NationMaster - Encyclopedia: Oligonucleotides

Oligonucleotides are short sequences of nucleotides (RNA or DNA), typically with twenty or fewer bases. Automated synthesizers allow the synthesis of oligonucleotides up to 160 to 200 bases. The length of a synthesized base is usually denoted by 'mer', for example a fragment of 25 bases would be called a 25-mer. Oligonucleotides are often used as probes for detecting complementary DNA or RNA because they bind readily to their complements. Examples of procedures that use oligonucleotides are DNA microarrays, Southern blots, fluorescent in situ hybridization (FISH), and the synthesis of artificial genes. A nucleotide is a chemical compound that consists of a heterocyclic base, a sugar, and one or more phosphate groups. ... This article or section does not adequately cite its references or sources. ... The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ... Look up primer in Wiktionary, the free dictionary. ... Look up primer in Wiktionary, the free dictionary. ... On the left: nucleotides that forms the DNA and their complementary. ... Example of an approximately 40,000 probe spotted oligo microarray with enlarged inset to show detail. ... A Southern blot is a method in molecular biology of enhancing the result of an agarose gel electrophoresis by marking specific DNA sequences. ... A metaphase cell positive for the bcr/abl rearrangement using FISH. The chromosomes can be seen in blue. ...

Oligonucleotides composed of DNA (deoxyoligonucleotides) are often used in the polymerase chain reaction (PCR), a procedure that can be employed to amplify almost any piece of DNA. In this instance, the oligonucleotide is often referred to as a primer, or a short piece of DNA that binds to its complementary target sequence. This generates a place for a polymerase to bind and extend the primer by the addition of nucleotides to make a copy of the target sequence. Polymerase chain reaction (PCR) is a biochemistry and molecular biology technique[1] for enzymatically replicating DNA without using a living organism, such as E. coli or yeast. ... ITaq DNA polymerase A polymerase (EC 2. ... A nucleotide is an organic molecule consisting of a heterocyclic nucleobase (a purine or a pyrimidine), a pentose sugar (deoxyribose in DNA or ribose in RNA), and a phosphate or polyphosphate group. ...

Antisense oligonucleotides

Antisense oligonucleotides are single strands of DNA or RNA that are complementary to a chosen sequence. In the case of antisense RNA they prevent translation of complementary RNA strands by binding to it. Antisense DNA can be used to target a specific, complementary (coding or non-coding) RNA. If binding takes places this DNA/RNA hybrid can be degraded by the enzyme RNase H. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein. ... The enzyme RNase H (EC 3. ...

DNA MicroArray

One subtype of DNA MicroArrays can be described as substrates (nylon, glass etc.) to which oligonucleotides have been bound at high density. Currently there exist three applications of DNA MicroArrays: polymorphism studies, gene expression studies, and tracking down certain diseases.

Synthesis

Oligonucleotides are chemically synthesized using nucleotides, called phosphoramidites, normal nucleotides which have protection groups: preventing amine, hydroxyl groups and phosphate groups interacting incorrectly. One phophoramidite is added at the time, the product's 5' phosphate is deprotected and a new base is added and so on (backwards), at the end, all the protection groups are removed. Nethertheless, being a chemical process, several incorrect interactions occur leading to some defective products. The longer the oligonucleotide sequence that is being synthesized, the more defects there are, thus this process is only practical for producing short sequences of nucleotides. HPLC can be used to isolate products with the proper sequence. Nucleoside phosphoramidites are used to synthesise short nucleic acid chains. ... Chromatography is a family of analytical chemistry techniques for the separation of mixtures. ...

