DdCBEs

DdCBEs, or DddA-derived cytosine base editors, are programmable genome editing tools designed to make precise C to T transitions in mitochondrial DNA (mtDNA). The system combines two DNA-binding domains based on TALEs with split fragments of the DddA cytosine deaminase toxin, along with a mitochondrial targeting sequence to direct the editor to mitochondria and a uracil glycosylase inhibitor to enhance editing efficiency. When the two TALEs bind to adjacent sites on opposite strands, the DddA halves reconstitute an active deaminase that deaminates cytosines within a defined editing window; after replication or repair, the resulting uracil is read as thymine, producing a C•G to T•A change in mtDNA.

DdCBEs are distinguished from CRISPR-based approaches by their reliance on TALE DNA-binding domains rather than guide RNAs, a design that accommodates the challenges of delivering editing components to mitochondria. They enable targeted edits without relying on double-strand breaks in mtDNA, which can be particularly relevant for mitochondrial genomes.

Applications of DdCBEs include modeling mitochondrial diseases, studying heteroplasmy dynamics, and exploring potential therapeutic avenues for pathogenic mtDNA mutations. Editing efficiency and specificity depend on the target sequence, the design of the TALEs, and cellular context. Off-target activity within mtDNA and potential, though less well characterized, effects in the nuclear genome remain considerations in ongoing development.

History and development began in the late 2010s, with initial demonstrations showing that split DddA-derived cytosine deaminases could effect targeted mtDNA edits in human cells, followed by refinements aimed at expanding targeting scope and improving specificity.