription factors (NF-1 and SP-1) in this region were important for the basal FXIII expression. It was also revealed that an upstream region (-806 to -290) had enhancer activity in MEG-01 but silencer activity in U937. DNA sequences for binding of myeloid-enriched factors (GATA-1 and Ets-1) were recognized in this region, and the GATA-1 element was found to be responsible for the enhancer activity. These transcription factors play a major role in the cell type-specific expression of FXIIIA, which differs from other transglutaminases. (+info)

Base pairing of anhydrohexitol nucleosides with 2,6-diaminopurine, 5-methylcytosine and uracil asbase moiety. (6/6278)

Hexitol nucleic acids (HNAs) with modified bases (5-methylcytosine, 2,6-diaminopurine or uracil) were synthesized. The introduction of the 5-methylcytosine base demonstrates that N -benzoylated 5-methylcytosyl-hexitol occurs as the imino tautomer. The base pairing systems (G:CMe, U:D, T:D and U:A) obey Watson-Crick rules. Substituting hT for hU, hCMefor hC and hD for hA generally leads to increased duplex stability. In a single case, replacement of hC by hCMedid not result in duplex stabilization. This sequence-specific effect could be explained by the geometry of the model duplex used for carrying out the thermal stability study. Generally, polypurine HNA sequences give more stable duplexes with their RNA complement than polypyrimidine HNA sequences. This observation supports the hypothesis that, besides changes in stacking pattern, the difference in conformational stress between purine and pyrimidine nucleosides may contribute to duplex stability. Introduction of hCMeand hD in HNA sequences further increases the potential of HNA to function as a steric blocking agent. (+info)

Hairpin-shaped DNA duplexes with disulfide bonds in sugar-phosphate backbone as potential DNA reagents for crosslinking with proteins. (7/6278)

Convenient approaches were described to incorporate -OP(=O)O(-)-SS-O(-)(O=)PO- bridges in hairpin-shaped DNA duplexes instead of regular phosphodiester linkages: (i) H2O2- or 2,2'-dipyridyldisulfide-mediated coupling of 3'- and 5'-thiophosphorylated oligonucleotides on complementary template and (ii) more selective template-guided autoligation of a preactivated oligonucleotide derivative with an oligomer carrying a terminal thiophosphoryl group. Dithiothreitol was found to cleave completely modified internucleotide linkage releasing starting oligonucleotides. The presence of complementary template as an intrinsic element of the molecule protects the hairpin DNA analog from spontaneous exchange of disulfide-linked oligomer fragments and makes it a good candidate for auto-crosslinking with cysteine-containing proteins. (+info)

The use of terminal blocking groups for the specific joining of oligonucleotides in RNA ligase reactions containing equimolar concentrations of acceptor and donor molecules. (8/6278)

Under the conditions that RNA ligase converts the tetranucleotide, pA-A2-A, to larger polynucleotides, no such polymerization can be detected with the derivative, pA-A2-A(MeOEt), that possesses a terminal 2'-0-(alpha-methoxyethyl) group. The protection against self condensation offered by the methoxyethyl group in this system allows the specific joining of donor and acceptor oligonucleotides in reaction mixtures containing equimolar concentrations of the two species. Thus, the enzyme, together with ATP, converts equimolar quantities of A-A2-A and pA-A2-A(MeOEt) to A-A6-A(MeOEt) in 55% yield, while a similar reaction with A-A2-A and pU-U2-U(MeOEt) results in a 40% yield of A-A3-U3-U(MeOEt). The intermediate in these ligations is a disubstituted pyrophosphate composed of the donor molecule and the adenylate moiety deriving from ATP. In the case of the intermediate arising from the blocked adenosine tetranucleotide, the assigned structure, A5'pp5'A-A2-A(MeOEt), has been confirmed by chemical synthesis. The pyrophosphate derivative is able to participate in joining reactions in the absence of ATP. These observations constitute an efficient approach to the synthesis of larger polynucleotides from a specific series of oligonucleotide blocks since (i), the methoxyethyl group can be easily introduced into each oligonucleotide using the single addition reaction catalyzed by polynucleotide phosphorylase in the presence of a 2'-0-(alpha-methoxyethyl)nucleoside 5'-diphosphate, and (ii), the blocking group may be readily removed under mild conditions after each successive ligation reaction. Two other octanucleotides, I-I2-A-U3-U and U-U2-C-I3-A, have also been synthesized by this method, and these molecules correspond (with I substituting for G) to sequences appearing near the 3' terminus of the 6S RNA transcribed from phage lambda DNA. The terminal 3'-phosphate group serves equally well as a blocking group for specific ligation reactions in that the ligase converts equimolar amounts of A-A2-A and pA-A2-Ap to A-A6-Ap in 50% yield. (+info)

Oligonucleotides. 13 (6): 479-489. doi:10.1089/154545703322860799. PMID 15025914. Herdewijn P, Marlière P (June 2009). "Toward ...

https://en.wikipedia.org/wiki/Xeno_nucleic_acid

Triplex-Forming Oligonucleotide Target Sequence Search Tool: A Searching Tool to find Polypurine and Polypyrimidine stretches ... PPRHs could be used as gene silencing tools acting by different mechanisms than triplex forming oligonucleotides (TFOs), ... Polypurine reverse-Hoogsteen hairpins (PPRHs) are non-modified oligonucleotides containing two polypurine domains, in a mirror ... antisense oligonucleotides or siRNAs. Upon binding to their targets, PPRHs can decrease the mRNA and protein levels of the ...

