spacerDNA

Spacer DNA refers to the short DNA segments embedded within the CRISPR (clustered regularly interspaced short palindromic repeats) loci of many bacteria and archaea. These spacers are separated by short repeat sequences and collectively form a history of past encounters with foreign genetic elements such as bacteriophages and plasmids. Most spacers are about 20 to 40 base pairs in length, though exact sizes vary by organism.

Spacer DNA is acquired by the CRISPR adaptation machinery, principally the Cas1-Cas2 complex, which integrates new spacers into the CRISPR array. Transcription of the array yields a precursor RNA that is processed into small CRISPR RNAs (crRNAs) containing a spacer sequence. The spacer-derived crRNA, in combination with Cas proteins, guides the complex to complementary sequences in invading genomes, enabling targeted cleavage.

The collection of spacers provides a molecular memory of prior infections, and spacer content can differ even among closely related strains. New spacers are typically added at the leader end of the array, allowing rapid adaptation to evolving threats. Spacers may be lost or rearranged over time, reflecting ongoing arms races between microbes and their invaders.

In biotechnology, spacer sequences are central to CRISPR-based genome editing. Synthetic spacers are designed to match specific genomic targets and are incorporated into guide RNAs that direct nucleases such as Cas9 or Cas12 to the desired site. Spacer design is a critical factor in targeting specificity and efficiency, and research continues to optimize spacer selection and delivery.