Self-assembly of DNA into nanoscale three-dimensional shapes

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Self-assembly of DNA into nanoscale three-dimensional shapes

Vol 459 |21 May 2009 |doi:10.1038/nature08016LETTERSSelf-assembly of DNA into nanoscalethree-dimensional shapesShawn M. Douglas 1,2,3 , Hendrik Dietz 1,2 , Tim Liedl 1,2 , Björn Högberg 1,2 , Franziska Graf 1,2,3 & William M. Shih 1,2,3Molecular self-assembly offers a ‘bottom-up’ route to fabricationwith subnanometre precision of complex structures from simplecomponents 1 . DNA has proved to be a versatile building block 2–5for programmable construction of such objects, including twodimensionalcrystals 6 , nanotubes 7–11 , and three-dimensional wireframenanopolyhedra 12–17 . Templated self-assembly of DNA 18 intocustom two-dimensional shapes on the megadalton scale hasbeen demonstrated previously with a multiple-kilobase ‘scaffoldstrand’ that is folded into a flat array of antiparallel helices byinteractions with hundreds of oligonucleotide ‘staple strands’ 19,20 .Here we extend this method to building custom three-dimensionalshapes formed as pleated layers of helices constrained to ahoneycomb lattice. We demonstrate the design and assembly ofnanostructures approximating six shapes—monolith, square nut,railed bridge, genie bottle, stacked cross, slotted cross—withprecisely controlled dimensions ranging from 10 to 100 nm. Wealso show hierarchical assembly of structures such as homomultimericlinear tracks and heterotrimeric wireframe icosahedra.Proper assembly requires week-long folding times and calibratedmonovalent and divalent cation concentrations. We anticipate thatour strategy for self-assembling custom three-dimensional shapeswill provide a general route to the manufacture of sophisticateddevices bearing features on the nanometre scale.The assembly of a target three-dimensional shape using thehoneycomb-pleat-based strategy described here can be conceptualizedas laying down the scaffold strand into an array of antiparallelhelices (Fig. 1a) where helix m 1 1 has a preferred attachment angle tohelix m of 6120u degrees with respect to the attachment of helix m 2 1to helix m (Fig. 1b, c). This angle is determined by the relative registeralong the helical axes of the Holliday-junction crossovers that connecthelix m 1 1 to helix m versus those that connect helix m 2 1tohelix m.Branching flaps are allowed as well (Supplementary Note S1).The design procedure is analogous to sculpture from a porouscrystalline block. Here the block is a honeycomb lattice of antiparallelscaffold helices (Fig. 1d). Complementary staple strands wind in anantiparallel direction around the scaffold strands to assemble B-formdouble helices that are assigned initial geometrical parameters (thatcan later be adjusted to account for interhelical repulsion) of 2.0 nmdiameter, 0.34 nm per base-pair rise, and 34.3u per base-pair meantwist (or 21 base pairs every two turns). Crossovers between adjacentstaple helices are restricted to intersections between the block andevery third layer of a stack of planes orthogonal to the helical axes,spaced apart at intervals of seven base pairs or two-thirds of a turn(Fig. 1c). Crossovers between adjacent scaffold helices are permittedat positions displaced upstream or downstream of the correspondingstaple-crossover points by five base pairs or a half-turn.The first steps in the design process are carving away duplex segmentsfrom the block to define the target shape, and then introducingscaffold crossovers at a subset of allowed positions so as to create asingular scaffold path that visits all remaining duplex segments. Next,staple crossovers are added at all permitted positions on the shapethat are not five base pairs away from a scaffold crossover; this exceptionmaintains the local crossover density along any helix–helix interfaceat roughly one per 21 base pairs. Nicks are introduced into staplehelices to define staple strands whose lengths are between 18 and 49bases inclusive, with a mean between 30 and 42 bases. Sometimesstaple