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Oligonucleotide
 
 
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An oligonucleotide is a short nucleic acid
Nucleic acid

A nucleic acid is a macromolecule composed of chains of monomeric nucleotides. In biochemistry these molecules carry genetic information or form structures within Cell ....
 polymer, typically with twenty or fewer bases
Nucleotide

Nucleotides are molecules that comprise the structural units of RNA and DNA. Additionally, nucleotides play central roles in metabolism. In that capacity, they serve as sources of chemical energy , participate in cell signaling , and are incorporated into important cofactors of enzymatic reactions ....
. Although they can be formed by bond cleavage
Bond cleavage

Bond cleavage, or scission, is the splitting of chemical bonds.If the two electrons in a cleaved covalent bond are divided between the products, the process is known as homolytic fission or homolysis....
 of longer segments, they are now more commonly synthesized by polymerizing individual nucleotide precursors. Automated synthesizers allow the synthesis of oligonucleotides up to 160 to 200 bases.

The length of the oligonucleotide is usually denoted by "mer
Monomer

A monomer is a small molecule that may become Chemistry chemical bonding to other monomers to form a polymer....
" (from Greek
Greek language

Greek is an Indo-European languages native to the southern Balkan peninsula, the language of the Greek people. It forms an independent branch within Indo-European....
 meros, "part").






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An oligonucleotide is a short nucleic acid
Nucleic acid

A nucleic acid is a macromolecule composed of chains of monomeric nucleotides. In biochemistry these molecules carry genetic information or form structures within Cell ....
 polymer, typically with twenty or fewer bases
Nucleotide

Nucleotides are molecules that comprise the structural units of RNA and DNA. Additionally, nucleotides play central roles in metabolism. In that capacity, they serve as sources of chemical energy , participate in cell signaling , and are incorporated into important cofactors of enzymatic reactions ....
. Although they can be formed by bond cleavage
Bond cleavage

Bond cleavage, or scission, is the splitting of chemical bonds.If the two electrons in a cleaved covalent bond are divided between the products, the process is known as homolytic fission or homolysis....
 of longer segments, they are now more commonly synthesized by polymerizing individual nucleotide precursors. Automated synthesizers allow the synthesis of oligonucleotides up to 160 to 200 bases.

The length of the oligonucleotide is usually denoted by "mer
Monomer

A monomer is a small molecule that may become Chemistry chemical bonding to other monomers to form a polymer....
" (from Greek
Greek language

Greek is an Indo-European languages native to the southern Balkan peninsula, the language of the Greek people. It forms an independent branch within Indo-European....
 meros, "part"). For example, a fragment of 25 bases would be called a 25-mer. Because oligonucleotides readily bind to their respective complementary
Complementarity (molecular biology)

In molecular biology, complementarity is a property of double-stranded nucleic acids such as DNA and RNA as well as DNA:RNA duplexes. Each strand is complementary to the other in that the base pairs between them are non-covalent bond connected via two or three hydrogen bonds....
 nucleotide, they are often used as probes
Hybridization probe

In molecular biology, a hybridization probe is a fragment of DNA or RNA of variable length , which is used to detect in DNA or RNA samples the presence of nucleotide sequences that are Complementarity to the sequence in the probe....
 for detecting DNA or RNA. Examples of procedures that use oligonucleotides include DNA microarray
DNA microarray

A DNA microarray is a multiplex technology used in molecular biology and in medicine. It consists of an arrayed series of thousands of microscopic spots of DNA oligonucleotides, called features, each containing picoMole s of a specific DNA sequence....
s, Southern blot
Southern blot

A Southern blot is a method routinely used in molecular biology to check for the presence of a DNA sequence in a DNA sample. Southern blotting combines agarose gel electrophoresis electrophoresis for size separation of DNA with methods to transfer the size-separated DNA to a filter membrane for probe hybridization....
s, ASO analysis
Allele specific oligonucleotide

An Allele Specific Oligonucleotide is a short piece of synthetic DNA complementary to the sequence of a variable target DNA. It acts as a Hybridization probe for the presence of the target in a Southern blot assay or, more commonly, in the simpler Dot blot assay....
, fluorescent in situ hybridization
Fluorescent in situ hybridization

FISH is a cytogenetics technique that can be used to detect and localize the presence or absence of specific DNA DNA sequence on chromosomes. It uses hybridization probe that bind to only those parts of the chromosome with which they show a high degree of sequence similarity....
 (FISH), and the synthesis of artificial genes.