https://en.wikipedia.org/wiki/Polypurine_reverse-Hoogsteen_hairpin

Ding X, Yang J, Wang S (Mar-Apr 2011). "Antisense oligonucleotides targeting abhydrolase domain containing 2 block human ... hepatitis B virus propagation". Oligonucleotides. 21 (2): 77-84. doi:10.1089/oli.2011.0280. PMID 21466387. Yamanoi, Koji; ...

https://en.wikipedia.org/wiki/ABHD2

Triplex-forming oligonucleotides (TFO) are one potential method to achieve therapeutic gene modulation. TFOs are approximately ... January 2003). "Triplex-forming oligonucleotides as modulators of gene expression". Int J Biochem Cell Biol. 35 (1): 22-31. doi ... There are three major categories of agents that act as transcriptional gene modulators: triplex-forming oligonucleotides (TFOs ... Simon, P.; Cannata, F.; Concordet, JP.; Giovannangeli, C. (August 2008). "Targeting DNA with triplex-forming oligonucleotides ...

https://en.wikipedia.org/wiki/Therapeutic_gene_modulation

Two oligonucleotides. or their analogues, are linked via chemical groups to precursors of chemical compounds. The ... oligonucleotides recognize specific nucleic acids and are hybridized sterically close to each other. Afterwards, the chemical ...

https://en.wikipedia.org/wiki/Nucleic_acid_templated_chemistry

... is a form of treatment that uses antisense oligonucleotides (ASOs) to target messenger RNA (mRNA). ASOs are ... In 2019, a report was published detailing the development of milasen, an antisense oligonucleotide drug for Batten disease, ... As of 2020 more than 50 antisense oligonucleotides were in clinical trials, including over 25 in advanced clinical trials ( ... Over the following years, an antisense oligonucleotide later named nusinersen was developed by Ionis Pharmaceuticals under a ...

https://en.wikipedia.org/wiki/Antisense_therapy

Oligonucleotides 18(3), 257-268. Fahmy, R. et al (2006) Suppression of vascular permeability and inflammation by targeting of ... Oligonucleotides 16, 297-312. Goodchild, A. et al (2007) Cytotoxic G-rich oligode-oxynucleotides: putative protein targets and ... Kim, M.-G. et al (2015) Biomimetic DNA nanoballs for oligonucleotide delivery. Biomaterials 62, 155-163. Marquardt, K. et al ( ...

https://en.wikipedia.org/wiki/Dz13

The incorporation of BNAs into oligonucleotides allows the production of modified synthetic oligonucleotides with equal or ... and good aqueous solubility of the resulting oligonucleotides when compared to regular DNA or RNA oligonucleotides. New BNA ... The same group, also in 2012, reported that the 2',4'-BNANC[NMe] analog when used in antisense oligonucleotides showed ... BNA nucleotides can be incorporated into DNA or RNA oligonucleotides at any desired position. Such oligomers are synthesized ...

https://en.wikipedia.org/wiki/Bridged_nucleic_acid

The potential of antisense oligonucleotides to treat neurodegenerative diseases was reviewed by Tabrizi in Science in 2020. ... "Full Results from Huntingtin Lowering Antisense Oligonucleotides Trial now published". UCL Queen Square Institute of Neurology ... Leavitt, Blair R.; Tabrizi, Sarah J. (27 March 2020). "Antisense oligonucleotides for neurodegeneration". Science. 367 (6485): ... or huntingtin-lowering antisense oligonucleotide (ASO) drug in Huntington's disease patients. The announcement of the 'top line ...

https://en.wikipedia.org/wiki/Sarah_Tabrizi

The probe types used for non-polymorphic arrays include cDNA, BAC clones (e.g., BlueGnome), and oligonucleotides (e.g., Agilent ... Other terms used to describe the arrays used for karyotyping include SOMA (SNP oligonucleotide microarrays) and CMA (chromosome ... "Customized oligonucleotide array-based comparative genomic hybridization as a clinical assay for genomic profiling of chronic ... Santa Clara, CA, USA or Nimblegen, Madison, WI, USA). Commercially available oligonucleotide SNP arrays can be solid phase ( ...

https://en.wikipedia.org/wiki/Virtual_karyotype

"Characteristic archaebacterial 16S rRNA oligonucleotides". Syst. Appl. Microbiol. 7 (2-3): 194-197. doi:10.1016/S0723-2020(86) ...

https://en.wikipedia.org/wiki/Korarchaeota

Many of these schemes use a covalent attachment scheme, using oligonucleotides with amide or thiol functional groups as a ... The nucleic acids themselves are then synthesized using standard oligonucleotide synthesis methods, usually automated in an ... Methods: Ellington A, Pollard JD (1 May 2001). Synthesis and Purification of Oligonucleotides. Current Protocols in Molecular ... Methods: Ellington A, Pollard JD (1 May 2001). Purification of Oligonucleotides Using Denaturing Polyacrylamide Gel ...

https://en.wikipedia.org/wiki/DNA_nanotechnology

"Characteristic archaebacterial 16S rRNA oligonucleotides". Syst. Appl. Microbiol. 7 (2-3): 194-197. doi:10.1016/S0723-2020(86) ...

https://en.wikipedia.org/wiki/Thermoproteota

TLR8 recognizes G-rich oligonucleotides. TLR8 is an endosomal receptor that recognizes single stranded RNA (ssRNA), and can ...

https://en.wikipedia.org/wiki/Toll-like_receptor_8

In vivo applications of antisense oligonucleotides showed that toxicity is largely due to impurities in the oligonucleotide ... Some results show that nuclear localisation signals can be irreversibly linked to one end of the oligonucleotides, forming an ... Brysch, Wolfgang; Schlingensiepen, Karl-Hermann (1994). "Design and application of antisense oligonucleotides in cell culture, ... Lebedeva, Irina; Stein, CA (2001). "Antisense oligonucleotides: promise and reality". Annual Review of Pharmacology and ...

