Figure 3: The distribution of backbone nicks affects folding success.
From: Magnesium-free self-assembly of multi-layer DNA objects
(a) Schematic illustration of four backbone nick distribution rules. Thick solid lines represent scaffold strand. The horizontal crossover spacing is 7 bp for honeycomb-type packing. (b) The distribution of length of dsDNA domains formed by staple strands with the scaffold strand resulting when applying backbone nick rules 1 to 4 to a 42-helix bundle object in honeycomb-type packing. (c) Left panel (middle panel): photograph of a ethidium-bromide-stained 2% agarose gel on which folding products of 42-helix bundle versions designed according to rules 1 to 4 obtained after 1.5-day-long (12-day-long) thermal annealing in the presence of 2.4 M NaCl were electrophoresed. M, 1 kb marker; ref, scaffold DNA. (d) As in (c) left panel, but for reactions run in the presence of 20 mM MgCl2. M, 1 kb marker; ref, scaffold DNA.
