Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA.

The identification and differentiation of a large number of distinct molecular species with high temporal and spatial resolution is a major challenge in biomedical science. Fluorescence microscopy is a powerful tool, but its multiplexing ability is limited by the number of spectrally distinguishable fluorophores. Here, we used (deoxy)ribonucleic acid (DNA)-origami technology to construct submicrometre nanorods that act as fluorescent barcodes. We demonstrate that spatial control over the positioning of fluorophores on the surface of a stiff DNA nanorod can produce 216 distinct barcodes that can be decoded unambiguously using epifluorescence or total internal reflection fluorescence microscopy. Barcodes with higher spatial information density were demonstrated via the construction of super-resolution barcodes with features spaced by ∼40 nm. One species of the barcodes was used to tag yeast surface receptors, which suggests their potential applications as in situ imaging probes for diverse biomolecular and cellular entities in their native environments.

[1]  Chenxiang Lin,et al.  Recovery of intact DNA nanostructures after agarose gel–based separation , 2011, Nature Methods.

[2]  Hao Zhang,et al.  Controlled fabrication of fluorescent barcode nanorods. , 2010, ACS nano.

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

[4]  D. Ingber,et al.  Self-assembly of three-dimensional prestressed tensegrity structures from DNA , 2010 .

[5]  S. Hell Far-field optical nanoscopy , 2010 .

[6]  Jan Vogelsang,et al.  Superresolution microscopy on the basis of engineered dark states. , 2008, Journal of the American Chemical Society.

[7]  Paul R. Selvin,et al.  Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5-nm Localization , 2003, Science.

[8]  Hao Yan,et al.  DNA Origami: A Quantum Leap for Self‐Assembly of Complex Structures , 2012 .

[9]  Ricardo Henriques,et al.  Superresolution imaging of HIV in infected cells with FlAsH-PALM , 2012, Proceedings of the National Academy of Sciences.

[10]  Dan Luo,et al.  Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes , 2005, Nature Biotechnology.

[11]  R. G. Freeman,et al.  Submicrometer metallic barcodes. , 2001, Science.

[12]  Jan Vogelsang,et al.  Make them blink: probes for super-resolution microscopy. , 2010, Chemphyschem : a European journal of chemical physics and physical chemistry.

[13]  Michael J Sailor,et al.  Biomolecular screening with encoded porous-silicon photonic crystals , 2002, Nature Materials.

[14]  W. B. Knowlton,et al.  Programmable Periodicity of Quantum Dot Arrays with DNA Origami Nanotubes , 2010, Nano letters.

[15]  S. Nie,et al.  Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules , 2001, Nature Biotechnology.

[16]  Robert H Singer,et al.  Single-Cell Gene Expression Profiling , 2002, Science.

[17]  X. Zhuang,et al.  Fast three-dimensional super-resolution imaging of live cells , 2011, Nature Methods.

[18]  X. Zhuang,et al.  Breaking the Diffraction Barrier: Super-Resolution Imaging of Cells , 2010, Cell.

[19]  J. Lippincott-Schwartz,et al.  Imaging Intracellular Fluorescent Proteins at Nanometer Resolution , 2006, Science.

[20]  R. W. Draft,et al.  Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system , 2007, Nature.

[21]  Alex Rhee,et al.  Facile and rapid one-step mass preparation of quantum-dot barcodes. , 2008, Angewandte Chemie.

[22]  Shawn M. Douglas,et al.  Folding DNA into Twisted and Curved Nanoscale Shapes , 2009, Science.

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

[24]  Ralf Jungmann,et al.  DNA origami as a nanoscopic ruler for super-resolution microscopy. , 2009, Angewandte Chemie.

[25]  Michael J Rust,et al.  Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) , 2006, Nature Methods.

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

[27]  Chenxiang Lin,et al.  Knitting Complex Weaves with Dna Origami This Review Comes from a Themed Issue on Nucleic Acids Edited Dna and the Biosynthetic Advantage Single-layer Dna Origami Multi-layer Dna Origami Scaling to Greater Complexity Conclusions and Future Outlook , 2022 .

