Fig. 1: Determining the topology of individual DNA molecules using AFM.
From: Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy
a 4-node DNA catenane visualised using AFM with helical structure visible (of N = 1010 total DNA plasmid, knot and catenane molecules imaged). Scale bar: 20 nm. Colour bar: −2 to 6 nm. b Schematic of the right-handed 4-node catenane in a with crossing orders determined by eye. c Schematic of the expected crossing height profiles of over-(lime green) and under-passing (hot pink) DNA duplexes at a crossing. d tilted 3D height profiles of each catenane crossing, schematics of each crossing in 3D, and manual line profiles of each crossing (numbered as in a). The large circle is coloured blue and small purple. The crossing order of each crossing is determined visually and agrees with the known topology of the catenane. e Automated tracing and topological determination of DNA structures from AFM images, for: i, relaxed (N = 67) and; ii, supercoiled plasmid (2260 bp) (N = 78); iii, 5-node twist knot produced from pDIR (2260 bp) (N = 108) and; iv, catenated (1253 bp, 398 bp) plasmids produced from p4CAT (N = 604). Automated traces (blue) show under-passing (hot pink) and over-passing (lime) segments at crossings. Scale bar: 50 nm. Height scale: −2 to 6 nm. Source data is provided as a Source Data file.
