A Caltech Library Service

Folding DNA to create nanoscale shapes and patterns

Rothemund, Paul W. K. (2006) Folding DNA to create nanoscale shapes and patterns. Nature, 440 (7082). pp. 297-302. ISSN 0028-0836. doi:10.1038/nature04586.

PDF (Notes on the design process; helix bending and the inter-helix gap; models and sequences; experimental methods; control experiments; patterning with dumbbell hairpins; the combination of shapes into larger structures; secondary structure of the scaffold a) - Supplemental Material
See Usage Policy.

PDF (Full designs for all structures. Staple sequences are drawn out explicitly where they occur in the design. Because the designs are very large and the fonts are very small, this file will not print legibly. Instead of printing this file, open it in a PDF v) - Supplemental Material
See Usage Policy.


Use this Persistent URL to link to this item:


‘Bottom-up fabrication’, which exploits the intrinsic properties of atoms and molecules to direct their self-organization, is widely used to make relatively simple nanostructures. A key goal for this approach is to create nanostructures of high complexity, matching that routinely achieved by ‘top-down’ methods. The self-assembly of DNA molecules provides an attractive route towards this goal. Here I describe a simple method for folding long, single-stranded DNA molecules into arbitrary two-dimensional shapes. The design for a desired shape is made by raster-filling the shape with a 7-kilobase single-stranded scaffold and by choosing over 200 short oligonucleotide ‘staple strands’ to hold the scaffold in place. Once synthesized and mixed, the staple and scaffold strands self-assemble in a single step. The resulting DNA structures are roughly 100 nm in diameter and approximate desired shapes such as squares, disks and five-pointed stars with a spatial resolution of 6 nm. Because each oligonucleotide can serve as a 6-nm pixel, the structures can be programmed to bear complex patterns such as words and images on their surfaces. Finally, individual DNA structures can be programmed to form larger assemblies, including extended periodic lattices and a hexamer of triangles (which constitutes a 30-megadalton molecular complex).

Item Type:Article
Related URLs:
URLURL TypeDescription Material ReadCube access
Rothemund, Paul W. K.0000-0002-1653-3202
Contact Email
Additional Information:© 2006 Macmillan Publishers Limited. Received 7 September 2005; Accepted 12 January 2006. Acknowledgements I thank E. Winfree for discussions and providing a stimulating laboratory environment; B. Yurke for the term ‘nanobreadboard’; N. Papadakis, L. Adleman, J. Goto, R. Barish, R. Schulman, R. Hariadi, M. Cook and M. Diehl for discussions; B. Shaw for a gift of AFM tips; A. Schmidt for coordinating DNA synthesis; and K. Yong, J. Crouch and L. Hein for administrative support. This work was supported by National Science Foundation Career and Nano grants to E. Winfree as well as fellowships from the Beckman Foundation and Caltech Center for the Physics of Information.
Funding AgencyGrant Number
Arnold and Mabel Beckman FoundationUNSPECIFIED
Caltech Center for the Physics of InformationUNSPECIFIED
Issue or Number:7082
Record Number:CaltechAUTHORS:20110216-103904901
Persistent URL:
Official Citation:Rothemund, P. W. K. (2006). "Folding DNA to create nanoscale shapes and patterns." Nature 440(7082): 297-302.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:22244
Deposited By: Dr. Paul W.K. Rothemund
Deposited On:16 Feb 2011 19:46
Last Modified:09 Nov 2021 16:04

Repository Staff Only: item control page