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. Author manuscript; available in PMC: 2013 Apr 1.
Published in final edited form as: Nat Chem. 2012 Oct;4(10):832–839. doi: 10.1038/nchem.1451

Figure 1. Design of the DNA-nanorod-based barcode.

Figure 1

(a) Two schematics of the Blue--Red-Green (BRG) barcode with a segment diagram on the top and a three-dimensional (3D) view at the bottom. The main-body of the barcode is a DNA nanorod formed by dimerizing two origami monomers, each consisting of 28 segments of 42 base pairs (~14 nm in length). The grey segment in the middle represents the junction where the two monomers are joined together. Three 84-bp zones of the nanorod are fluorescently labeled (shown as blue, red and green segments) to produce the BRG barcode. (b) 3D cartoons showing the details of one fluorescently labeled zone. Left: a strand model of an 84-bp zone before labeling. Each of the twelve 63-base staples (rainbow colors) contains two parts: the 42-base region at the 5′-end to fold the scaffold (black) into a six-helix bundle nanorod, and the 21-base extension at the 3′-end protrudes out for fluorescent labeling. Middle: a simplified model to emphasize the six-helix bundle structure (each helix shown as a semi-transparent grey cylinder) and the positioning of the twelve staple extensions (light-grey curls). Right: the zone with “green” fluorescent labeling. The labeling is achieved by hybridizing the Cy3 (glowing green spheres) modified strands to the staple extensions.