crossovers are removed at the edges of the shapes to allowadjustment of staple lengths to preferred values. Unpaired scaffoldbases are often introduced at the ends of helices to minimizeundesired multimerization, or else to accommodate later additionof connecting staple strands that mediate desired multimerization.The final step is to thread the actual scaffold sequence on the targetscaffold path to determine the Watson–Crick-complementarysequences of the staple strands.Design steps and assignment of staple sequences for the shapespresented here were aided by manual rendering of strand diagramsin Adobe Illustrator and by writing ad hoc computer programs toproduce staple sequences corresponding to those diagrams. Thisprocess was very time-consuming and error-prone even for trainedDNA nanotechnologists. More recently, we have developed caDNAno,a graphical-interface-based computer-aided-design environmentfor assisting in honeycomb-pleated-origami design 21 , and have portedall the objects described in this article into this framework(Supplementary Note S2). With caDNAno, an individual with noprior knowledge of programming or DNA structure can complete ashort tutorial and then be capable of generating sequences within a dayfor building a new shape comparable in complexity to the examplesdemonstrated here.As with flat DNA origami 19 , assembly of three-dimensional,honeycomb-pleated DNA origami proceeds in a one-pot reaction,after rapid heating followed by slow cooling, between a scaffoldstrand and the hundreds of oligonucleotide staple strands that directits folding into the target shape. Successful folding was observed for apanel of five structural targets (detailed schematics in SupplementaryNote S2) each produced by mixing 10 nM scaffold strands derivedfrom the single-stranded genome of the M13 bacteriophage (preparationdescribed in Supplementary Note S1), 50 nM of every oligonucleotidestaple strand, purified by reverse-phase cartridge(Bioneer Inc.), buffer and salts including 5 mM Tris 1 1mMEDTA (pH 7.9 at 20 uC), 16 mM MgCl 2 , and subjecting the mixtureto a thermal-annealing ramp that cooled from 80 uCto60uC over thecourse of 80 min and then cooled from 60 uCto24uC over the courseof 173 h. Objects were electrophoresed on a 2% agarose gel containing45 mM Tris borate 1 1 mM EDTA (pH 8.3 at 20 uC), and 11 mMMgCl 2 at 70 V for four hours cooled by an ice-water bath, monomerbands were excised, DNA was recovered by physical extraction fromthe excised band, and the objects were imaged using transmissionelectron microscopy after negative-staining by uranyl formate. The1 Department of Cancer Biology, Dana-Farber Cancer Institute, 2 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts02115, USA. 3 Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts 02138, USA.414©2009 Macmillan Publishers Limited. All rights reserved


NATURE | Vol 459 | 21 May 2009LETTERSabcdefp7560p8064p7704pEGFP-N1p73081.2 3 6 12 18 37 74 1730 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30320 160 80 40 20 10 5 0Folding time (h) [MgCl 2 ] (mM) [NaCl] (mM)Figure 3 | Gel and TEM analysis of folding conditions for three-dimensionalDNA origami. a, Cylinder models of shapes: monolith, stacked cross, railedbridge, and two versions of genie bottle, with corresponding scaffoldsequences. Labels indicate the source of scaffold used for folding the object(for example, p7560 is an M13-based vector of length 7,560 bases). b, Shapeswere folded in 5 mM Tris 1 1 mM EDTA (pH 7.9 at 20 uC) and 16 mM MgCl 2and analysed by gel electrophoresis (2% agarose, 45 mM Tris borate 1 1mMEDTA (pH 8.3 at 20 uC), 11 mM MgCl 2 ) using different thermal-annealingramps. For the 1.2 h ramp, the temperature was lowered from 95 uCto20uCat a rate of 1.6 min uC 21 . For the 3 h, 6 h, 12 h, 18 h, 37 h, 74 h and 173 hramps, the temperature was lowered from 80 uCto60uC at 4 min uC 21 , andthen from 60 uC to24uC at rates of 5, 10, 20, 30, 60, 120 or 280 min uC 21 ,respectively). c–e, TEM and gel analysis of influence of MgCl 2 concentrationon folding