A colony-forming assay for determining the establishment efficiency of S/MAR-containing nonviral episomal expression vectors.

As with all eukaryotic replicons, the stable establishment of S/MAR (scaffold/matrix attached region) vectors is a stochastic event that depends on poorly understood epigenetic factors such as chromatin structure and nuclear localization. Establishment efficiency describes the percentage of cells in which a particular S/MAR vector is stably retained as an episome after an initial selection period. Expected establishment efficiency for S/MAR vectors is 1-5%. This article describes a colony-forming assay that may be used either to determine establishment efficiency or to generate single cell clones.