https://en.wikipedia.org/wiki/Computational_gene

Oligonucleotides are annealed and ligated; the preferential ligation by DNA ligase for matching sequences results in a signal ... Use of oligonucleotides of defined sequence as primers in DNA sequence analysis". Biochem. Biophys. Res. Commun. 48 (5): 1295- ... Here, a pool of all possible oligonucleotides of a fixed length are labeled according to the sequenced position. ... oligonucleotides), also called DNA probes, to reconstruct a target DNA sequence. Non-specific hybrids are removed by washing ...

https://en.wikipedia.org/wiki/DNA_sequencing

doi:10.1016/S0040-4039(00)87907-1. Takaku, Hiroshi; Kamaike, Kazuo; Tsuchiya, Hiromichi (1984-01-01). "Oligonucleotide ...

https://en.wikipedia.org/wiki/Benzyl_group

This reaction led to death in some cases and raises significant concerns about siRNA delivery when PEGylated oligonucleotides ... Woolf TM, Melton DA, Jennings CG (August 1992). "Specificity of antisense oligonucleotides in vivo". Proceedings of the ... Some methods for siRNA delivery adjoin polyethylene glycol (PEG) to the oligonucleotide reducing excretion and improving ... Gene knockdown Gene silencing Oligonucleotide synthesis EsiRNA NatsiRNA Viroid VIRsiRNAdb CRISPR Dharmacon Persomics Laganà A, ...

https://en.wikipedia.org/wiki/Small_interfering_RNA

... is a second-generation phosphorothioate antisense oligonucleotide. Phosphorothioates are oligonucleotides with a ... An antisense oligonucleotide (ASO) is a single-strand DNA sequence complementary to a desired messenger RNA (mRNA) sequence. ... Second-generation oligonucleotides are highly specific to the target mRNA sequence, increasing the affinity of the compound. ... Antisense therapy targets gene sequences using antisense oligonucleotides by binding the ASO to the mRNA strand. This creates ...

https://en.wikipedia.org/wiki/Custirsen

1986). "Characteristic archaebacterial 16S rRNA oligonucleotides". Syst. Appl. Microbiol. 7 (2-3): 194-7. doi:10.1016/S0723- ...

https://en.wikipedia.org/wiki/Nanoarchaeota

RNase H-dependent oligonucleotides cause the target mRNA molecules to be degraded, while steric-blocker oligonucleotides ... The antisense oligonucleotides can affect gene expression in two ways: by using an RNase H-dependent mechanism or by using a ... Oligonucleotides, which are short nucleic acid fragments, bind to complementary target mRNA molecules when added to the cell. ... Ribozymes, antisense oligonucleotides, and more recently RNAi have been used to target mRNA molecules involved in asthma. These ...

https://en.wikipedia.org/wiki/Gene_silencing

Oligonucleotide chips are microarrays of oligonucleotides. They can be used for detection of mutations and expression ... Using inkjet technology, nucleotides are printed onto a surface drop by drop to form oligonucleotides cDNA microarrays are ... Selected major technical achievements during bio-MEMS development of the 1990s include: In 1991, the first oligonucleotide chip ... This process can be repeated to synthesize oligonucleotides of relatively short lengths on the surface, nucleotide by ...

https://en.wikipedia.org/wiki/Bio-MEMS

"Paper of the Year - Oligonucleotide Therapeutics Society". Oligonucleotide Therapeutics Society. Retrieved 2018-10-30. " ... Oligonucleotide Therapeutics Society Recipient, Chancellor's Medal for Excellence in Scholarship, University of Massachusetts ...

https://en.wikipedia.org/wiki/Phillip_D._Zamore

Anti-thrombin aptamers - Oligonucleotides which recognize the exosites of human thrombin Deoxyribozyme - DNA oligonucleotides ... "DNA Oligonucleotide Synthesis". Millipore Sigma. Retrieved 4 July 2022. Ellington AD, Szostak JW (August 1990). "In vitro ... which are mostly oligonucleotides, is very different from the amino acid-based structure of antibodies, which are proteins. ... the researcher introduces a series of random and blocker oligonucleotides to an immobilization field before introduction to the ...

https://en.wikipedia.org/wiki/Aptamer

"5th International Workshop on Lung Health, Asthma and COPD - Personalised Medicine: From Myth to Real Life". Oligonucleotide ...

https://en.wikipedia.org/wiki/International_Workshop_on_Lung_Health

". "Interview with Jeannie T. Lee". Oligonucleotide Therapeutics Society. August 13, 2016. Viegas, J (2015). "QnAs with Jeannie ...

https://en.wikipedia.org/wiki/Jeannie_T._Lee

"Modified oligonucleotides: synthesis and strategy for users". Annual Review of Biochemistry. 67: 99-134. doi:10.1146/annurev. ... Study of how temperature affects the nucleic acid structure Oligonucleotide synthesis - Chemical synthesis of relatively short ...

https://en.wikipedia.org/wiki/Nucleic_acid

... and other nucleic acids are the basis of aptamers, synthetic oligonucleotide ligands for specific target molecules used in ... Verma S, Eckstein F (1998). "Modified oligonucleotides: synthesis and strategy for users". Annual Review of Biochemistry. 67: ...

https://en.wikipedia.org/wiki/DNA

"Isothermal reactions for the amplification of oligonucleotides". Proceedings of the National Academy of Sciences of the United ...