See also

In chemistry, an amino acid is any molecule that contains both amino and carboxylic acid functional groups. ... An antigen is a substance that stimulates an immune response, especially the production of antibodies. ... Schematic of antibody binding to an antigen An antibody or immunoglobulin is a large Y-shaped protein used by the immune system to identify and neutralize foreign objects like bacteria and viruses. ... Aptamers are oligo nucliec acid or peptide molecules selected from large randome sequence pool to bind to specific target molecule. ... THERE ARE NOW 30 CHROMOSOMES!!!!!! Figure 1: A representation of a condensed eukaryotic chromosome, as seen during cell division. ... The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ... An epitope is the part of a macromolecule that is recognized by the immune system, specifically by antibodies, B cells, or cytotoxic T cells. ... For other meanings of this term, see gene (disambiguation). ... Morpholino oligos are an antisense technology used to block access of other molecules to specific sequences within nucleic acid molecules. ... In biology, polymorphism can be defined as the occurrence in the same habitat of two or more forms of a trait in such frequencies that the rarer cannot be maintained by recurrent mutation alone. ... Polynucleotide literally means many nucleotides. ... Recombinant deoxyribonucleic acid(rDNA) is an artificial DNA sequence resulting from the combining of two other DNA sequences in a plasmid. ...

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Category: Genetics Biochemistry is the study of the chemical processes and transformations in living organisms. ... Peptides (from the Greek Ï€ÎµÏ€Ï„Î¿Ï‚, digestible), are the family of short molecules formed from the linking, in a defined order, of various Î±-amino acids. ... Phenylalanine is one of the standard amino acids. ... This article or section does not cite its references or sources. ... Lactose is a disaccharide found in milk. ... A polyunsaturated triglyceride. ... Many terpenes are derived from conifer resins, here a pine. ... Carotenoids are organic pigments that are naturally occurring in plants and some other photosynthetic organisms like algae, some types of fungus and some bacteria. ... Polypyrrole A Polypyrrole (PPy) is a chemical compound formed from a number of connected pyrrole ring structures. ... A cofactor is any substance that needs to be present in addition to an enzyme to catalyze a certain reaction. ... Steroid skeleton of lanosterol. ... Molecular structure of flavone The term flavonoid refers to a class of plant secondary metabolites based around a phenylbenzopyrone structure. ... Diagram of Ephedrine An alkaloid, strictly speaking, is a naturally-occurring amine produced by a plant,[1] but amines produced by animals and fungi are also called alkaloids. ... Polyketides are secondary metabolites from bacteria, fungi, plants, and animals. ... A glycoside is a molecule where a sugar group is bonded through its anomeric carbon to a nonsugar group by either an oxygen or a nitrogen atom. ... This article or section does not cite its references or sources. ... Adenine Guanine Thymine Cytosine ... Adenine is one of the two purine nucleobases used in forming nucleotides of the nucleic acids DNA and RNA. In DNA, adenine binds to thymine via two hydrogen bonds to assist in stabilizing the nucleic acid structures. ... For the similarly-spelled vitamin compound, see Thiamine Thymine, also known as 5-methyluracil, is a pyrimidine nucleobase. ... Uracil is a pyrimidine which is common and naturally occurring. ... Guanine is one of the five main nucleobases found in the nucleic acids DNA and RNA; the others being adenine, cytosine, thymine, and uracil. ... Cytosine is one of the 5 main nucleobases used in storing and transporting genetic information within a cell in the nucleic acids DNA and RNA. It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an amine group at position 4 and a keto group at... Purine is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring. ... Pyrimidine is a heterocyclic aromatic organic compound similar to benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of the six-member ring [1]. It is isomeric with two other forms of diazine. ... Nucleosides are glycosylamines made by attaching