An oligonucleotide (or oligo) is a short segment of RNA or DNA, typically with twenty or fewer bases. Although they can be formed by 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 Greekmeros, "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 (deoxyoligonucleotides) are often used in the polymerase chain reaction (PCR), 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.
Oligonucleotides are chemically synthesized using nucleotides, called phosphoramidites, normal nucleotides that have protection groups: preventing amine, hydroxyl groups and phosphate groups 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 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. Currently there exist three applications of DNA microarrays: polymorphism studies, gene expression studies, and tracking down certain diseases.
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
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