DNA loop domain organization as revealed by single-cell gel electrophoresis.

Abstract At higher order levels chromatin is organized into loops. This looping, which plays an important role in transcription regulation and other processes, remains poorly understood. We investigated the kinetics of DNA loop migration during single cell gel electrophoresis (the comet assay). The migration of a part of the loops was shown to be reversible after switching off electrophoresis and to be sensitive to intercalation-induced changes in supercoiling. Another group of the loops migrates rapidly, the rate being insensitive to the supercoiling level. The largest part of the loops cannot migrate at all, presumably because of their large size. The loop ends can be detached in the presence of high concentrations of intercalators or protein denaturants, thus increasing the fraction of DNA that cannot migrate in the gel. The distribution of the loop length up to 100 kilobases appears to be consistent with the fractal globule organization.