a nucleobase (often reffered to simply as bases) to a ribose ring. ... The chemical structure of adenosine Adenosine is a nucleoside comprised of adenine attached to a ribose (ribofuranose) moiety via a Î²-N9-glycosidic bond. ... Uridine is a molecule (known as a nucleoside) that is formed when uracil is attached to a ribose ring (also known as a ribofuranose) via a β-N1-glycosidic bond. ... The chemical structure of Guanosine Guanosine is a nucleoside comprising guanine attached to a ribose (ribofuranose) ring via a Î²-N9-glycosidic bond. ... Cytidine is a molecule (known as a nucleoside) that is formed when cytosine is attached to a ribose ring (also known as a ribofuranose) via a β-N1-glycosidic bond. ... The chemical structure of adenosine Adenosine is a nucleoside formed when adenine is attached to a ribose ring (also known as a ribofuranose) via a β-N9-glycosidic bond. ... The chemical structure of deoxythymidine Thymidine (more precisely called deoxythymidine can also be labelled deoxyribosylthymine, and thymine deoxyriboside) is a chemical compound, more precisely a pyrimidine deoxynucleoside. ... Guanosine is a molecule (known as a nucleoside) that is formed when guanine is attached to a ribose ring (also known as a ribofuranose) via a β-N9-glycosidic bond. ... Cytidine is a molecule (known as a nucleoside) that is formed when cytosine is attached to a ribose ring (also known as a ribofuranose) via a β-N1-glycosidic bond. ... A nucleotide is a chemical compound that consists of a heterocyclic base, a sugar, and one or more phosphate groups. ... Adenosine monophosphate, also known as 5-adenylic acid and abbreviated AMP, is a nucleotide that is found in RNA. It is an ester of phosphoric acid with the nucleoside adenosine. ... Uridine monophosphate, also known as 5-uridylic acid and abbreviated UMP, is a nucleotide that is found in RNA. It is an ester of phosphoric acid with the nucleoside uridine. ... Guanosine monophosphate, also known as 5-guanidylic acid and abbreviated GMP, is a nucleotide that is found in RNA. It is an ester of phosphoric acid with the nucleoside guanosine. ... Cytidine monophosphate, also known as 5-cytidylic acid and abbreviated CMP, is a nucleotide that is found in RNA. It is an ester of phosphoric acid with the nucleoside cytidine. ... Adenosine diphosphate, abbreviated ADP, is a nucleotide. ... Uridine diphosphate, abbreviated UDP, is a nucleotide. ... Cytidine diphosphate, abbreviated CDP, is a nucleotide. ... Adenosine 5-triphosphate (ATP) is a multifunctional nucleotide that is most important as a molecular currency of intracellular energy transfer. ... Adenosine 5-triphosphate (ATP) is a multifunctional nucleotide primarily known in biochemistry as the molecular currency of intracellular energy transfer. ... Guanosine triphosphate (GTP) is also known as guanosine-5-triphosphate. ... Adenosine 5-triphosphate (ATP) is a multifunctional nucleotide primarily known in biochemistry as the molecular currency of intracellular energy transfer. ... Structure of cAMP cAMP represented in three ways, the left with sticks-representation, the middle with structure formula, and the right with space filled representation. ... Cyclic ADP Ribose popularly known as cADPR is a cyclic adenine nucleotide (like cAMP) with two phosphate gruops present on 5 OH of the adenosine (like ADP), further connected to another ribose at the 5 position which in turn closes the cycle by glycosidic bonding to the Nitrogen1 of the... Cyclic guanosine monophosphate (cGMP) is a second messenger derived from GTP. Cyclic guanosine monophosphate (cGMP) is a cyclic nucleotide derived from guanosine triphosphate (GTP). ... A nucleotide is a monomer or the structural unit of nucleotide chains forming nucleic acids as RNA and DNA. A nucleotide consists of a heterocyclic nucleobase, a pentose sugar, and a phosphate or polyphosphate group. ... This article belongs in one or more categories. ... Thymidine monophosphate, also known as 5-thymidylic acid and abbreviated TMP, is a nucleotide that is found in RNA. It is an ester of phosphoric acid with the nucleoside thymidine. ... Deoxyguanosine monophosphate is a derivative of the common nucleic acid GTP, or guanosine triphosphate, in which the -OH (hydroxyl) group on the 2 carbon on the nucleotides pentose has been removed (hence the deoxy- part of the name). ... Cytidine is a molecule (known as a nucleoside) that is formed when cytosine is attached to a ribose ring (also known as a ribofuranose) via a β-N1-glycosidic bond. ... Deoxyadenosine diphosphate is a derivative of the common nucleic acid ATP, or adenosine triphosphate, in which the -OH (hydroxyl) group on the 2 carbon on the nucleotides pentose has been removed (hence the deoxy- part of the name). ... Thymidine diphosphate, abbreviated TDP, is a nucleotide. ... Deoxyguanosine diphosphate is a derivative of the common nucleic acid GTP, or guanosine triphosphate, in which the -OH (hydroxyl) group on the 2 carbon on the nucleotides pentose has been removed (hence the deoxy- part of the name). ... Please wikify (format) this article or section as suggested in the Guide to layout and the Manual of Style. ... Deoxy adenosine triphosphate produces energy within the cells and is the basis for normal functioning of all body systems and organs. ... 3D-Model of thymidine triphosphate Thymidine triphosphate or TTP is one of the four nucleoside triphosphates that make up DNA. It can be used by DNA ligase to create overlapping sticky ends so that protruding ends of opened microbial plasmids maybe closed up. ... The chemical structure of dGTP Deoxyguanosine triphosphate, normally shortened to dGTP has a chemical structure of Na4 â€¢ 3 H2O and a molecular weight of 649. ... This article or section is in need of attention from an expert on the subject. ... This article or section does not adequately cite its references or sources. ... This article or section does not adequately cite its references or sources. ... The life cycle of an mRNA in a eukaryotic cell. ... Piwi-interacting RNA (piRNA) is a class of small RNA molecules that is expressed uniquely in mammalian testes and forms RNA-protein complexes with Piwi proteins. ... It has been suggested that Queuine be merged into this article or section. ... A non-coding RNA (ncRNA) is any RNA molecule that functions without being translated into a protein. ... A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein. ... A short hairpin RNA (shRNA) is a sequence of RNA that makes a tight hairpin turn that can be used in gene expression silence. ... Small interfering RNA (siRNA), sometimes known as short interfering RNA, are a class of 20-25 nucleotide-long RNA molecules that interfere with the expression of genes. ... A non-coding RNA (ncRNA) is any RNA molecule that functions without being translated into a protein. ... The title given to this article is incorrect due to technical limitations. ... A non-coding RNA (ncRNA) is any RNA molecule that functions without being translated into a protein. ... A locked nucleic acid (LNA) is a modified RNA nucleotide. ... The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ... The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ... // Mitochondrial DNA (mtDNA) is DNA that is located in mitochondria. ... In genetics, complementary DNA (cDNA) is DNA synthesized from a mature mRNA template. ... Figure 1: Schematic drawing of a bacterium with plasmids enclosed. ... A cosmid is a type of plasmid (often used as a cloning vector) constructed by the insertion of cos sequences, DNA-Sequences of the Phage Lambda Virus. ... A bacterial artificial chromosome (BAC) is a DNA construct, based on a fertility plasmid (or F-plasmid), used for transforming and cloning in bacteria, usually E. coli. ... A yeast artificial chromosome (short YAC) is a vector used to clone large DNA fragments (larger than 100 kb and up to 3000 kb). ... A human artificial chromosome (short HAC) is a microchromosome that can act as a new chromosome in a population of human cells. ... This article or section does not cite its references or sources. ... GNA is glycol nucleic acid, a chemical similar to DNA or RNA but differing in the composition of its backbone. ... PNA is peptide nucleic acid, a chemical similar to DNA or RNA but differing in the composition of its backbone. ... TNA is threose nucleic acid, a chemical similar to DNA or RNA but differing in the composition of its backbone. ... Morpholino oligos are an antisense technology used to block access of other molecules to specific sequences within nucleic acid molecules. ...

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