Oligonucleotides are short
RNA molecules, oligomers, that have
a wide range of applications in genetic testing, research, and
forensics. Commonly made in the laboratory by solid-phase chemical
synthesis, these small bits of nucleic acids can be manufactured as
single-stranded molecules with any user-specified sequence, and so are
vital for artificial gene synthesis, polymerase chain reaction (PCR),
DNA sequencing, library construction and as molecular probes. In
nature, oligonucleotides are usually found as small
RNA molecules that
function in the regulation of gene expression (e.g. microRNA), or are
degradation intermediates derived from the breakdown of larger nucleic
Oligonucleotides are characterized by the sequence of nucleotide
residues that make up the entire molecule. The length of the
oligonucleotide is usually denoted by "-mer" (from Greek meros,
"part"). For example, an oligonucleotide of six nucleotides (nt) is a
hexamer, while one of 25 nt would usually 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
DNA microarrays, Southern blots, ASO
analysis, fluorescent in situ hybridization (FISH), PCR, and the
synthesis of artificial genes. Oligonucleotides are also indispensable
elements in antisense therapy.
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.
2 Antisense oligonucleotides
4 Mass spectrometry analysis
5 See also
7 Further reading
8 External links
Main article: oligonucleotide synthesis
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.
Main article: Antisense therapy
Antisense oligonucleotides are single strands of
RNA that are
complementary to a chosen sequence. In the case of antisense
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 place this
RNA hybrid can be degraded by the enzyme RNase H. The use of
morpholino-antisense oligonucleotides for gene knockdowns in
vertebrates, which is now a standard technique in developmental
biology and is used to study altered gene expression and gene
function, was first developed by Janet Heasman using Xenopus. 
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.
Mass spectrometry analysis
A mixture of
5-methoxysalicylic acid and spermine can be used as a
matrix for oligonucleotides analysis in MALDI mass spectrometry.
Aptamers, oligonucleotides with important biological applications
Morpholinos, oligos with non-natural backbones, which do not activate
RNase-H but can reduce gene expression or modify
Polymorphism, the appearance in a population of the same gene in
multiple forms because of mutations; can often be tested with ASO
CpG Oligodeoxynucleotide, an ODN with immunostimulatory properties
Polypurine reverse-Hoogsteen hairpins, PPRHs, oligonucleotides that
can bind either
RNA and decrease gene expression.
^ Weiss, B., ed. (1997). Antisense Oligodeoxynucleotides and Antisense
RNA : Novel Pharmacological and Therapeutic Agents. Boca Raton,
Florida: CRC Press
^ Weiss, B., Davidkova, G., and Zhou, LW (March 1999). "Antisense RNA
gene therapy for studying and modulating biological processes."
Cellular and Molecular Life Sciences : CMLS. 55 (3): 334–58.
doi:10.1007/s000180050296. PMID 10228554.
^ Beta-catenin signaling activity dissected in the early Xenopus
embryo: a novel antisense approach. Heasman J, Kofron M, Wylie C. Dev.
Biol. 2000. 222, 124-34
^ Distler, AM; Allison, J (2001). "5-Methoxysalicylic acid and
spermine: A new matrix for the matrix-assisted laser
desorption/ionization mass spectrometry analysis of oligonucleotides".
Journal of the American Society for Mass Spectrometry. 12 (4):
456–62. doi:10.1016/S1044-0305(01)00212-4. PMID 11322192.
Spingler, Bernhard (2012). "Chapter 3. Metal-Ion-Promoted
Conformational Changes of Oligonucleotides". In Astrid Sigel, Helmut
Sigel and Roland K. O. Sigel. Interplay between Metal Ions and Nucleic
Acids. Metal Ions in Life Sciences. 10. Springer. pp. 103–118.
RNAi Atlas: a database of RNAi libraries and their target analysis
physorg.com Genetic source of muscular dystrophy neutralized
Types of nucleic acids
precursor, heterogenous nuclear
Small Cajal Body RNAs
Trans-acting small interfering