quality. c, The fastest-migrating bands in the 4 mM MgCl 2 laneswere purified and imaged, revealing gross folding defects. d, Shapes werefolded with a 173 h ramp in 5 mM Tris 1 1 mM EDTA (pH 7.9 at 20 uC) andMgCl 2 concentrations varying from 0 to 30 mM. e, Asinc, leading bandswere purified from the 16 mM MgCl 2 lanes and found to exhibit higherqualityfolding when analysed by TEM. f, Excess NaCl inhibits properfolding. Shapes were folded with 173 h ramp in 5 mM Tris 1 1 mM EDTA(pH 7.9 at 20 uC), 16 mM MgCl 2 , and varying NaCl concentrations.with a length of 7,308 bases, where 2,800 bases of the scaffold strandwere left unpaired and dangling from the neck of the bottle (reminiscentof wisps of smoke in TEM images), while the other scaffoldsequence used was the 4,733-base forward strand of an expressionvector encoding the enhanced green fluorescent protein (pEGFP-N1,Clontech). Folding of the same shape under identical conditions gavesuperior yield with the M13-based scaffold sequence. Some foldingsuccess could be achieved with the pEGFP-N1 scaffold sequencewhen much higher scaffold and staple concentrations were used.One striking difference between the two scaffold sequences is thatthe M13 base composition is 43% cytosines and guanines whereas thepEGFP-N1 base composition is 53% cytosines and guanines. Higherlevels of GC base pairs might lead to a greater incidence of mispairingduring folding and a slower rate of unpairing in misfolded intermediates,which could explain why folding was more difficult withthe pEGFP-N1 scaffold sequence. On the other hand, local sequencediversity is potentially greatest at 50% GC content, and so a scaffoldsequence with GC content that is very low might not be well-suitedfor DNA origami. Systematic studies will be required in the future todetermine the optimal base composition.Hierarchical assembly of DNA-origami nanostructures can beachieved by programming staple strands to bridge separate scaffoldstrands. Figure 4a shows the stacked cross programmed to polymerizealong the long axes of the DNA helices of the pod domain. The scaffoldloops on the ends of the object were programmed with a length suchthat they form properly spaced scaffold crossovers in the presence ofbridging staple strands that link the two ends of the objects. Thisinduces head-to-tail polymerization. Shown are filaments that©2009 Macmillan Publishers Limited. All rights reservedadsorbed on the grid in two different orientations to illustrate theperiodic presentation of the C-shaped domain perpendicular to thefilament axis at a periodicity of 41 nm (63 nm s.d. over a 33mer),corresponding to a length per base pair of 0.33 nm (60.02 nm s.d.).Figure 4b shows a wireframe DNA-origami nanostructure whosestruts are six-helix-bundle nanotubes (strand diagrams inSupplementary Note S2). A single scaffold strand is folded into abranched tree that links two pairs of half-struts internally to producea double triangle (Fig. 4b). This operation is repeated twice morewith two completely different sets of staple strands, based on cyclicpermutation of the same 8,100-base scaffold sequence through thearchitecture of the double-triangle monomer. This produces threechemically distinct double-triangle monomers that vary according tothe sequences displayed at various positions. Every double triangledisplays ten terminal branches presenting scaffold and staplesequences that are programmed to pair specifically with five terminalbranches each on the two other double triangles (Fig. 4c). When thethree species are mixed together, heterotrimers in the shape of awireframe icosahedron with a diameter of about 100 nm are formed(Fig. 4d, and gel in Supplementary Note S1). The majority of particlesvisualized by transmission electron microscopy have missing struts,owing either to incomplete folding or to particle flattening andcollapse, commonly seen for spherical or cylindrical particles preparedby negative-stain protocols 27 .Previously, scaffolded DNA origami was employed to create flatstructures containing dozens of helices and nanotubes containing sixhelices 9,28,29 . The present work generalizes this method into three dimensionsby folding helices on a honeycomb lattice. Using caDNAno 21 ,417