https://en.wikipedia.org/wiki/Keck_Graduate_Institute

... is an oligonucleotide capable of antisense interactions with mRNA of human papillomavirus. It has been investigated ... "In vitro pharmacokinetics of phosphorothioate antisense oligonucleotides". The Journal of Pharmacology and Experimental ...

https://en.wikipedia.org/wiki/Afovirsen

2023 Integrated DNA Technologies, Inc.. Trademarks contained herein are the property of Integrated DNA Technologies, Inc. or their respective owners, and may be registered in the USA and/or other jurisdictions. For specific trademark information, see www.idtdna.com/trademarks.. ...

https://www.idtdna.com/site/order/oligoentry/index/UltraRNA

Oligonucleotide Process Chemistry job in Boston, MA with Entrada Therapeutics. Apply Today. ... Scientist, Oligonucleotide Process Chemistry. Employer. Entrada Therapeutics Location. Boston, MA. Start date. Nov 11, 2022. ... and characterization of small organic compounds and oligonucleotides produced within our Oligonucleotide Process Chemistry ... The Companys lead oligonucleotide programs include ENTR-601-44 targeting Duchenne muscular dystrophy (DMD) and ENTR-701 ...

https://www.biospace.com/job/2658240/scientist-oligonucleotide-process-chemistry/

Antisense Oligonucleotides. Class Summary. In a clinical trial, inotersen, an antisense oligonucleotide, has improved ... Berk JL, Barroso FA, Coelho A. Oligonucleotide Drugs for Transthyretin Amyloidosis. N Engl J Med. 2018 Nov 22. 379:2085-2086. [ ... Inotersen is an antisense oligonucleotide that causes degradation of mutant and wild-type transthyretin mRNA by binding TTR ...

https://www.medscape.com/answers/335301-163499/which-medications-in-the-drug-class-sirna-agents-are-used-in-the-treatment-of-transthyretin-related-amyloidosis

Custom LNA-enhanced oligonucleotides for a range of applications ... Custom LNA Oligonucleotide Large Scale (A). Cat. No. / ID: ... 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 ...

https://www.qiagen.com/th/products/discovery-and-translational-research/custom-lna-oligonucleotides/

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https://www.eurogentec.com/en/catalog/c47~calibration-oligonucleotides?catalog_product.ProductAttribute.190=20585

Panmicrobial Oligonucleotide Array for Diagnosis of Infectious Diseases On This Page Methods Results Discussion Cite This ... The 60-mer oligonucleotide arrays were synthesized on 70-mm × 20-mm glass slides by using an inkjet deposition system (Agilent ... Panmicrobial Oligonucleotide Array for Diagnosis of Infectious Diseases. Emerging Infectious Diseases. 2007;13(1):73. doi: ... Fluorescently labeled synthetic oligonucleotides complementary to the control probes were included in all hybridizations. ...

https://wwwnc.cdc.gov/eid/article/13/1/06-0837_article

... Nucleic Acids ... Methods to suppress expression of mRNAs include antisense oligonucleotides (ASOs) and RNA interference (RNAi). Antisense and ...

https://pubmed.ncbi.nlm.nih.gov/26578588/

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... The present invention relates to compounds which are capable of ...

https://www.ideaconnection.com/patents/14762-Pharmaceutical-Compounds-Comprising-Abasic-Oligonucle.html?c=17

... and to increase sustainability.Tailor-made oligonucleotide synthesisersTo ensure only the highest-quality oligonucleotide is ... s oligonucleotide manufacturing process uses unique, innovative equipment to deliver the highest-quality products ... Tailor-made oligonucleotide synthesisers. To ensure only the highest-quality oligonucleotide is supplied to customers, Bachem ... Continuous chromatography for oligonucleotide purification. To further optimise the process of oligonucleotide manufacturing, ...

https://www.pharmiweb.com/article/bachem-s-innovative-processes-are-transforming-oligonucleotide-manufacturing

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, ... Tosi, L., Sridhara, V., Yang, Y. et al. Long-adapter single-strand oligonucleotide probes for the massively multiplexed cloning ... Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265, 2085-2088 (1994). ...

https://www.nature.com/articles/s41551-017-0092?error=cookies_not_supported&code=fba52139-46ae-4016-826f-edb19936cf33

Modulating Anti-MicroRNA-21 Activity and Specificity Using Oligonucleotide Derivatives and Length Optimization ... Modulating Anti-MicroRNA-21 Activity and Specificity Using Oligonucleotide Derivatives and Length Optimization. ...

https://www.hindawi.com/journals/isrn/2012/407154/fig3/

... In: Endocytobiosis & Cell ...

https://epub.ub.uni-muenchen.de/60424/

Complementary oligonucleotides were hybridized to the surface-attached oligonucleotides with a density of 7 x 1012 DNA ... Complementary oligonucleotides were hybridized to the surface-attached oligonucleotides with a density of 7 x 1012 DNA ... Submicron patterning of DNA oligonucleotides on silicon. The covalent attachment of DNA oligonucleotides onto crystalline ... Yin, H.B., Brown, T., Wilkinson, J.S., Eason, R.W. and Melvin, T. (2004) Submicron patterning of DNA oligonucleotides on ...

https://eprints.soton.ac.uk/20346/

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. ...

https://www.biosearchtech.com/products/oligos-probes-and-primers/commercial-gmp-oligos

... at the 2nd Annual Oligonucleotide Therapeutics and Delivery Conference. The conference will take place on September 21 and 22, ... Platform Programs at the 2nd Annual Oligonucleotide Therapeutics and Delivery Conference. Read full article. ... at the 2nd Annual Oligonucleotide Therapeutics and Delivery Conference. The conference will take place on September 21 and 22, ... present-latest-developments-on-sirna-therapeutics-for-cancer-and-galaheadtm-platform-programs-at-the-2nd-annual-oligonucleotide ...

