Constructing Higher-Order DNA Nanoarchitectures with Highly Purified DNA Nanocages.

DNA nanostructures have attracted great attention due to their precisely controllable geometry and great potential in various areas including bottom-up self-assembly. However, construction of higher-order DNA nanoarchitectures with individual DNA nanostructures is often hampered with the purity and quantity of these "bricks". Here, we introduced size exclusion chromatography (SEC) to prepare highly purified tetrahedral DNA nanocages in large scale and demonstrated that precise quantification of DNA nanocages was the key to the formation of higher-order DNA nanoarchitectures. We successfully purified a series of DNA nanocages with different sizes, including seven DNA tetrahedra with different edge lengths (7, 10, 13, 17, 20, 26, 30 bp) and one trigonal bipyramid with a 20-bp edge. These highly purified and aggregation-free DNA nanocages could be self-assembled into higher-order DNA nanoarchitectures with extraordinarily high yields (98% for dimer and 95% for trimer). As a comparison, unpurified DNA nanocages resulted in low yield of 14% for dimer and 12% for trimer, respectively. AFM images cleraly presented the characteristic structure of monomer, dimer and trimer, impling the purified DNA nanocages well-formed the designed nanoarchitectures. Therefore, we have demonstrated that highly purified DNA nanocages are excellent "bricks" for DNA nanotechnology and show great potential in various applications of DNA nanomaterials.

[1]  J. Chao,et al.  Folding super-sized DNA origami with scaffold strands from long-range PCR. , 2012, Chemical communications.

[2]  Erik Winfree,et al.  Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. , 2010, Nature nanotechnology.

[3]  Andrew J Turberfield,et al.  Single-molecule protein encapsulation in a rigid DNA cage. , 2006, Angewandte Chemie.

[4]  J. Storhoff,et al.  A DNA-based method for rationally assembling nanoparticles into macroscopic materials , 1996, Nature.

[5]  Qin Xu,et al.  DNA nanostructure-based ultrasensitive electrochemical microRNA biosensor. , 2013, Methods.

[6]  Jiye Shi,et al.  Scaffolded biosensors with designed DNA nanostructures , 2013 .

[7]  Andrew J Turberfield,et al.  The single-step synthesis of a DNA tetrahedron. , 2004, Chemical communications.

[8]  J. Chao,et al.  RCA strands as scaffolds to create nanoscale shapes by a few staple strands. , 2013, Journal of the American Chemical Society.

[9]  Hao Yan,et al.  Encapsulation of gold nanoparticles in a DNA origami cage. , 2011, Angewandte Chemie.

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

[11]  Peng Yin,et al.  Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA. , 2012, Nature chemistry.

[12]  Qiangbin Wang,et al.  DNA origami directed large-scale fabrication of nanostructures resembling room temperature single-electron transistors. , 2013, Small.

[13]  Lei Liu,et al.  Three-step synthesis of sialic acids and derivatives. , 2006, Angewandte Chemie.

[14]  M. Ali,et al.  Rolling circle amplification: applications in nanotechnology and biodetection with functional nucleic acids. , 2008, Angewandte Chemie.

[15]  Grigory Tikhomirov,et al.  DNA-based programming of quantum dot valency, self-assembly and luminescence. , 2011, Nature nanotechnology.

[16]  Hao Yan,et al.  Challenges and opportunities for structural DNA nanotechnology. , 2011, Nature nanotechnology.

[17]  Christof M. Niemeyer,et al.  DNA Origami: The Art of Folding DNA. , 2012 .

[18]  Yonggang Ke,et al.  Two design strategies for enhancement of multilayer-DNA-origami folding: underwinding for specific intercalator rescue and staple-break positioning. , 2012, Chemical science.

[19]  B. Ren,et al.  DNA-directed gold nanodimers with tunable sizes and interparticle distances and their surface plasmonic properties. , 2013, Small.

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

[21]  이혁진.  Molecularly Self-Assembled Nucleic Acid Nanoparticles for Targeted In Vivo siRNA Delivery , 2012 .

[22]  H. Pei,et al.  Self-assembled multivalent DNA nanostructures for noninvasive intracellular delivery of immunostimulatory CpG oligonucleotides. , 2011, ACS nano.

[23]  Weihai Ni,et al.  Bifacial DNA origami-directed discrete, three-dimensional, anisotropic plasmonic nanoarchitectures with tailored optical chirality. , 2013, Journal of the American Chemical Society.

[24]  Hao Yan,et al.  A route to scale up DNA origami using DNA tiles as folding staples. , 2010, Angewandte Chemie.

[25]  A. Herrmann,et al.  Drug delivery systems based on nucleic acid nanostructures. , 2013, Journal of controlled release : official journal of the Controlled Release Society.

[26]  Hao Yan,et al.  Immobilization and one-dimensional arrangement of virus capsids with nanoscale precision using DNA origami. , 2010, Nano letters.

[27]  Shawn M. Douglas,et al.  Self-assembly of DNA into nanoscale three-dimensional shapes , 2009, Nature.

[28]  Adam T Woolley,et al.  Polymerase chain reaction based scaffold preparation for the production of thin, branched DNA origami nanostructures of arbitrary sizes. , 2009, Nano letters.

[29]  Hao Yan,et al.  DNA Sensors: A DNA Nanostructure‐based Biomolecular Probe Carrier Platform for Electrochemical Biosensing (Adv. Mater. 42/2010) , 2010 .

[30]  Yonggang Ke,et al.  Designer three-dimensional DNA architectures. , 2014, Current opinion in structural biology.

[31]  A. Paul Alivisatos,et al.  Pyramidal and chiral groupings of gold nanocrystals assembled using DNA scaffolds. , 2009, Journal of the American Chemical Society.

[32]  Qiangbin Wang,et al.  DNA-programmed self-assembly of photonic nanoarchitectures , 2014 .

[33]  Jiye Shi,et al.  Smart Drug Delivery Nanocarriers with Self‐Assembled DNA Nanostructures , 2013, Advanced materials.

[34]  Russell P. Goodman,et al.  A self-assembled DNA bipyramid. , 2007, Journal of the American Chemical Society.

[35]  Ick Chan Kwon,et al.  Drug delivery by a self-assembled DNA tetrahedron for overcoming drug resistance in breast cancer cells. , 2013, Chemical communications.

[36]  H. Sleiman,et al.  Development and characterization of gene silencing DNA cages. , 2014, Biomacromolecules.

[37]  D. Lelie,et al.  DNA-guided crystallization of colloidal nanoparticles , 2008, Nature.

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

[39]  Hao Yan,et al.  Dna Origami: a History and Current Perspective This Review Comes from a Themed Issue on Nanotechnology and Miniaturization Edited Structural Development Assembly Approaches Single-molecule Detection Material Organization , 2022 .