Purifying and Imaging Nucleic Acid Polygons

The samples of each RNA and DNA polygons were purified using gel electrophoresis prior to imaging. The assembled DNA and RNA polygons (2 μM concentration of each strand, in 50 μL TMS buffer) were subjected to the 6% native PAGE. After band visualization by UV-shadowing, the gel pieces with corresponding nucleic acid complexes were cut and eluted overnight into 200 μL of TMS buffer. The samples were concentrated using a 3KDa molecular-weight cutoff filter device (Ultracel-3, Millipore) and resuspended into 100 μL of TMS buffer. AFM imaging was conducted at RT using silicon probes (NCH 320 kHz resonance frequency and 42 N/m spring constant, www.nanoworld.com) on the MultiMode AFM NanoScope IV system (Veeco), following the well-developed protocol.^{74 (link)}