Oligonucleotides composed of DNA (deoxyoligonucleotides) are often used in the polymerase chain reaction
Polymerase chain reaction

The polymerase chain reaction is a technique widely used in molecular biology. It derives its name from one of its key components, a DNA polymerase used to amplify a piece of DNA by in vitro enzyme DNA replication....
, a procedure that can greatly amplify almost any small piece of DNA. There, the oligonucleotide is referred to as a primer
Primer (molecular biology)

A primer is a strand of nucleic acid that serves as a starting point for DNA replication. They are required because the enzymes that catalyze replication, DNA polymerases, can only add new nucleotides to an existing strand of DNA....
, allowing DNA polymerase
DNA polymerase

A DNA polymerase is an enzyme that catalyze the polymerization of deoxyribonucleotides into a DNA strand. DNA polymerases are best-known for their role in DNA replication, in which the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand....
 to extend the oligonucleotide and replicate the complementary strand.

Synthesis


Oligonucleotides are chemically synthesized using nucleotides, called phosphoramidite
Phosphoramidite

Nucleoside phosphoramidites are used to oligonucleotide synthesis short nucleic acid chains.The chemical process allows several modifications, such as linker arms or using Nucleic acid analogues, such as LNA or morpholino or 2' group modified or abasic, non-canon bases or bases with a fluorescent group, linker arm to attach a fluorescent...
s, normal nucleotides that have protection groups: preventing amine, hydroxyl groups and phosphate groups from 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, 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 practical only for producing short sequences of nucleotides. HPLC can be used to isolate products with the proper sequence.

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 protein translation of certain messenger RNA
Messenger RNA

Messenger ribonucleic acid is a molecule of RNA encoding a chemical "blueprint" for a protein product. mRNA is transcription from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes....
 strands by binding to them. Antisense DNA can be used to target a specific, complementary (coding or non-coding
Non-coding RNA

A non-coding RNA is a functional RNA molecule that is not Translation into a protein. Less-frequently used synonyms are non-protein-coding RNA , non-messenger RNA , small non-messenger RNA , functional RNA ....
) RNA. If binding takes places this DNA/RNA hybrid can be degraded by the enzyme RNase H
RNase H

The enzyme RNase H is a ribonuclease that cleaves the 3'-O-P-bond of RNA in a DNA/RNA duplex to produce 3'-hydroxyl and 5'-phosphate terminated products....
.

DNA microarray


One subtype of DNA microarrays can be described as substrates (nylon, glass, etc.) to which oligonucleotides have been bound at high density. There are a number of applications of DNA microarrays
DNA microarray

A DNA microarray is a multiplex technology used in molecular biology and in medicine. It consists of an arrayed series of thousands of microscopic spots of DNA oligonucleotides, called features, each containing picoMole s of a specific DNA sequence....
 within the life sciences.

See also


  • Aptamer
    Aptamer

    Aptamers are oligonucleotide or peptide molecules that bind a specific target molecule. Aptamers are usually created by selecting them from a large random Sequencing pool, but natural aptamers also exist in riboswitches....
     — oligonucleotides with important biological applications
  • Morpholino
    Morpholino

    In molecular biology, a Morpholino is a molecule used to modify gene expression. Morpholino oligomers are an antisense technology used to block access of other molecules to specific sequences within nucleic acid....
     — oligos with non-natural backbones, which do not activate RNase-H but can reduce gene expression or modify RNA splicing
  • Polymorphism
    Polymorphism (biology)

    Polymorphism in biology occurs when two or more clearly different phenotypes exist in the same population of a species ? in other words, the occurrence of more than one form or morph....
     — the appearance in a population of the same gene in multiple forms because of mutations; can often be tested with ASO probes
  • Polynucleotide
    Polynucleotide

    A polynucleotide molecule is an organic chemistry polymer molecule composed of nucleotide monomers covalently bonded in a chain. DNA and RNA are examples of polynucleotides with distinct biological function....