An oligonucleotide (from Greek prefix oligo-, "having few, having little") 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 microarrays, Southern blots, 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.



Oligonucleotides are chemically synthesized using building blocks, protected phosphoramidites of natural or chemically modified nucleosides 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

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 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.

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

  • Aptamer — oligonucleotides with important biological applications
  • Morpholino — oligos with non-natural backbones, which do not activate RNase-H but can reduce gene expression or modify RNA splicing
  • Polymorphism — the appearance in a population of the same gene in multiple forms because of mutations; can often be tested with ASO probes
  • Genomic signature
  • Polynucleotide
  • CpG Oligodeoxynucleotide - an ODN with immunostimulatory properties
  • K-mer

External links


  • Pierce, "GENETICS: A Conceptual Approach", 2005
  • Weiss, B. (ed.): Antisense Oligodeoxynucleotides and Antisense RNA : Novel Pharmacological and Therapeutic Agents, CRC Press, Boca Raton, FL, 1997
  • Weiss, B., Davidkova, G., and Zhou, L-W.: Antisense RNA gene therapy for studying and modulating biological processes. Cell. Mol. Life Sci., 55:334-358, 1999
  • Hartwell, L. H., Hood, L., Goldberg, M. L., Reynolds, A. E., Silver, L. M., and Veres, R. C. 2008. In: Genetics from Genes to Genomes 3rd edition. pp. G-14.

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Look at other dictionaries:

  • Oligonucleotide — Oligonucléotide Les oligonucléotides sont des courtes séquences de nucléotides (ARN ou ADN), simple brin et longs de quelques dizaines de bases. Ils sont en général obtenus par synthèse chimique. Sommaire 1 Synthèse des oligonucléotides 2… …   Wikipédia en Français

  • oligonucleotide — oligonucleotide. См. олигонуклеотид. (Источник: «Англо русский толковый словарь генетических терминов». Арефьев В.А., Лисовенко Л.А., Москва: Изд во ВНИРО, 1995 г.) …   Молекулярная биология и генетика. Толковый словарь.

  • oligonucléotide — [ɔligonykleɔtid] n. m. ÉTYM. Av. 1963; de oligo , et nucléotide. ❖ ♦ Biochim. Chaîne de nucléotides (mononucléotides) comportant un nombre d éléments relativement petit, généralement inférieur ou égal à dix (opposé à polynucléotide). || « Parmi… …   Encyclopédie Universelle

  • oligonucleotide — [äl΄i gōno͞o′klē ō tīd΄, äl΄i qōnyo͞o′kle ō tīd΄] n. a short piece of nucleic acid, usually with less than twenty nucleotides, used in genetic engineering and research …   English World dictionary

  • Oligonucléotide — Les oligonucléotides sont des courts segments d acides nucléiques (ARN ou ADN), longs de quelques dizaines de nucléotides. Ils sont en général obtenus par synthèse chimique, sous forme simple brin. Sommaire 1 Synthèse des oligonucléotides 2… …   Wikipédia en Français

  • Oligonucleotide — A small DNA molecule composed of a few nucleotide bases. The term oligonucleotide applies similarly to RNA. * * * A compound made up of the condensation of a small number (typically fewer than 20) of nucleotides. Cf.:polynucleotide. * * *… …   Medical dictionary

  • oligonucleotide — oligonukleotidas statusas T sritis chemija apibrėžtis Nukleotidas, susidedantis iš 2–20 nukleotidų, susijungusių fosfodiesteriniais ryšiais. atitikmenys: angl. oligonucleotide rus. олигонуклеотид …   Chemijos terminų aiškinamasis žodynas

  • oligonucleotide — noun Date: 1942 a relatively short nucleic acid chain usually consisting of up to approximately 20 nucleotides …   New Collegiate Dictionary

  • oligonucleotide — Linear sequence of up to 20 nucleotides joined by phosphodiester bonds. Above this length the term polynucleotide begins to be used …   Dictionary of molecular biology

  • oligonucleotide — /ol i goh nooh klee euh tuyd , nyooh /, n. Biochem. a chain of a few nucleotides. [1940 45; OLIGO + NUCLEOTIDE] * * * …   Universalium

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