https://finance.yahoo.com/news/sirnaomics-present-latest-developments-sirna-141000175.html

Oligonucleotides. The use of synthetic oligonucleotides in gene therapy is to inactivate the genes involved in the disease ...

https://www.genetherapynet.com/non-viral-vectors/oligonucleotides.html

Towards the application of triplex-forming oligonucleotides as therapeutic agents at University of Portsmouth, listed on ... Oligonucleotides that might prove useful in this manner are known as triplex-forming oligonucleotides, on account of their ... Synthetic oligonucleotides are short strands of DNA that can be used to treat or manage a wide range of diseases, for example ... Towards the application of triplex-forming oligonucleotides as therapeutic agents. University of Portsmouth School of Pharmacy ...

https://www.findaphd.com/phds/project/towards-the-application-of-triplex-forming-oligonucleotides-as-therapeutic-agents/?p137777

We will develop an antisense oligonucleotide, or DNA therapy for diverse forms of amyotrophic lateral sclerosis (ALS). ...

https://www.cirm.ca.gov/our-progress/awards/development-syf2-antisense-oligonucleotide-aso-treatment-als

Complex of the DNA binding core domain of the transcription factor MEF2A with a 20mer oligonucleotide ... Complex of the DNA binding core domain of the transcription factor MEF2A with a 20mer oligonucleotide. *PDB DOI: 10.2210/ ... and a 20mer DNA oligonucleotide comprising the consensus sequence CTA(A/T)(4)TAG has been solved by NMR. The protein comprises ... and a 20mer DNA oligonucleotide comprising the consensus sequence CTA(A/T)(4)TAG has been solved by NMR. The protein comprises ...

https://www.rcsb.org/structure/1c7u

US-5952201-A chemical patent summary.

https://pubchem.ncbi.nlm.nih.gov/patent/US-5952201-A

In tissues, the midkine antisense oligonucleotides were mainly distributed in the liver, presenting liver-targeting properties ... Encapsulating the antisense oligonucleotide drug MK-ASODN with nanoliposomes greatly improved its potency and targeting to the ... Encapsulating the antisense oligonucleotide drug MK-ASODN with nanoliposomes greatly improved its potency and targeting to the ... Encapsulating the antisense oligonucleotide drug MK-ASODN with nanoliposomes greatly improved its potency and targeting to the ...

https://www.frontiersin.org/articles/10.3389/fphar.2021.769538/full

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 /EINPresswire.com/ -- The global Oligonucleotide Synthesis Market1 is forecasted to be ...

https://www.einpresswire.com/article_print/585344004/oligonucleotide-synthesis-market-future-development-key-business-strategies-and-deep-exploration-till-2027

... end of oligonucleotides using the H-phosphonate approach. The photoenol-functionalized DNA is subsequently employed for the ... Photo-induced chemistry for the design of oligonucleotide conjugates and surfaces A. Vigovskaya, D. Abt, I. Ahmed, C. M. ... A photocaged diene is introduced at the 5′-end of oligonucleotides using the H-phosphonate approach. The photoenol- ...

https://pubs.rsc.org/en/content/articlelanding/2016/tb/c5tb02207j

... dc.contributor.author. Wilkinson, Adrian J.. en. ...

https://era.ed.ac.uk/handle/1842/11574?show=full

Correction of IKBKAP exon 20 splicing by splice switching oligonucleotides. G. H. Bruun, T. K. Doktor, J. S. Andersen, A. G. B ... Correction of IKBKAP exon 20 splicing by splice switching oligonucleotides. / Bruun, G. H.; Doktor, T. K.; Andersen, J. S. et ... Correction of IKBKAP exon 20 splicing by splice switching oligonucleotides. In: European Journal of Human Genetics. 2018 ; Vol ... Correction of IKBKAP exon 20 splicing by splice switching oligonucleotides. European Journal of Human Genetics. 2018 Oct;26:627 ...

https://portal.findresearcher.sdu.dk/en/publications/correction-of-ikbkap-exon-20-splicing-by-splice-switching-oligonu

Wackerbarth, H., Grubb, M., Marie, R. C. W., Boisen, A., & Ulstrup, J. (2004). Self-Assembly of Sulfur Achored Oligonucleotide. ... Wackerbarth, H, Grubb, M, Marie, RCW, Boisen, A & Ulstrup, J 2004, Self-Assembly of Sulfur Achored Oligonucleotide., ... Self-Assembly of Sulfur Achored Oligonucleotide.. Hainer Wackerbarth, Mikala Grubb, Rodolphe Charly Willy Marie, Anja Boisen, ... Self-Assembly of Sulfur Achored Oligonucleotide. / Wackerbarth, Hainer; Grubb, Mikala; Marie, Rodolphe Charly Willy et al. ...

https://orbit.dtu.dk/en/publications/self-assembly-of-sulfur-achored-oligonucleotide

... we anticipate the overall oligonucleotide synthesis market to grow at over 10% CAGR ... Driven by the rising demand for oligonucleotides and increase in number of oligonucleotide synthesis companies, ... Oligonucleotide Synthesis Market, Oligonucleotides Modification Market and Oligonucleotides Purification Market: Focus on ... Type of Oligonucleotide Manufactured (Antisense, siRNA, shRNA, miRNA and Others), Scale of Operation, Purpose of Production (In ...

https://www.rootsanalysis.com/reports/oligonucleotide-synthesis/ask-question.html

