Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA
Open accessAbstract
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.
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Single-molecule total internal reflection fluorescence (TIRF) microscopy can decode fluorescent barcodes assembled on DNA nanostructures.
“Through the use of single-molecule total internal reflection fluorescence (TIRF) microscopy, it is possible to decode fluorescent barcodes assembled on DNA nanostructures.120”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [120]
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Cites
Imaging Intracellular Fluorescent Proteins at Nanometer Resolution
Betzig, E., Patterson, G. H., Sougrat, R., Lindwasser, O. W., Olenych, S. G., Bonifacino, J. S., Davidson, M. W., Lippincott‐Schwartz, J., & Hess, H. F. (2006) · Science · doi:10.1126/science.1127344 · Cited by 8,802 · see citing works
Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)
Rust, M. J., Bates, M., & Zhuang, X. (2006) · Nature Methods · doi:10.1038/nmeth929 · Cited by 8,109 · see citing works
Folding DNA to create nanoscale shapes and patterns
Rothemund, P. W. K. (2006) · Nature · doi:10.1038/nature04586 · Cited by 7,320 · see citing works
Hell, S. W. (2007) · Science · doi:10.1126/science.1137395 · Cited by 2,967 · see citing works
Growth of nanowire superlattice structures for nanoscale photonics and electronics
Gudiksen, M. S., Lauhon, L. J., Wang, J., Smith, D. C., & Lieber, C. M. (2002) · Nature · doi:10.1038/415617a · Cited by 2,709 · see citing works
Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules
Han, M., Gao, X., Su, J. Z., & Nie, S. (2001) · Nature Biotechnology · doi:10.1038/90228 · Cited by 2,632 · see citing works
Self-assembly of DNA into nanoscale three-dimensional shapes
Douglas, S. M., Dietz, H., Liedl, T., Högberg, B., Graf, F., & Shih, W. M. (2009) · Nature · doi:10.1038/nature08016 · Cited by 2,579 · see citing works
Self-citationNucleic acid junctions and lattices
Seeman, N. C. (1982) · Journal of Theoretical Biology · doi:10.1016/0022-5193(82)90002-9 · Cited by 2,505 · see citing works
Direct multiplexed measurement of gene expression with color-coded probe pairs
Geiss, G. K., Bumgarner, R. E., Birditt, B., Dahl, T., Dowidar, N., Dunaway, D. L., Fell, H. P., Ferree, S., George, R. D., Grogan, T., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1385 · Cited by 2,066 · see citing works
A general method for the covalent labeling of fusion proteins with small molecules in vivo
Keppler, A., Gendreizig, S., Gronemeyer, T., Pick, H. M., Vogel, H., & Johnsson, K. (2002) · Nature Biotechnology · doi:10.1038/nbt765 · Cited by 1,964 · see citing works
Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system
Livet, J., Weissman, T. A., Kang, H., Draft, R. W., Lu, J., Bennis, R. A., Sanes, J. R., & Lichtman, J. W. (2007) · Nature · doi:10.1038/nature06293 · Cited by 1,876 · see citing works
Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5-nm Localization
Yildiz, A., Forkey, J., McKinney, S., Ha, T., Goldman, Y., & Selvin, P. (2003) · Science · doi:10.1126/science.1084398 · Cited by 1,870 · see citing works
Self-assembly of a nanoscale DNA box with a controllable lid
Andersen, E. S., Dong, M., Nielsen, M. M., Jahn, K., Subramani, R., Mamdouh, W., Golas, M. M., Sander, B. O., Stark, H., Oliveira, C. L. P., et al. (2009) · Nature · doi:10.1038/nature07971 · Cited by 1,628 · see citing works
Folding DNA into Twisted and Curved Nanoscale Shapes
Dietz, H., Douglas, S. M., & Shih, W. M. (2009) · Science · doi:10.1126/science.1174251 · Cited by 1,340 · see citing works
Self-citationDNA Origami with Complex Curvatures in Three-Dimensional Space
Han, D., Pal, S., Nangreave, J., Deng, Z., Liu, Y., & Yan, H. (2011) · Science · doi:10.1126/science.1202998 · Cited by 1,216 · see citing works
Submicrometer Metallic Barcodes
Peña, S. R. N., Freeman, R. G., Reiss, B. D., He, L., Peña, D. J., Walton, I. D., CROMER, R., Keating, C. D., & Natan, M. J. (2001) · Science · doi:10.1126/science.294.5540.137 · Cited by 1,212 · see citing works
Standardizing immunophenotyping for the Human Immunology Project
Maecker, H. T., McCoy, J. P., & Nussenblatt, R. B. (2012) · Nature reviews. Immunology · doi:10.1038/nri3158 · Cited by 1,174 · see citing works
Breaking the Diffraction Barrier: Super-Resolution Imaging of Cells
