The Circular DNA Size Code

Circular DNA molecules—mitochondrial DNA (mtDNA) and extrachromosomal circular DNA (ecDNA)—are fundamental genetic elements whose structural integrity is essential for cellular homeostasis. Pathological alterations in their length, caused by deletions or duplications, are directly implicated in a broad spectrum of human diseases, from inherited mitochondrial disorders to aggressive cancers. This review provides a comprehensive methodological guide for detecting these specific structural changes. We systematically evaluate classical techniques (long-range PCR, Southern blotting, electron microscopy) that offer direct visualization and validation, and modern high-throughput approaches (short- and long-read sequencing) that enable genome-wide discovery. Special emphasis is placed on quantitative clinical tools like digital droplet PCR (ddPCR) for ultrasensitive monitoring. By presenting a comparative framework, we guide the selection of optimal methods based on resolution, throughput, and clinical applicability. We conclude that an integrated, multi-method strategy is indispensable for robust analysis, positioning the precise detection of circular DNA length alterations as a cornerstone of emerging precision diagnostics and therapeutic strategies.