A Study to Investigate the Safety and Tolerability of Single and Multiple Ascending Doses of Antisense Oligonucleotide STK-001 ...

https://www.mayo.edu/research/clinical-trials/cls-20490427?p=1

Methods to suppress expression of mRNAs include antisense oligonucleotides (ASOs) and RNA interference (RNAi). (nih.gov)
This invention relates to the design and synthesis of antisense oligonucleotides which can be administered to inhibit the replication of cytomegalovirus and treat cytomegalovirus infections. (justia.com)
Here, we identified potent next-generation constrained ethyl (cEt) antisense oligonucleotides (ASOs) to selectively target either human or mouse YAP1 and evaluated these in several preclinical models of both HCC and HNSCC. (aacrjournals.org)
A recently proposed therapeutic strategy has been the use of antisense oligonucleotides (AOs) to manipulate pre-mRNA splicing to remove exons from the dystrophin transcript such that the DMD mutation is removed or bypassed to allow a semi-functional protein to be produced. (edu.au)
Conclusions: : The inhibition of α-synuclein production in dopamine neurons and its accumulation in cortical/striatal projection areas may alleviate the early deficits of dopamine function, showing the high translational value of antisense oligonucleotides as a disease modifying therapy for PD and related synucleinopathies. (elsevier.com)
Multiple factor XI inhibitors are currently under evaluation in clinical trials, including parenterally administered antisense oligonucleotides, monoclonal antibodies, and orally active small-molecule inhibitors. (medscape.com)

Here, we show that long-adapter single-strand oligonucleotide (LASSO) probes can capture and clone thousands of kilobase DNA fragments in a single reaction. (nature.com)
Padlock probes: circularizing oligonucleotides for localized DNA detection. (nature.com)
The selection of suitable oligonucleotide probes remains a bottleneck in the microarray workflow [ 2 ]. (biomedcentral.com)
We tested human whole genome microarrays for cross-species reactivity with AGM transcripts using both long oligonucleotide arrays (60-mer probes) and short oligonucleotide arrays (25-mer). (archives-ouvertes.fr)
This qualitative in-vitro diagnostics test uses oligonucleotide probes labeled with four different fluorescent dyes. (cdc.gov)
Oligonucleotide probes. (who.int)
Perioperative genomic profiles using structure-specific oligonucleotide probes. (cdc.gov)

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. (einpresswire.com)
VANCOUVER, BC, CANADA, August 10, 2022 / EINPresswire.com / -- 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. (einpresswire.com)
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. (einpresswire.com)
This report aims to provide detailed insights into the Oligonucleotide Synthesis Market . (express-press-release.net)
therefore, an increase in government-funded projects will positively impact the overall growth of the oligonucleotide synthesis market. (express-press-release.net)

Detection and typing of NDV, IBV, or AIV using oligonucleotide microarrays. (biomedcentral.com)
Long oligonucleotide microarrays for African green monkey gene expression profile analysis. (archives-ouvertes.fr)

The conjugation of small molecules that interact with nucleic acids through intercalation, edge and groove binding has been shown to improve the strength and specificity of oligonucleotide hybridisation, whilst the conjugation of compounds that chemically react with nucleic acids has been used to invoke cross-linking and cleavage reactions at oligonucleotide target sites. (port.ac.uk)

Oligonucleotide therapeutics - the emerging medicine class - are harnessing the therapeutic benefit of targeting genetic material via antisense, mRNA, RNAi, saRNA and siRNA. (pharmanews.eu)

GAITHERSBURG, Md. and SUZHOU, China , Sept. 20, 2022 /PRNewswire/ -- Sirnaomics Ltd . (the " Company " or " Sirnaomics ", stock code: 2257.HK), a leading biopharmaceutical company in discovery and development of RNAi therapeutics, announced today that it will present the latest developments on delivery of novel RNAi therapies for cancer, and its GalAhead™ platform and programs, at the 2nd Annual Oligonucleotide Therapeutics and Delivery Conference. (yahoo.com)
SMi's inaugural Oligonucleotide Therapeutics and Delivery conference is here to keep you updated. (pharmanews.eu)
Established on the success of our RNA Therapeutics series, we look forward to welcoming you at Oligonucleotide Therapeutics and Delivery to join the conversation around maximizing the potential of oligo-based treatments. (pharmanews.eu)
Phase 2/3 clinical trials by ProQR Therapeutics is testing RNA antisense oligonucleotide gene therapy. (medscape.com)
Dr Crooke has received numerous honours and awards for his pioneering work in RNA-targeted therapeutics including the prestigious Massry Prize, the Oligonucleotide Therapeutics Society Lifetime Achievement Award, the American Chemical Society's E.B. Hershberg Award for Important Discoveries in Medicinally Active Substances, the Prix Galien Best Biotechnology Award for Spinraza, the Scrip Lifetime Achievement Award, and BIO's Helix Award for the most important innovation. (pharmafile.com)

In this position you will be responsible for the synthesis, purification, and characterization of small organic compounds and oligonucleotides produced within our Oligonucleotide Process Chemistry group. (biospace.com)
Erratum: Evaluation of oligonucleotide sequence capture arrays and comparison of next-generation sequencing platforms for use in molecular diagnostics (Clinical Chemistry (2010) 56 (1297-1306) DOI: 10.1373/clinchem. (elsevier.com)

Although this has been hugely successful, a better strategy would be to use oligonucleotides to target genomic DNA directly to prevent messenger RNA expression altogether. (findaphd.com)

The aim of this review is to summarize the properties of some of these small molecule-oligonucleotide conjugates, with an emphasis on their biological applications. (port.ac.uk)
Fox, Keith R. / Small molecule-oligonucleotide conjugates . (port.ac.uk)