Huang, B., Babcock, H. P., & Zhuang, X. (2010) · Cell · doi:10.1016/j.cell.2010.12.002 · Cited by 1,159 · see citing works
An Engineered Protein Tag for Multiprotein Labeling in Living Cells
Gautier, A., Juillerat, A., Heinis, C., et al. (2008) · Chemistry & Biology · doi:10.1016/j.chembiol.2008.01.007 · Cited by 1,096 · see citing works
Assembling Materials with DNA as the Guide
Aldaye, F. A., Palmer, A. L., & Sleiman, H. F. (2008) · Science · doi:10.1126/science.1154533 · Cited by 978 · see citing works
Molecular robots guided by prescriptive landscapes
Lund, K., Manzo, A. J., Dabby, N., Michelotti, N., Johnson-Buck, A. E., Nangreave, J., Taylor, S. K., Pei, R., Stojanović, M. N., Walter, N. G., et al. (2010) · Nature · doi:10.1038/nature09012 · Cited by 942 · see citing works
Jungmann, R., Steinhauer, C., Scheible, M. B., Kuzyk, A., Tinnefeld, P., & Simmel, F. C. (2010) · Nano Letters · doi:10.1021/nl103427w · Cited by 907 · see citing works
Self-citationFast, three-dimensional super-resolution imaging of live cells
Jones, S. A., Shim, S., He, J., & Zhuang, X. (2011) · Nature Methods · doi:10.1038/nmeth.1605 · Cited by 752 · see citing works
Multifunctional Encoded Particles for High-Throughput Biomolecule Analysis
Pregibon, D. C., Toner, M., & Doyle, P. S. (2007) · Science · doi:10.1126/science.1134929 · Cited by 727 · see citing works
Single-Cell Gene Expression Profiling
Levsky, J. M., Shenoy, S. M., Pezo, R. C., & Singer, R. H. (2002) · Science · doi:10.1126/science.1072241 · Cited by 526 · see citing works
Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes
Li, Y., Cu, Y., & Luo, D. (2005) · Nature Biotechnology · doi:10.1038/nbt1106 · Cited by 517 · see citing works
DNA-nanotube-induced alignment of membrane proteins for NMR structure determination
Douglas, S. M., Chou, J. J., & Shih, W. M. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0700930104 · Cited by 481 · see citing works
Self-citationDNA origami: a quantum leap for self-assembly of complex structures
Tørring, T., Voigt, N. V., Nangreave, J., Yan, H., & Gothelf, K. V. (2011) · Chemical Society Reviews · doi:10.1039/c1cs15057j · Cited by 475 · see citing works
Biomolecular screening with encoded porous-silicon photonic crystals
Cunin, F., Schmedake, T. A., Link, J. R., Li, Y. Y., Koh, J., Bhatia, S. N., & Sailor, M. J. (2002) · Nature Materials · doi:10.1038/nmat702 · Cited by 409 · see citing works
Self-assembly of three-dimensional prestressed tensegrity structures from DNA
Liedl, T., Högberg, B., Tytell, J. D., Ingber, D. E., & Shih, W. M. (2010) · Nature Nanotechnology · doi:10.1038/nnano.2010.107 · Cited by 382 · see citing works
Self-citationWestphal, V., Rizzoli, S. O., Lauterbach, M. A., Kamin, D., & Hell, S. W. (2009) · OSA Optics and Photonics Congress: Advances in Imaging · doi:10.1364/ntm.2009.nma1 · Cited by 365 · see citing works
Do-it-yourself guide: how to use the modern single-molecule toolkit
Walter, N. G., Huang, C., Manzo, A. J., & Sobhy, M. A. (2008) · Nature Methods · doi:10.1038/nmeth.1215 · Cited by 335 · see citing works
Folding and cutting DNA into reconfigurable topological nanostructures
Han, D., Pal, S., Liu, Y., & Yan, H. (2010) · Nature Nanotechnology · doi:10.1038/nnano.2010.193 · Cited by 329 · see citing works
A New Wave of Cellular Imaging
Toomre, D. K., & Bewersdorf, J. (2010) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100109-104048 · Cited by 321 · see citing works
DNA‐Origami‐Directed Self‐Assembly of Discrete Silver‐Nanoparticle Architectures
Pal, S., Deng, Z., Ding, B., Yan, H., & Liu, Y. (2010) · Angewandte Chemie International Edition · doi:10.1002/anie.201000330 · Cited by 314 · see citing works
DNA Origami as a Nanoscopic Ruler for Super‐Resolution Microscopy
Steinhauer, C., Jungmann, R., Sobey, T. L., Simmel, F. C., & Tinnefeld, P. (2009) · Angewandte Chemie International Edition · doi:10.1002/anie.200903308 · Cited by 276 · see citing works
Self-citationMultiplexed SNP genotyping using the QbeadTM system: a quantum dot-encoded microsphere-based assay
Xu, H. (2003) · Nucleic Acids Research · doi:10.1093/nar/gng043 · Cited by 269 · see citing works
Designer DNA Nanoarchitectures
Lin, C., Liu, Y., & Yan, H. (2009) · Biochemistry · doi:10.1021/bi802324w · Cited by 261 · see citing works
Self-citationLive-cell dSTORM with SNAP-tag fusion proteins
