Oligonucleotide
Encyclopedia
An oligonucleotide is a short nucleic acid
polymer, typically with fifty or fewer bases
. Although they can be formed by bond cleavage
of longer segments, they are now more commonly synthesized
, in a sequence-specific manner, from individual nucleoside phosphoramidites. Automated synthesizers allow the synthesis of oligonucleotides up to about 200 bases.
Oligonucleotides are characterized by the sequence of nucleotide residues that comprise the entire molecule. The length of the oligonucleotide is usually denoted by "mer
" (from Greek
meros, "part"). For example, a fragment of 25 bases would be called a 25-mer. Oligonucleotides readily bind, in a sequence-specific manner, to their respective complementary
oligonucleotides, DNA, or RNA to form duplexes or, less often, hybrids of a higher order. This basic property serves as a foundation for the use of oligonucleotides as probes
for detecting DNA or RNA. Examples of procedures that use oligonucleotides include DNA microarray
s, Southern blot
s, ASO analysis
, fluorescent in situ hybridization
(FISH), and the synthesis of artificial genes.
Oligonucleotides composed of 2'-deoxyribonucleotides
(oligodeoxyribonucleotides) are fragments of DNA
and are often used in the polymerase chain reaction
, a procedure that can greatly amplify almost any small amount of DNA. There, the oligonucleotide is referred to as a primer
, allowing DNA polymerase
to extend the oligonucleotide and replicate the complementary strand.
s of natural or chemically modified nucleoside
s or, to a lesser extent, of non-nucleosidic compounds. The oligonucleotide chain assembly proceeds in the direction from 3'- to 5'-terminus by following a routine procedure referred to as a "synthetic cycle". Completion of a single synthetic cycle results in the addition of one nucleotide residue to the growing chain. A less than 100% yield of each synthetic step and the occurrence of side reactions set practical limits of the efficiency of the process so that the maximum length of synthetic oligonucleotides hardly exceeds 200 nucleotide residues. HPLC
and other methods can be used to isolate products with the desired sequence
strands by binding to them. 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
.
Nucleic acid
Nucleic acids are biological molecules essential for life, and include DNA and RNA . Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information...
polymer, typically with fifty or fewer bases
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular 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 and free redicals are generated by homolytic cleavage the process is known as homolytic fission or homolysis...
of longer segments, they are now more commonly synthesized
Oligonucleotide synthesis
Oligonucleotide synthesis is the chemical synthesis of relatively short fragments of nucleic acids with defined chemical structure . The technique is extremely useful in current laboratory practice because it provides a rapid and inexpensive access to custom-made oligonucleotides of the desired...
, in a sequence-specific manner, from individual nucleoside phosphoramidites. Automated synthesizers allow the synthesis of oligonucleotides up to about 200 bases.
Oligonucleotides are characterized by the sequence of nucleotide residues that comprise the entire molecule. The length of the oligonucleotide is usually denoted by "mer
Monomer
A monomer is an atom or a small molecule that may bind chemically to other monomers to form a polymer; the term "monomeric protein" may also be used to describe one of the proteins making up a multiprotein complex...
" (from Greek
Greek language
Greek is an independent branch of the Indo-European family of languages. Native to the southern Balkans, it has the longest documented history of any Indo-European language, spanning 34 centuries of written records. Its writing system has been the Greek alphabet for the majority of its history;...
meros, "part"). For example, a fragment of 25 bases would be called a 25-mer. Oligonucleotides readily bind, in a sequence-specific manner, to their respective complementary
Complementarity (molecular biology)
In molecular biology, complementarity is a property of double-stranded nucleic acids such as DNA, as well as DNA:RNA duplexes. Each strand is complementary to the other in that the base pairs between them are non-covalently connected via two or three hydrogen bonds...
oligonucleotides, DNA, or RNA to form duplexes or, less often, hybrids of a higher order. This basic property serves as a foundation for the use of oligonucleotides as probes
Hybridization probe
In molecular biology, a hybridization probe is a fragment of DNA or RNA of variable length , which is used in DNA or RNA samples to detect the presence of nucleotide sequences that are complementary 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 collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome...
s, Southern blot
Southern blot
A Southern blot is a method routinely used in molecular biology for detection of a specific DNA sequence in DNA samples. Southern blotting combines transfer of electrophoresis-separated DNA fragments to a filter membrane and subsequent fragment detection by probe hybridization. The method is named...