Using the long oligonucleotide arrays, we detected 4-fold more AGM transcripts than with the short oligonucleotide technology. (archives-ouvertes.fr)
The specificity of the signals obtained with the long oligonucleotide arrays was determined by analyzing the transcriptome of concanavalin A-activated CD4+ T cells vs. nonactivated T cells of two monkey species AGM and macaque. (archives-ouvertes.fr)
High-density oligonucleotide arrays (HDONAs) are a powerful tool for assessing differential mRNA expression levels. (biomedcentral.com)
Here we have used "gene chip" technology (high density DNA-oligonucleotide arrays) to identify potential biomarkers of asphalt fume condensate (AFC) exposure. (cdc.gov)

Sequence Verification of Oligonucleotides Containing Multiple Arylamine Modifications by Enzymatic Digestion and Liquid Chromatography Mass Spectrometry (LC/MS)." Journal of the American Society for Mass Spectrometry 19, 8 (2008): 1147-1155. (uri.edu)
Analysis of the epitranscriptome with ion-pairing reagent free oligonucleotide mass spectrometry. (kaiser-lab.de)

Phosphorothioate Oligonucleotides" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (uams.edu)
This graph shows the total number of publications written about "Phosphorothioate Oligonucleotides" by people in UAMS Profiles by year, and whether "Phosphorothioate Oligonucleotides" was a major or minor topic of these publications. (uams.edu)
Below are the most recent publications written about "Phosphorothioate Oligonucleotides" by people in Profiles over the past ten years. (uams.edu)

Thus, to address the challenge of more highly multiplexed differential diagnoses, we established an oligonucleotide microarray platform. (cdc.gov)

1-4 Non-DNA components provide additional functionality, usually in the form of chemically-modified oligonucleotides that are hybridized to the nanostructures and that are typically manufactured by a DNA synthesizing company. (rsc.org)
The cost for chemically modified oligonucleotides renders the synthesis of DNA nanostructures expensive if many modifications are to be incorporated. (rsc.org)

Custom LNA Oligonucleotides are ideal for studies involving short or very similar sequences. (qiagen.com)
Oligonucleotides that might prove useful in this manner are known as triplex-forming oligonucleotides, on account of their binding to specific duplex sequences and generating a triplex structure. (findaphd.com)
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. (sussex.ac.uk)
Q2: Are the oligonucleotide sequences published or available? (cdc.gov)
The sequences for the oligonucleotides along with all characteristics and performance evaluations of the assay have been published. (cdc.gov)

Our research group has recently overcome a long-standing problem associated with these molecules using oligonucleotides containing modified DNA bases ( https://academic.oup.com/nar/article/49/13/7256/6316833?login=true ). (findaphd.com)
His early research focused on oligonucleotides, small molecules of DNA or RNA. (asu.edu)

You will become part of exclusive group of scientists who will synthesize oligonucleotides, peptides via solid-phase synthesis. (biospace.com)
Bachem is a leading, innovation-driven company specialising in the development and manufacture of peptides and oligonucleotides. (pharmiweb.com)

abstract = "The hybridization of exogenous oligonucleotides to cellular RNA and DNA offers a means to modulate the expression of specific genes, with applications in the treatment of viral infections, cancer and other diseases. (port.ac.uk)

Kostov O, Liboska R, Páv O, Novák P, Rosenberg I. Solid-Phase Synthesis of Phosphorothioate/Phosphonothioate and Phosphoramidate/Phosphonamidate Oligonucleotides. (ucdenver.edu)

The use of synthetic oligonucleotides in gene therapy is to inactivate the genes involved in the disease process. (genetherapynet.com)
Synthetic oligonucleotides are short strands of DNA that can be used to treat or manage a wide range of diseases, for example by gene silencing. (findaphd.com)
After seeing the exploding need for synthetic genes and developing an industry-leading platform for creating short, single-stranded DNA (oligonucleotides), the company made a $21 million investment in DNA synthesis start-up Gen9 that combined each company's sequencing library in return for an equity stake and a position on the board. (fool.com)

Methods: We used a non-viral gene therapy based on a new indatraline-conjugated antisense oligonucleotide (IND-ASO) to disrupt the α-synuclein mRNA transcription selectively in monoamine neurons of a PD-like mouse model and elderly nonhuman primates. (elsevier.com)

The use of oligonucleotides to activate the splicing of selected exons is limited by a poor understanding of the mechanisms affected. (strath.ac.uk)

Once the synthesis is complete, and the same column has been installed onto the C&D skid, the first step is to deprotect the cyanoethyl groups before the cleavage of the oligonucleotide from its solid support. (pharmiweb.com)

We will develop an antisense oligonucleotide, or DNA therapy for diverse forms of amyotrophic lateral sclerosis (ALS). (ca.gov)

Oligonucleotides and derivatives thereof are useful candidate drugs, for example, for cancer therapy. (justia.com)

RNA extracted from sediment was probed with radiolabeled oligonucleotides targeting bacterial, archaeal, and eukaryotic SSU rRNAs, as well as with a universal probe. (cmich.edu)

In accordance with the preferred embodiments, oligonucleotides such as ISIS 2922 are designed to bind with portions of the CMV mRNAs which code for the IE1, IE2 or DNA polymerase proteins. (justia.com)
The results suggest that splicing limited by weak signals can be rescued by rapid exchange of TOES oligonucleotides in various complexes and raise the possibility that SR proteins associate transiently with ESEs. (strath.ac.uk)
The cellular environment, at an average macromolecular concentration of 300 - 400 mg/mL, naturally forces proteins, oligonucleotides and other biomacromolecules into close proximity with each other. (wyatt.com)