Klein, T., Löschberger, A., Proppert, S., Wolter, S., van de Linde, S., & Sauer, M. (2010) · Nature Methods · doi:10.1038/nmeth0111-7b · Cited by 247 · see citing works
Programmable Periodicity of Quantum Dot Arrays with DNA Origami Nanotubes
Bui, H., Onodera, C., Kidwell, C., Tan, Y., Graugnard, E., Kuang, W., Lee, J., Knowlton, W. B., Yurke, B., & Hughes, W. L. (2010) · Nano Letters · doi:10.1021/nl101079u · Cited by 244 · see citing works
Rare earth-doped glass microbarcodes
Dejneka, M. J., Streltsov, A. M., Pal, S., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0236044100 · Cited by 209 · see citing works
Make them Blink: Probes for Super‐Resolution Microscopy
Vogelsang, J., Steinhauer, C., Forthmann, C., et al. (2010) · ChemPhysChem · doi:10.1002/cphc.201000189 · Cited by 199 · see citing works
DNA origami: a history and current perspective
Nangreave, J., Han, D., Liu, Y., & Yan, H. (2010) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2010.06.182 · Cited by 190 · see citing works
DNA Origami as a Nanoscopic Ruler For Super-Resolution Microscopy
Jungmann, R., Steinhauer, C., Sobey, T. L., Tinnefeld, P., & Simmel, F. C. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2009.12.986 · Cited by 187 · see citing works
Self-citationEncoding microcarriers by spatial selective photobleaching
Braeckmans, K., Smedt, S. C. D., Roelant, C., Leblans, M., Pauwels, R., & Demeester, J. (2003) · Nature Materials · doi:10.1038/nmat828 · Cited by 165 · see citing works
Facile and Rapid One‐Step Mass Preparation of Quantum‐Dot Barcodes
Fournier‐Bidoz, S., Jennings, T. L., Klostranec, J. M., et al. (2008) · Angewandte Chemie International Edition · doi:10.1002/anie.200800409 · Cited by 149 · see citing works
Knitting complex weaves with DNA origami
Shih, W. M., & Lin, C. (2010) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2010.03.009 · Cited by 133 · see citing works
Self-citationSelf-Assembled Combinatorial Encoding Nanoarrays for Multiplexed Biosensing
Lin, C., Liu, Y., & Yan, H. (2007) · Nano Letters · doi:10.1021/nl062998n · Cited by 117 · see citing works
Self-citationMatesanz-Isabel, J., Sintes, J., Llinàs, L., de Salort, J., Lázaro, A., & Engel, P. (2010) · Immunology Letters · doi:10.1016/j.imlet.2010.09.019 · Cited by 72 · see citing works
Controlled Fabrication of Fluorescent Barcode Nanorods
Li, X., Wang, T., Zhang, J., et al. (2010) · ACS Nano · doi:10.1021/nn9017137 · Cited by 60 · see citing works
Direct determination of haplotypes from single DNA molecules
Xiao, M., Wan, E., Chu, C., Hsueh, W., Cao, Y., & Kwok, P. (2009) · Nature Methods · doi:10.1038/nmeth.1301 · Cited by 35 · see citing works
Marcon, L., Battersby, B. J., Rühmann, A., et al. (2009) · Molecular BioSystems · doi:10.1039/b909087h · Cited by 18 · see citing works
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Jones, M. R., Seeman, N. C., & Mirkin, C. A. (2015) · Science · doi:10.1126/science.1260901 · Cited by 1,347 · see citing works
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Schnitzbauer, J., Strauss, M. T., Schlichthaerle, T., Schueder, F., & Jungmann, R. (2017) · Nature Protocols · doi:10.1038/nprot.2017.024 · Cited by 1,047 · see citing works
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- Authors
- Lin, C., Jungmann, R., Leifer, A. M., Li, C., Levner, D., Church, G. M., Shih, W. M., & Yin, P.
- Affiliations
- Harvard University (US)
- Corresponding author
- Shih, William M.
- Yin, Peng
- ORCID
- Venue
- Nature Chemistry
- Published
- 2012-09-24
- Volume
- 4
- Issue
- 10
- Pages
- 832-839
- ISSN
- 1755-4330 (ISSN-L)
- 1755-4349
- PMC
- PMC3523708
- OpenAlex
- W2052275870
- Cited by
- 302
- References
- 52
- Citations by year
- 2026: 15 · 2025: 21 · 2024: 17 · 2023: 20 · 2022: 18 · 2021: 21 · 2020: 19 · 2019: 26 · 2018: 29 · 2017: 26 · 2016: 21 · 2015: 13 · 2014: 31 · 2013: 21 · 2012: 3
- FWCI
- 8.73
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (acceptedVersion)
- Funders
- National Institutes of Health (1dp2od007292-01, 1dp2od004641-01)
- National Human Genome Research Institute (P50HG005550)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- DNA origami, DNA nanorods, multiplexed fluorescence imaging, total internal reflection fluorescence microscopy, epifluorescence microscopy
- MeSH terms
- DNA, Fluorescent Dyes, Microscopy, Fluorescence, Nanotubes
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