nonanucleotide

A nonanucleotide is a sequence composed of nine nucleotides. In molecular biology, the term is often used to describe conserved nine-nucleotide motifs located at origins of replication in certain circular single-stranded DNA viruses. These motifs are typically embedded within a stem-loop structure in the viral genome and play a key role in initiating replication.

In many plant-associated viruses, including those in the families Geminiviridae and Nanoviridae, the replication origin contains a conserved nonanucleotide motif just upstream of the stem-loop. The viral replication initiator protein, commonly referred to as Rep, introduces a site-specific nick at or near this motif, producing a 3'-OH end that starts rolling-circle replication of the circular genome. While the exact sequence can vary, the motif is highly conserved within groups and is crucial for efficient replication.

A frequently cited example is the motif TAATATTAC, often described as a canonical nonanucleotide in geminiviruses. Related viruses may display minor sequence variation, but the overall concept remains the same: the nonanucleotide motif marks the origin of replication and serves as the target for initiation by replication proteins.

Beyond its role in replication, the presence and conservation of nonanucleotide motifs aid in the annotation, comparison, and taxonomy of circular ssDNA viruses. They provide a recognizable feature for identifying replication origins and understanding genome organization across related viral lineages.