Inotersen is an antisense oligonucleotide that causes degradation of mutant and wild-type transthyretin mRNA by binding TTR mRNA. (medscape.com)
Compositions and methods for modulating the effects of cytomegalovirus (CMV) infections are disclosed, comprising contacting CMV mRNA with an oligonucleotide which can bind with at least portions of the CMV RNA. (justia.com)

In recent years, various oligonucleotides have made it through clinical trials and have now reached the clinic to some fanfare. (findaphd.com)

Nusinersen injection is in a class of medications called antisense oligonucleotide inhibitors. (medlineplus.gov)

Bachem, the Swiss pharmaceutical company, invested in a capacity expansion for large-scale production of oligonucleotide active pharmaceutical ingredients (APIs). (pharmiweb.com)

The unique phospholipid bilayer of the nanoliposomes effectively protects the encapsulated oligonucleotides from degradation by enzymes or other active substances. (frontiersin.org)
IMSEAR at SEARO: Enzymatic degradation and circular dichroism of deoxyguanosine oligonucleotides. (who.int)

After synthesis has taken place, an oligonucleotide has to undergo a process of cleaving and deprotection (C&D). To improve efficiency, Bachem has equipped their oligonucleotide production line with an automated, large-scale C&D system which uses a two-step process. (pharmiweb.com)
The second step of the process is the deprotection of the protecting groups from the oligonucleotide. (pharmiweb.com)
Acta, Vol 83 (2000) p.1417-1423 disclose deprotection of β-cyanoethyl protected oligonucleotides with a 0.5 M concentrated DBU solution in acetonitrile. (justia.com)
It has been found, surprisingly, that the process according to the invention allows for particularly efficient deprotection of phosphorus protected oligonucleotides, in particular of β-cyanoethyl protective groups, with high selectivity and yield. (justia.com)

Initial characterization of isolates by RNase T1 oligonucleotide fingerprinting was inconclusive. (cdc.gov)

The covalent attachment of DNA oligonucleotides onto crystalline silicon (100) surfaces, in patterns with submicron features, in a straightforward, two-step process is presented. (soton.ac.uk)
The N-hydroxysuccinimide ester surface acted as a template for the subsequent covalent attachment of aminohexyl-modified DNA-oligonucleotides. (soton.ac.uk)

FIG. 1 shows IP-HPLC data from the analysis of the oligonucleotide product of Example 1 . (justia.com)
FIG. 2 shows LC/MS data from the analysis of the oligonucleotide product of Example 1 . (justia.com)
FIG. 3 shows RP-HPLC data from the analysis of the oligonucleotide product of Example 2 . (justia.com)
FIG. 8 shows RP-HPLC data from the analysis of the oligonucleotide product of Example 5 . (justia.com)
Analysis of oligonucleotides with the A. (selectscience.net)

To ensure only the highest-quality oligonucleotide is supplied to customers, Bachem designed a large-scale oligonucleotide synthesiser. (pharmiweb.com)
This synthesiser optimises the process of oligonucleotide synthesis and has been qualified for GMP batches from a 0.2 mol to 2 mol scale. (pharmiweb.com)
To further optimise the process of oligonucleotide manufacturing, Bachem has set up the first continuous chromatography equipment for use at an industrial scale. (pharmiweb.com)

Can your Mix-n-Stain™ kits be used to label oligonucleotides with CF® Dyes or enzymes? (biotium.com)

Additionally, over the anticipated timeframe, the expanding applications of synthesised oligonucleotides are also predicted to support market expansion. (einpresswire.com)

For more information about Sirnaomics' presentation, please visit the event website at https://www.smgconferences.com/pharmaceuticals/uk/conference/oligonucleotide-discovery-delivery . (yahoo.com)

The solution structure of the 33 kDa complex between the dimeric DNA-binding core domain of the transcription factor MEF2A (residues 1-85) and a 20mer DNA oligonucleotide comprising the consensus sequence CTA(A/T)(4)TAG has been solved by NMR. (rcsb.org)

The market is expanding in this sector to fulfil the demands of the enormous number of individuals suffering from chronic diseases, which is driven by the increased number of inpatient and outpatient hospitalizations as well as the growing need for oligonucleotide medications. (einpresswire.com)

Custom LNA Oligonucleotides are intended for molecular biology applications. (qiagen.com)

The present invention relates to a process for the manufacture of oligonucleotides. (justia.com)

Mirkin, C & Elghanian, R Nov. 11 2003, NANOPARTICLES HAVING OLIGONUCLEOTIDES ATTACHED THERETO AND USES THEREFORE , Patent No. 6645721. (northwestern.edu)
Affymetrix first filed a patent infringement suit against Incyte in January 1998, alleging that Incyte was infringing on its patent number 5,445,934, which covers an "array of oligonucleotides on a solid substrate. (genomeweb.com)

Plus, an interactive half day pre-conference workshop on Oligonucleotide drug discovery: Target selection, delivery, molecular design and lead identification. (pharmanews.eu)

Each step within the company's oligonucleotide manufacturing process uses unique, innovative equipment to deliver the highest-quality products and to increase sustainability. (pharmiweb.com)
This project aims to revolutionize the manufacturing of oligonucleotides through a collaboration with AstraZeneca, Exactmer, Novartis, and the UK Research & Innovation. (express-press-release.net)

The unique, custom-built synthesiser, C&D system and MCSGP equipment will all enhance the quality, sustainability and cost-effectiveness of oligonucleotide API production. (pharmiweb.com)