An oligonucleotide is a short nucleic acid polymer, typically with twenty or fewer bases. Although they can be formed by bond cleavage 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" (from Greek ''meros'', "part"). For example, a fragment of 25 bases would be called a 25-mer.
Because oligonucleotides readily bind to their respective complementary nucleotide, they are often used 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 DNA (oligodeoxyribonucleotides) are often used in the polymerase chain reaction, a procedure that can greatly amplify almost any small piece of DNA.
There, the oligonucleotide is referred to as a primer, allowing DNA polymerase to extend the oligonucleotide and replicate the complementary strand.
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.
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