Visualizing DNA Minicircles for Poloidal Bias

Short DNA exhibits anisotropic bending due to sequence-dependent base pair geometry (such as roll, tilt, and twist). Consequently, when circularized into a minicircle, it tends to adopt a specific poloidal (inside-out) orientation to minimize bending energy. While computational studies suggest a poloidal bias in DNA minicircles, experimental evidence has been limited. In our recent surface-based single-molecule assay, we observed that poloidal bias is strongly influenced by surface attachment rather than by sequence. To reduce surface artifacts, we are now using atomic force microscopy to image protein-bound DNA minicircles. The spatial distribution of the protein relative to the minicircle reveals the intrinsic poloidal bias of DNA minicircles.