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. Author manuscript; available in PMC: 2012 Jun 1.
Published in final edited form as: Methods. 2010 Dec 14;54(2):239–250. doi: 10.1016/j.ymeth.2010.12.010

Fig. 5.

Fig. 5

A 2D cartoon representation of a tectosquare assembly protocol used by NanoTiler. Only two out of four L-shaped monomers are shown. The full tectosquare is built out of the right angle (RA) junctions and kissing loop (KL) complexes (gray boxes) which are connected by idealized linker helices (red arrows and boxes). A linker helix of size 0 may be viewed as a special case where only the RA and KL building blocks are best-fit together. Linker helices are used by NanoTiler to introduce small distortions required to connect all the building blocks together. By default the junctions used in the design are not subjected to any adjustments by the program. Our mating of the MD states of the junctions with the adjustable linkers increases the versatility of the overall approach.