[28]  Thomas Tørring,et al.  DNA origami: a quantum leap for self-assembly of complex structures. , 2011, Chemical Society reviews.

[29]  Kevin Braeckmans,et al.  Encoding microcarriers by spatial selective photobleaching , 2003, Nature materials.

[30]  Holden T. Maecker,et al.  Erratum: Standardizing immunophenotyping for the Human Immunology Project , 2012, Nature Reviews Immunology.

[31]  Marcel A. Lauterbach,et al.  Far-Field Optical Nanoscopy , 2009 .

[32]  Erik Winfree,et al.  Molecular robots guided by prescriptive landscapes , 2010, Nature.

[33]  Jennifer L. Osborn,et al.  Direct multiplexed measurement of gene expression with color-coded probe pairs , 2008, Nature Biotechnology.

[34]  R. Schleif,et al.  Size fractionation of double-stranded DNA by precipitation with polyethylene glycol. , 1975, Nucleic acids research.

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

[36]  F. Simmel,et al.  Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. , 2010, Nano letters.

[37]  Anthony J. Manzo,et al.  Do-it-yourself guide: how to use the modern single-molecule toolkit , 2008, Nature Methods.

[38]  P. Kwok,et al.  Direct determination of haplotypes from single DNA molecules , 2009, Nature Methods.

[39]  Anthony G. Frutos,et al.  Rare earth-doped glass microbarcodes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[40]  H. Vogel,et al.  A general method for the covalent labeling of fusion proteins with small molecules in vivo , 2003, Nature Biotechnology.

[41]  B. Kurien,et al.  Extraction of nucleic acid fragments from gels. , 2002, Analytical biochemistry.

[42]  Mehmet Toner,et al.  Multifunctional Encoded Particles for High-Throughput Biomolecule Analysis , 2007, Science.

[43]  P. Engel,et al.  New B-cell CD molecules. , 2011, Immunology letters.

[44]  Hao Yan,et al.  DNA-origami-directed self-assembly of discrete silver-nanoparticle architectures. , 2010, Angewandte Chemie.

[45]  Sebastian van de Linde,et al.  Live-cell dSTORM with SNAP-tag fusion proteins. , 2011, Nature methods.

[46]  Kai Johnsson,et al.  An engineered protein tag for multiprotein labeling in living cells. , 2008, Chemistry & biology.

[47]  M. Trau,et al.  'On-the-fly' optical encoding of combinatorial peptide libraries for profiling of protease specificity. , 2010, Molecular bioSystems.

[48]  Hao Yan,et al.  Self-assembled combinatorial encoding nanoarrays for multiplexed biosensing. , 2007, Nano letters.

[49]  Hao Yan,et al.  Designer DNA nanoarchitectures. , 2009, Biochemistry.

[50]  Charles M. Lieber,et al.  Growth of nanowire superlattice structures for nanoscale photonics and electronics , 2002, Nature.

[51]  Hao Yan,et al.  DNA origami: a history and current perspective. , 2010, Current opinion in chemical biology.

[52]  J. Kjems,et al.  Self-assembly of a nanoscale DNA box with a controllable lid , 2009, Nature.

[53]  Hao Yan,et al.  Folding and cutting DNA into reconfigurable topological nanostructures. , 2010, Nature nanotechnology.

[54]  Faisal A. Aldaye,et al.  Assembling Materials with DNA as the Guide , 2008, Science.

[55]  J. Treadway,et al.  Multiplexed SNP genotyping using the Qbead system: a quantum dot-encoded microsphere-based assay. , 2003, Nucleic acids research.

[56]  D. Toomre,et al.  A new wave of cellular imaging. , 2010, Annual review of cell and developmental biology.

[57]  Hao Yan,et al.  DNA Origami with Complex Curvatures in Three-Dimensional Space , 2011, Science.