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Encyclopedia > Oligonucleotide

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' (from 'Greek' meros "part"). 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. ... Ribonucleic acid or RNA is a nucleic acid polymer consisting of nucleotide monomers that plays several important roles in the processes that translate genetic information from deoxyribonucleic acid (DNA) into protein products; RNA acts as a messenger between DNA and the protein synthesis complexes known as ribosomes, forms vital portions... The structure of part of a DNA double helix Deoxyribonucleic acid, or DNA, is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all known living organisms. ... In chemistry, a monomer (from Greek mono one and meros part) is a small molecule that may become chemically bonded to other monomers to form a polymer. ... In chemistry, a monomer (from Greek mono one and meros part) is a small molecule that may become chemically bonded to other monomers to form a polymer. ... On the left: nucleotides that forms the DNA and their complementary. ... It has been suggested that Gene chip technology be merged into this article or section. ... A Southern blot is a method routinely used in molecular biology to check for the presence of a DNA sequence in a DNA sample. ... 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. PCR tubes in a stand after a colony PCR The polymerase chain reaction (PCR) is a biochemistry and molecular biology technique[1] for exponentially amplifying DNA, via enzymatic replication, 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. ...


Oligonucleotides are sometimes referred to as oligos.

Contents

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

Main article: oligonucleotide 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 phosphoramidite 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. Nevertheless, 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. Oligonucleotide synthesis is the non-biological, chemical synthesis of defined short sequences of nucleic acids. ... 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

  • Amino acids are the building blocks of proteins. There are 20 natural amino acids.
  • Antigen is a substance which, after take-up by an organism, elicits an immune response.
  • Antibody is a protein produced by the immune system in order to protect the body against a foreign substance (antigen).
  • Aptamer Oligonucleotides with important biological applications
  • ChromosomeComponents in a cell that contain genetic information. Each chromosome contains numerous genes. Chromosomes occur in pairs: one obtained from the mother; the other from the father. Chromosomes of different pairs are often visibly different from each other (see also DNA).
  • DNA The material inside the nucleus of cells that carries genetic information. The scientific name for DNA is deoxyribonucleic acid.
  • Epitope is the smallest part of an antigen that can be recognised by an antibody.
  • Gene The fundamental physical and functional unit of hereditary.
  • Morpholino oligos have non-natural backbones which do not activate RNase-H but can knockdown gene expression or modify splicing.
  • Polymorphism The appearance in a population of the same gene in multiple forms because of mutations.
  • Polynucleotide
  • Recombinant DNA is DNA formed by the artificial combination of several existing DNA strands.

In chemistry, an amino acid is any molecule that contains both amino and carboxylic acid functional groups. ... This article does not cite any references or sources. ... Each antibody binds to a specific antigen; an interaction similar to a lock and key. ... Aptamers are oligo nucliec acid or peptide molecules selected from large randome sequence pool to bind to specific target molecule. ... 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, or DNA, is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all known 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 a non-technical introduction to the topic, see Introduction to Genetics. ... Segment of a Morpholino-RNA heteroduplex, 8-mer shown In molecular biology, a Morpholino is a kind of molecule used to modify gene expression. ... 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 DNA (rDNA) is an artificial DNA sequence resulting from the combination of different DNA sequences. ...

References

Pierce, "GENETICS: A Conceptual Approach", 2005


External Links


v  d  e
Major families of biochemicals
Peptides | Amino acids | Nucleic acids | Carbohydrates | Lipids | Terpenes | Carotenoids | Tetrapyrroles | Enzyme cofactors | Steroids | Flavonoids | Alkaloids | Polyketides | Glycosides
Analogues of nucleic acids: Types of Nucleic Acids Analogues of nucleic acids:
Nucleobases: Purine (Adenine, Guanine) | Pyrimidine (Uracil, Thymine, Cytosine)
Nucleosides: Adenosine/Deoxyadenosine | Guanosine/Deoxyguanosine | Uridine | Thymidine | Cytidine/Deoxycytidine
Nucleotides: monophosphates (AMP, UMP, GMP, CMP) | diphosphates (ADP, UDP, GDP, CDP) | triphosphates (ATP, UTP, GTP, CTP) | cyclic (cAMP, cGMP, cADPR)
Deoxynucleotides: monophosphates (dAMP, TMP, dGMP, dCMP) | diphosphates (dADP, TDP, dGDP, dCDP) | triphosphates (dATP, TTP, dGTP, dCTP)
Ribonucleic acids: RNA | mRNA | piRNA | tRNA | rRNA | ncRNA | gRNA | shRNA | siRNA | snRNA | miRNA | snoRNA
Deoxyribonucleic acids: DNA | mtDNA | cDNA | plasmid | Cosmid | BAC | YAC | HAC
Analogues of nucleic acids: GNA | PNA | TNA | Morpholino | LNA

  Results from FactBites:
 
Oligonucleotide Theraputic Society- Homepage (199 words)
OTS is an open, non-profit forum to foster academia and industry-based research and development of oligonucleotide therapeutics (RNAi, CpG, antisense, and others).
OTS membership is open to all individuals from industry, academia and other institutions worldwide who are interested in research and development of oligonucleotide therapeutics (RNAi, CpG, antisense, ribozymes, and others).
Membership includes a 1-year subscription to the society's journal "Oligonucleotides".
Oligonucleotide - Wikipedia, the free encyclopedia (321 words)
Oligonucleotides are often used as probes for detecting complementary DNA or RNA because they bind readily to their complements.
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.
Antisense Oligonucleotides are strands of RNA that prevent translation of complementary RNA strands by binding to it.
  More results at FactBites »

 
 

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