Folding DNA to create nanoscale shapes and patterns

Abstract

Supplementary Note S1: Design of DNA origamiThe program used for designing DNA origami, multishapes.m, may be downloaded from:http://www.dna.caltch.edu/SupplementaryMaterial/ Below is a description of how design proceeds using this program. It is not meant to be a manual but rather to show the level of abstraction at which the origami are designed, and to show the various types of diagrams that the program can draw to aid in design. If scaffolded DNA origami becomes widely used, a better CAD design tool will have to be written. Given a desired shape (for example the red outline in Fig. 1a) design of a DNA origami to approximate it proceeds in five phases (two manual design steps and three passes of the program):1. Generation of a block diagram. By hand, a rough geometric model is generated. It is comprised of rectangular blocks in which each block is taken to be one turn of DNA wide and one DNA helix plus the interhelix gap in height. (Such a block diagram sloppily overestimates the height of a structure by one inter-helix gap.) An example block diagram is in Supplementary Fig. S1 step 1.This step is performed with an eye towards the next step (generation of a folding path), in some cases the block diagram is conceived almost simultaneously with the folding path. The phase of the underlying periodic crossover lattice is chosen as well; generally this phasing is chosen so that seams and long edges of the shape align with columns of periodic crossovers. For blocks on the edge of the diagram, it is useful to keep track of the relationship of such blocks to the underlying crossover lattice. For an origami with 1.5-turn spacing between crossovers there are 3 possible offsets that an edge may have with respect to the underlying lattice-call them 0, +1 and -1 (Origami with 2.5 turn spacing have 5 possible offsets). For designs with a central seam, blocks on edges of offset 0 are colored red and blocks on edges of offset +1 and -1 are colored yellow and orange, depending on whether they occur to the left or right of the central seam. At this point the placement of seams may already be apparent; if so, half-blocks are used along seams. Adjacent half-blocks involved in the same scaffold crossover are colored the same (one of either green or purple) but adjacent half-blocks that participate in different crossovers are given different colors.2. Generation of a folding path, by raster fill, through the block diagram. For a given shape there are many compatible raster fill patterns; currently the raster fill pattern must be hand-designed. For any helical domain in which the scaffold is to start and end on the same side of the helix (top or bottom), an integral number of turns (blocks) is traversed. For any helical domain in which the scaffold starts and ends on opposite sides sides of the helix, the scaffold traverses an odd number of half-turns (half-blocks). An example folding path is in Supplementary Fig. S1 step 2.3. Generation of a first pass design based on the block diagram and folding path. The lengths of various heli...

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