ARTICLES NATURETVol 440 16 March 2006 y-direction. As noticed before in DNA lattices, parallel helices in tangent point between helices. Thus for the scaffold such structures are not close-packed, perhaps owing to electrostatic progressively from one helix to another and onto a third, the repulsion. Thus the exact y-resolution depends on the gap between between successive scaffold crossovers must be an odd numbe helices. The gap, in turn, appears to depend on the spacing of turns. Conversely, where the raster reverses direction vertically and crossovers. In Fig. la crossovers occur every 1.5 turns along alter- returns to a previously visited helix, the distance between scaffold nating sides of a helix, but any odd number ofhalf-turns may be used. crossovers must be an even number of half-turns. Note that the In this study, data are consistent with an inter-helix gap of I nm folding path shown in Fig. Ib is compatible with a circular scaffold for 1.5-turn spacing and 1.5 nm for 2.5-turn spacing, yielding a and leaves a'seam'(a contour which the path does not cross) y-resolution of 6 or 7 nm, respectively. Once the geometric model and a folding path are designed, they Conceptually, the second step(illustrated in Fig. Ib) proceeds by are represented as lists of DNA lengths and offsets in units of half- folding a single long scaffold strand(900 nucleotides(nt) in Fig turns. These lists, along with the DNA sequence of the actual scaffold back and forth in a raster fill pattern so that it comprises one of the to be used, are input to a computer program. Rather than assuming two strands in every helix; progression of the scaffold from one helix 10.5 base pairs(bp)per turn(which corresponds to standard B-DNA to another creates an additional set of crossovers, the scaffold twist), the program uses an integer number of bases between periodi crossovers'(indicated by small red crosses in Fig. 1b). The funda- crossovers(for example, 16 bp for 1.5 turns). It then performs the mental constraint a folding path is that the scaffold can form a third step, the design of a set of staple strands'( the coloured dNA crossover only at those locations where the DNA twist places it at a strands in Fig. Ic)that provide Watson-Crick complements for the 嘉羋 AL mmm Nw~ANA吵0N 厘C Figure 1 Design of DNA origami. a, A shape(red ith coloured lines, and major/minor grooves by large/small ouble helices joined by periodic crossovers(blue). b, A scaffold(black) runs them. Arrows in c point to nicks sealed to create green strands in d. Yellow through every helix and forms more crossovers(red). c, As first designed, diamonds in c and d indicate a position at which staples may be cut staples bind two helices and ands resealed to bridge the seam. e, A finished design after merges and drawn as helices. Red triangles point to scaffold crossovers, black triangles to rearrangements along the seam. Most staples are 32-mers spanning three periodic crossovers with minor grooves on the top face of the shape, blue helices Insets show a dumbbell hairpin(d)and a 4-Tloop(e), modifications rers with minor grooves on bottom Cross- used in Fig 3 sections of crossovers(1, 2, viewed from left)indicate backbone positions 298 2006 Nature Publishing Group© 2006 Nature Publishing Group y-direction. As noticed before in DNA lattices15, parallel helices in such structures are not close-packed, perhaps owing to electrostatic repulsion. Thus the exact y-resolution depends on the gap between helices. The gap, in turn, appears to depend on the spacing of crossovers. In Fig. 1a crossovers occur every 1.5 turns along alter￾nating sides of a helix, but any odd number of half-turns may be used. In this study, data are consistent with an inter-helix gap of 1 nm for 1.5-turn spacing and 1.5 nm for 2.5-turn spacing, yielding a y-resolution of 6 or 7 nm, respectively. Conceptually, the second step (illustrated in Fig. 1b) proceeds by folding a single long scaffold strand (900 nucleotides (nt) in Fig. 1b) back and forth in a raster fill pattern so that it comprises one of the two strands in every helix; progression of the scaffold from one helix to another creates an additional set of crossovers, the ‘scaffold crossovers’ (indicated by small red crosses in Fig. 1b). The funda￾mental constraint on a folding path is that the scaffold can form a crossover only at those locations where the DNA twist places it at a tangent point between helices. Thus for the scaffold to raster progressively from one helix to another and onto a third, the distance between successive scaffold crossovers must be an odd number of half turns. Conversely, where the raster reverses direction vertically and returns to a previously visited helix, the distance between scaffold crossovers must be an even number of half-turns. Note that the folding path shown in Fig. 1b is compatible with a circular scaffold and leaves a ‘seam’ (a contour which the path does not cross). Once the geometric model and a folding path are designed, they are represented as lists of DNA lengths and offsets in units of half￾turns. These lists, along with the DNA sequence of the actual scaffold to be used, are input to a computer program. Rather than assuming 10.5 base pairs (bp) per turn (which corresponds to standard B-DNA twist), the program uses an integer number of bases between periodic crossovers (for example, 16 bp for 1.5 turns). It then performs the third step, the design of a set of ‘staple strands’ (the coloured DNA strands in Fig. 1c) that provide Watson–Crick complements for the Figure 1 | Design of DNA origami. a, A shape (red) approximated by parallel double helices joined by periodic crossovers (blue). b, A scaffold (black) runs through every helix and forms more crossovers (red). c, As first designed, most staples bind two helices and are 16-mers. d, Similar to c with strands drawn as helices. Red triangles point to scaffold crossovers, black triangles to periodic crossovers with minor grooves on the top face of the shape, blue triangles to periodic crossovers with minor grooves on bottom. Cross￾sections of crossovers (1, 2, viewed from left) indicate backbone positions with coloured lines, and major/minor grooves by large/small angles between them. Arrows in c point to nicks sealed to create green strands in d. Yellow diamonds in c and d indicate a position at which staples may be cut and resealed to bridge the seam. e, A finished design after merges and rearrangements along the seam. Most staples are 32-mers spanning three helices. Insets show a dumbbell hairpin (d) and a 4-T loop (e), modifications used in Fig. 3. ARTICLES NATURE|Vol 440|16 March 2006 298