What is an Oligonucleotide?

By Dr Ananya Mandal, MD

Oligonucleotides are short nucleic acid polymers used in research, genetic testing and forensics.

Oligonucleotides are usually made up of 13 to 25 nucleotides and are designed to hybridize specifically to DNA or RNA sequences. Solid-phase clinical synthesis is used to manufacture these small bits of nucleic acid for use in polymerase chain reaction (PCR), DNA sequencing, library construction and artificial gene synthesis.

The term oligonucleotide is derived from the Greek “oligo,” which means few or small. The length of the oligonucleotide is usually denoted by the term “mer,”which is Greek for “part.”

Oligonucleotides are used as probes for detecting specific sequences that are complementary to the oligonucleotides. When a certain sequence needs to be detected, a complementary oligonucleotide is synthesized in the laboratory. It is then bound to a fluorescent marker and allowed to bind to the specific segment of RNA or DNA it was designed to detect. Using the molecules as probes for detection is one of the most important functions of oligonucleotides.

Examples of procedures that use oligonucleotides in this manner include DNA microarrays, Southern blot assay, ASO analysis, fluorescent in situ hybridization (FISH).

Oligonucleotides made up of 2’-deoxyribonucleotides are the molecules used in polymerase chain reaction (PCR). These are referred to as primers and are used to massively amplify a small amount of DNA. The primer binds to the specific DNA sequence and DNA polymerase is used to extend the oligonucleotide and replicate the complementary strand.

Reviewed by , BSc

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Last Updated: Sep 10, 2014

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