LETTERS NATURE | Vol 459 | 21 May 2009abdFigure 4 | Two-step hierarchical assembly of larger three-dimensionalstructures and polymers. a, Left panel, Cylinder model of stacked-crossmonomer (Fig. 2e), with dotted line indicating direction of assembly. Rightpanels, typical TEM micrographs showing stacked-cross polymers. Purifiedstacked-cross samples were mixed with a fivefold molar excess of connectorstaple strands in the presence of 5 mM Tris 1 1 mM EDTA (pH 7.9 at 20 uC),16 mM MgCl 2 at 30 uC for 24 h. Monomers were folded in separatechambers, purified, and mixed with connector staple strands designed tobridge separate monomers. b, Cylinder model (left) and transmissionelectron micrograph (right) of a double-triangle shape comprised of 20 sixhelixbundle half-struts. c, Heterotrimerization of the icosahedra was donewith a 1:1:1 mixture of the three unpurified monomers at 50 uC for 24 h.d, Orthographic projection models and TEM data of four icosahedronparticles. Scale bars in a, b and d: 100 nm.staple sequences for folding newly conceived objects can be generatedquickly. Design, acquisition of commercially synthesized staple strands,thermal folding, and initial transmission-electron-microscopic imagingcan all be completed in as little as two weeks.Improvements in the rate and yield of folding will be critical forenabling the robust assembly of larger and more complicated DNAnanostructures. Potential steps in this direction include enzymaticsynthesis for higher-quality staple strands, artificial scaffold sequencesthat are more amenable to robust folding, folding with formamidedilution instead of thermal ramps to reduce thermal damage to theDNA 29 , and hierarchical assembly with monomer architectures thathave been identified as being particularly well-behaved.Three-dimensional origami structures should expand the range ofpossible applications with an increased range of spatial positioningthat is not accessible by flat structures, including those requiringencapsulation or space-filling functionalities. For example, manynatural biosynthetic machines, such as polymerases, ribosomes, chaperones,and modular synthases, use three-dimensional scaffoldingto control assembly of complex products. Similar capabilities forsynthetic machines are thus more accessible with this convenient,generalizable facility to fabricate custom-shaped three-dimensionalstructures from DNA.Received 16 December 2008; accepted 24 March 2009.1. Whitesides, G. M., Mathias, J. P. & Seto, C. T. Molecular self-assembly andnanochemistry: a chemical strategy for the synthesis of nanostructures. Science254, 1312–1319 (1991).2. Seeman, N. C. Nucleic acid junctions and lattices. J. Theor. Biol. 99, 237–247 (1982).418c©2009 Macmillan Publishers Limited. All rights reserved3. Fu, T. J. & Seeman, N. C. DNA double-crossover molecules. Biochemistry 32,3211–3220 (1993).4. Li, X. J., Yang, X. P., Qi, J. & Seeman, N. C. Antiparallel DNA double crossovermolecules as components for nanoconstruction. J. Am. Chem. Soc. 118, 6131–6140(1996).5. Seeman, N. C. DNA in a material world. Nature 421, 427–431 (2003).6. Winfree, E., Liu, F., Wenzler, L. A. & Seeman, N. C. Design and self-assembly oftwo-dimensional DNA crystals. Nature 394, 539–544 (1998).7. Yan, H., Park, S. H., Finkelstein, H., Reif, J. H. & LaBean, T. H. DNA-templated selfassemblyof protein arrays and highly conductive nanowires. Science 301,1882–1884 (2003).8. Rothemund, P. W. et al. Design and characterization of programmable DNAnanotubes. J. Am. Chem. Soc. 126, 16344–16352 (2004).9. Mathieu, F. et al. Six-helix bundles designed from DNA.Nano Lett. 5, 661–665 (2005).10. Liu, D., Park, S. H., Reif, J. H. & LaBean, T. H. DNA nanotubes self-assembled fromtriple-crossover tiles as templates for conductive nanowires. Proc. Natl Acad. Sci.USA 101, 717–722 (2004).11. Yin, P. et al. Programming DNA tube circumferences. Science 321, 824–826 (2008).12. Goodman, R. P. et al. Rapid chiral assembly of rigid DNA building blocks formolecular nanofabrication. Science 310, 1661–1665 (2005).13. Chen, J. H. & Seeman, N. C. Synthesis from DNA of a molecule with theconnectivity of a cube. Nature 350, 631–633 (1991).14. Zhang, Y. & Seeman, N. C. The construction of a DNA truncated octahedron. J.Am. Chem. Soc. 116, 1661–1669 (1994).15. He, Y. et al. Hierarchical self-assembly of DNA into symmetric supramolecularpolyhedra. Nature 452, 198–201 (2008).16. Zhang, C. et al. Conformational flexibility facilitates self-assembly of complexDNA nanostructures. Proc. Natl Acad. Sci. USA 105, 10665–10669 (2008).17. Shih, W. M., Quispe, J. D. & Joyce, G. F. A 1.7-kilobase single-stranded DNA thatfolds into a nanoscale octahedron. Nature 427, 618–621 (2004).18. Whitesides, G. M. & Grzybowski, B. Self-assembly at all scales. Science 295,2418–2421 (2002).19. Rothemund, P. W. Folding DNA to create nanoscale shapes and patterns. Nature440, 297–302 (2006).20. Yan, H., LaBean, T. H., Feng, L. & Reif, J. H. Directed nucleation assembly of DNAtile complexes for barcode-patterned lattices. Proc. Natl Acad. Sci. USA 100,8103–8108 (2003).21. Douglas, S. M. et al. Rapid prototyping of three-dimensional DNA-origami shapeswith caDNAno. Nucleic Acids Res. (in the press).22. Mandelkern, M., Elias, J. G., Eden, D. & Crothers, D. M. The dimensions of DNA insolution. J. Mol. Biol. 152, 153–161 (1981).23. Diekmann, S. & Lilley, D. M. J. The anomalous gel migration of a stable cruciform:temperature and salt dependence, and some comparisons with curved DNA.Nucleic Acids Res. 15, 5765–5774 (1987).24. Budker, V., Trubetskoy, V. & Wolff, J. A. Condensation of nonstoichiometric DNA/polycation complexes by divalent cations. Biopolymers 83, 646–657 (2006).25. Hibino, K. et al. Na1 more strongly inhibits DNA compaction by spermidin(31)than K1. Chem. Phys. Lett. 426, 405–409 (2006).26. Garcia, H. G. et al. Biological consequences of tightly bent DNA: the other life of amacromolecular celebrity. Biopolymers 85, 115–130 (2007).27. Harris, J. R., Gerber, M., Gebauer, W., Wernicke, W. & Markl, J. Negative stainscontaining trehalose: application to tubular and filamentous structures. Microsc.Microanal. 2, 43–52 (1996).28. Douglas, S. M., Chou, J. J. & Shih, W. M. DNA-nanotube-induced alignment ofmembrane proteins for NMR structure determination. Proc. Natl Acad. Sci. USA104, 6644–6648 (2007).29. Jungmann, R., Liedl, T., Sobey, T. L., Shih, W. & Simmel, F. C. Isothermal assemblyof DNA origami structures using denaturing agents. J. Am. Chem. Soc. 130,10062–10063 (2008).Supplementary Information is linked to the online version of the paper atwww.nature.com/nature.Acknowledgements We thank X. Su for assistance in cloning M13-based scaffoldsequences and G. Hess for pilot studies on the railed-bridge design. This work wassupported by a Claudia Adams Barr Program Investigator grant, a Wyss Institutefor Biologically Inspired Engineering at Harvard grant, and an NIH New Investigatorgrant (1DP2OD004641-01) to W.M.S., a Humboldt Fellowship to H.D., DeutscherAkademischer Austauschdienst (DAAD) Fellowship to T.L., and Swedish ScienceCouncil (Vetenskapsrådet) Fellowship to B.H.Author Contributions S.M.D. designed the monolith and square nut, and providedcaDNAno software support; H.D. designed the stacked cross; T.L. designed therailed bridge; B.H. designed the slotted cross; F.G. designed the genie bottle;W.M.S. designed the icosahedron; S.M.D. and W.M.S. developed thehoneycomb-pleated-origami design rules; H.D., S.M.D., T.L., B.H. and W.M.S.optimized the folding and imaging conditions. All authors collected and analyseddata and contributed to preparing the manuscript.Author Information Reprints and permissions information is available atwww.nature.com/reprints. The authors declare competing financial interests:details accompany the paper on www.nature.com/nature. Correspondence andrequests for materials should be addressed to W.M.S.(william_shih@dfci.harvard.edu).

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