A primer to scaffolded DNA origami

Abstract

Molecular self-assembly with scaffolded DNA origami enables building custom-shaped nanometer-scale objects with molecular weights in the megadalton regime. Here we provide a practical guide for design and assembly of scaffolded DNA origami objects. We also introduce a computational tool for predicting the structure of DNA origami objects and provide information on the conditions under which DNA origami objects can be expected to maintain their structure.

Programmable disorder in random DNA tilings

“…We suspect that the opposite-side binding was thermodynamically more favorable due to the sequence variation of stacking bonds on four sides of the tile. Table S2 and Edg-TiRjC7 (i = 1, 2, 3, 4 and j = 00, 04, 06, 08, 12,14,16,20) in Table S4.…”

“…Thus we believe it is desirable to use an edge design with a low binding energy such that the melting temperature of origami arrays is significantly lower than that of the origami tile itself, which is commonly between 55 and 65 • C for DNA origami folded using staples of 20 to 60 nucleotides. 12 For example, the origami arrays shown in Figs. S18 to S21 had a melting temperature close to 35 • C, measured using both fluorescence experiments ( Fig.…”

“…12 Edge staples in comb-connected 3 by 3 arrays Table S26: Edge staples of Tile 1 in the comb-connected 3 by 3 arrays (Fig. S54).…”

Automated design of DNA origami

“…Underlying the increasing complexity of shapes are ever-more potent computational tools for designing and analyzing such objects. For example, researchers routinely use the design software caDNAno and the finite-element-based simulation software CanDo for prototyping and predicting the shape of multilayer DNA structures in honeycomb and square lattice geometries 5 . In addition, computational frameworks for making lattice-free DNA structures are available 6 .…”

“…After designing the shape and obtaining the sequences, researchers fabricate the structures using standard annealing routines. The DAEDALUS software (http://daedalus-dna-origami.org/) not only generates a list of staple strands but also produces atomistic models of the designed structures, whereas the CanDo software (http://cando-dnaorigami.org/) 5,6 can be used to simulate shapes of the objects in aqueous solution.…”