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 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 cytogenetic technique developed by biomedical researchers in the early 1980s that is used to detect and localize the presence or absence of specific DNA sequences on chromosomes. FISH uses fluorescent probes that bind to only those parts of the chromosome with which they show a high...
(FISH), and the synthesis of artificial genes.
Oligonucleotides composed of 2'-deoxyribonucleotides
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
(oligodeoxyribonucleotides) are fragments of DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
and are often used in the polymerase chain reaction
Polymerase chain reaction
The polymerase chain reaction is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence....
, a procedure that can greatly amplify almost any small amount 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 synthesis. They are required for DNA replication because the enzymes that catalyze this process, 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 helps catalyze in the polymerization of deoxyribonucleotides into a DNA strand. DNA polymerases are best known for their feedback 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 building blocks, protected phosphoramiditePhosphoramidite
Nucleoside phosphoramidites are derivatives of natural or synthetic nucleosides. They are used to synthesize oligonucleotides, relatively short fragments of nucleic acid and their analogs. Nucleoside phosphoramidites were first introduced in 1981 by Beaucage and Caruthers...
s of natural or chemically modified nucleoside
Nucleoside
Nucleosides are glycosylamines consisting of a nucleobase bound to a ribose or deoxyribose sugar via a beta-glycosidic linkage...
s or, to a lesser extent, of non-nucleosidic compounds. The oligonucleotide chain assembly proceeds in the direction from 3'- to 5'-terminus by following a routine procedure referred to as a "synthetic cycle". Completion of a single synthetic cycle results in the addition of one nucleotide residue to the growing chain. A less than 100% yield of each synthetic step and the occurrence of side reactions set practical limits of the efficiency of the process so that the maximum length of synthetic oligonucleotides hardly exceeds 200 nucleotide residues. HPLC
High-performance liquid chromatography
High-performance liquid chromatography , HPLC, is a chromatographic technique that can separate a mixture of compounds and is used in biochemistry and analytical chemistry to identify, quantify and purify the individual components of the mixture.HPLC typically utilizes different types of stationary...
and other methods can be used to isolate products with the desired 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 RNAMessenger RNA
Messenger RNA is a molecule of RNA encoding a chemical "blueprint" for a protein product. mRNA is transcribed from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes. Here, the nucleic acid polymer is translated into a polymer of amino acids: a protein...
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 translated into a protein. Less-frequently used synonyms are non-protein-coding RNA , non-messenger RNA and functional RNA . The term small RNA is often used for short bacterial ncRNAs...
) 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 non-specific endonuclease and catalyzes the cleavage of RNA via a hydrolytic mechanism. Members of the RNase H family can be found in nearly all organisms, from archaea to bacteria and eukaryota....
.
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 within the life sciences.See also
- AptamerAptamerAptamers are oligonucleic acid or peptide molecules that bind to a specific target molecule. Aptamers are usually created by selecting them from a large random sequence pool, but natural aptamers also exist in riboswitches. Aptamers can be used for both basic research and clinical purposes as...
— oligonucleotides with important biological applications - MorpholinoMorpholinoIn molecular biology, a Morpholino is a molecule in a particular structural family that is 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 - PolymorphismPolymorphism (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 - Genomic signatureGenomic signatureThe genomic signature refers to the characteristic frequency of oligonucleotides in a genome or sequence. It has been observed that the genomic signature of phylogenetically related genomes is similar....
- PolynucleotidePolynucleotideA polynucleotide molecule is a biopolymer composed of 13 or more nucleotide monomers covalently bonded in a chain. DNA and RNA are examples of polynucleotides with distinct biological function. The prefix poly comes from the ancient Greek πολυς...
- CpG OligodeoxynucleotideCpG OligodeoxynucleotideCpG oligodeoxynucleotides are short single-stranded synthetic DNA molecules that contain a cytosine "C" followed by a guanine "G". The "p" refers to the phosphodiester backbone of DNA, however some ODN have a modified phosphorothioate backbone. When these CpG motifs are unmethlyated, they act as...
- an ODN with immunostimulatory properties - K-merK-merThe term k-mer usually refers to a specific n-tuple or n-gram of nucleic acid or amino acid sequences that can be used to identify certain regions within biomolecules like DNA or proteins...
External links
- RNAi Atlas: a database of RNAi libraries and their target analysis results
- physorg.com | Genetic source of muscular dystrophy neutralized
- Oligonucleotides as drugs