Oligonucleotide (source code)

= 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>.https://iupac.qmul.ac.uk/class/nucle.html[IUPAC-IUBMB, Nucleic Acids and Component Units, oligonucleotides entry]{ref}

For an unmodified linear <DNA> example, $5'\text{-}\mathrm{AGTCG}\text{-}3'$ has five <nucleotides> and four connecting <phosphodiester bonds>. A fully complementary strand is $3'\text{-}\mathrm{TCAGC}\text{-}5'$. Writing that partner in the conventional $5'$-to-$3'$ direction gives $5'\text{-}\mathrm{CGACT}\text{-}3'$, 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.<Trinucleotide phosphoramidites: ideal reagents for the synthesis of mixed oligonucleotides for random mutagenesis by Bernhard Virnekas and others>[Abstract, codon building blocks and automated solid-phase synthesis]{ref} This separates designing an individual chain from designing the distribution of sequences in a collection.