Nonamer

Nonamer is a term used in genetics to denote a nine-nucleotide DNA sequence. In immunology it refers to the nonamer component of the recombination signal sequence (RSS) that flanks V, D, and J gene segments involved in V(D)J recombination. The RSS consists of a conserved heptamer, a spacer of 12 or 23 base pairs, and a conserved nonamer, arranged so that the nonamer and heptamer flank the spacer and together guide the recombination machinery to the appropriate target.

The nonamer is recognized by the RAG1/2 recombinase and helps establish the correct cleavage point relative to the heptamer, enabling the precise joining of gene segments. While the nonamer's sequence is not strictly fixed, there is a relatively conserved core motif with limited tolerance for variation, and the exact sequence can influence the efficiency of recombination.

Beyond immunogenetics, the term nonamer may be used more generally to denote any nine-nucleotide sequence, or, less commonly, any sequence or fragment consisting of nine units. In protein chemistry, the term nonapeptide is normally used for a nine-amino-acid sequence, while nonamer is more common for nucleotide sequences.

Etymology: from nonus, nine, plus -mer.