Oligonucleotides

Oligonucleotide - What is an Oligonucleotide?

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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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

This article is licensed under the Creative Commons Attribution-ShareAlike License. It uses material from the Wikipedia article on "Oligonucleotide" All material adapted used from Wikipedia is available under the terms of the Creative Commons Attribution-ShareAlike License. Wikipedia® itself is a registered trademark of the Wikimedia Foundation, Inc.