Oligonucleotide

An oligonucleotide is a short nucleic acid chain: an oligomer made from nucleotides, rather than from free nucleobases alone. It may be DNA or RNA. The description concerns chain length and composition, not a guarantee that the chain is single-stranded, naturally occurring or translated into a protein. IUPAC's terminology explicitly connects the word with oligo and nucleotides.^[ref]

For an unmodified linear DNA example, $5^{\prime }\text{-}\mathrm{AGTCG}\text{-}{3}^{\prime }$ has five nucleotides and four connecting phosphodiester bonds. A fully complementary strand is $3^{\prime }\text{-}\mathrm{TCAGC}\text{-}{5}^{\prime }$. Writing that partner in the conventional $5^{\prime }$-to-$3^{\prime }$ direction gives $5^{\prime }\text{-}\mathrm{CGACT}\text{-}{3}^{\prime }$, the reverse complement. Reversing the letters without complementing them would answer a different question. The five-position count also allows $4^5=1024$ possible strings over the standard four-letter DNA alphabet.

Chemical synthesis makes this sequence-level control experimentally useful. In 1994, researchers prepared three-nucleotide building blocks representing codons for all 20 amino acids and incorporated them during automated DNA synthesis. Adding whole triplets allowed mixed oligonucleotides to vary at the codon level rather than only one base at a time.^[ref] This separates designing an individual chain from designing the distribution of sequences in a collection.