Oligonucleotide

Oligonucleotides are short sequences of nucleotides (RNA or DNA), typically with twenty or fewer bases. Automated synthesizers allow the synthesis of oligonucleotides up to 160 to 200 bases. The length of a synthesized base is usually denoted by 'mer' (from 'Greek' meros "part"). For example, a fragment of 25 bases would be called a 25-mer. Oligonucleotides are often used as probes for detecting complementary DNA or RNA because they bind readily to their complements. Examples of procedures that use oligonucleotides are DNA microarrays, Southern blots, 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 be employed to amplify almost any piece of DNA. In this instance, the oligonucleotide is often referred to as a primer, or a short piece of DNA that binds to its complementary target sequence. This generates a place for a polymerase to bind and extend the primer by the addition of nucleotides to make a copy of the target sequence.

Oligonucleotides are sometimes referred to as oligos.

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 translation of complementary RNA strands by binding to it. 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.

Synthesis
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.