Self-assembly of a nanoscale DNA box with a controllable lid

The unique structural motifs and self-recognition properties of DNA can be exploited to generate self-assembling DNA nanostructures of specific shapes using a ‘bottom-up’ approach. Several assembly strategies have been developed for building complex three-dimensional (3D) DNA nanostructures. Recently, the DNA ‘origami’ method was used to build two-dimensional addressable DNA structures of arbitrary shape that can be used as platforms to arrange nanomaterials with high precision and specificity. A long-term goal of this field has been to construct fully addressable 3D DNA nanostructures. Here we extend the DNA origami method into three dimensions by creating an addressable DNA box 42 × 36 × 36 nm3 in size that can be opened in the presence of externally supplied DNA ‘keys’. We thoroughly characterize the structure of this DNA box using cryogenic transmission electron microscopy, small-angle X-ray scattering and atomic force microscopy, and use fluorescence resonance energy transfer to optically monitor the opening of the lid. Controlled access to the interior compartment of this DNA nanocontainer could yield several interesting applications, for example as a logic sensor for multiple-sequence signals or for the controlled release of nanocargos.

[1]  P. Debye,et al.  Molecular-weight determination by light scattering. , 1947, The Journal of physical and colloid chemistry.

[2]  N. Seeman.  Nucleic acid junctions and lattices. , 1982, Journal of theoretical biology.

[3]  Kell Mortensen,et al.  Analytical treatment of the resolution function for small-angle scattering , 1990 .

[4]  N. Seeman,et al.  Synthesis from DNA of a molecule with the connectivity of a cube , 1991, Nature.

[5]  D. Lilley,et al.  Fluorescence resonance energy transfer analysis of the structure of the four-way DNA junction. , 1992, Biochemistry.

[6]  R. Clegg.  Fluorescence resonance energy transfer and nucleic acids. , 1992, Methods in enzymology.

[7]  D. Svergun,et al.  CRYSOL : a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates , 1995 .

[8]  M van Heel,et al.  A new generation of the IMAGIC image processing system. , 1996, Journal of structural biology.

[9]  Jan Skov Pedersen,et al.  Analysis of small-angle scattering data from colloids and polymer solutions: modeling and least-squares fitting , 1997 .

[10]  A. Turberfield,et al.  A DNA-fuelled molecular machine made of DNA , 2022 .

[11]  H. Stark,et al.  Corrim-based alignment for improved speed in single-particle image processing. , 2003, Journal of structural biology.

[12]  H. Stark,et al.  Automatic CTF correction for single particles based upon multivariate statistical analysis of individual power spectra. , 2003, Journal of structural biology.

[13]  William M. Shih,et al.  A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron , 2004, Nature.

[14]  J. S. Pedersen.  A flux- and background-optimized version of the NanoSTAR small-angle X-ray scattering camera for solution scattering , 2004 .

[15]  Russell P. Goodman,et al.  Rapid Chiral Assembly of Rigid DNA Building Blocks for Molecular Nanofabrication , 2005, Science.

[16]  H. Stark,et al.  Advantages of CCD detectors for de novo three-dimensional structure determination in single-particle electron microscopy. , 2005, Journal of structural biology.

[17]  P. Rothemund.  Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[18]  N. Seeman,et al.  Operation of a DNA Robot Arm Inserted into a 2D DNA Crystalline Substrate , 2006, Science.

[19]  Hao Yan,et al.  Self-assembled peptide nanoarrays: an approach to studying protein-protein interactions. , 2007, Angewandte Chemie.

[20]  Nadrian C. Seeman,et al.  An Overview of Structural DNA Nanotechnology , 2007, Molecular biotechnology.

[21]  Shawn M. Douglas,et al.  DNA-nanotube-induced alignment of membrane proteins for NMR structure determination , 2007, Proceedings of the National Academy of Sciences.

[22]  C. Mao,et al.  Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra , 2008, Nature.

[23]  H. Sleiman,et al.  Templated synthesis of highly stable, electroactive, and dynamic metal-DNA branched junctions. , 2008, Angewandte Chemie.

[24]  D. Lilley,et al.  Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids , 2008, Proceedings of the National Academy of Sciences.

[25]  Mingdong Dong,et al.  DNA origami design of dolphin-shaped structures with flexible tails. , 2008, ACS nano.

[26]  Hao Yan,et al.  Self-Assembled Water-Soluble Nucleic Acid Probe Tiles for Label-Free RNA Hybridization Assays , 2008, Science.

[27]  Felicie F. Andersen,et al.  Assembly and structural analysis of a covalently closed nano-scale DNA cage , 2007, Nucleic acids research.

[28]  Russell P. Goodman,et al.  Reconfigurable, braced, three-dimensional DNA nanostructures. , 2008, Nature nanotechnology.

[29]  F. Simmel.  Three-Dimensional Nanoconstruction with DNA , 2008 .

[30]  Hao Yan,et al.  Toward reliable gold nanoparticle patterning on self-assembled DNA nanoscaffold. , 2008, Journal of the American Chemical Society.

[31]  Hao Yan,et al.  Self-assembled DNA nanostructures for distance-dependent multivalent ligand-protein binding. , 2008, Nature nanotechnology.