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ABSTRACT Rapid, multiplexed, sensitive and specific molecular detection is of great demand in gene profiling, drug screening, clinical diagnostics and environmental analysis1,2,3. One of the

major challenges in multiplexed analysis is to identify each specific reaction with a distinct label or 'code'4. Two encoding strategies are currently used: positional encoding,

in which every potential reaction is preassigned a particular position on a solid-phase support such as a DNA microarray5,6,7,8, and reaction encoding, where every possible reaction is

uniquely tagged with a code that is most often optical or particle based4,9,10,11,12,13. The micrometer size, polydispersity, complex fabrication process and nonbiocompatibility of current

codes limit their usability1,4,12. Here we demonstrate the synthesis of dendrimer-like DNA-based, fluorescence-intensity-coded nanobarcodes, which contain a built-in code and a probe for

molecular recognition. Their application to multiplexed detection of the DNA of several pathogens is first shown using fluorescence microscopy and dot blotting, and further demonstrated

using flow cytometry that resulted in detection that was sensitive (attomole) and rapid. Access through your institution Buy or subscribe This is a preview of subscription content, access

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USING BIOENGINEERED MULTIFUNCTIONAL YEAST NANOFRAGMENTS Article 08 June 2023 ULTRA-SENSITIVE AND RAPID DETECTION OF NUCLEIC ACIDS AND MICROORGANISMS IN BODY FLUIDS USING SINGLE-MOLECULE

TETHERING Article Open access 22 September 2020 PROGRAMMING BACTERIA FOR MULTIPLEXED DNA DETECTION Article Open access 10 April 2023 REFERENCES * Han, M., Gao, X.H., Su, J.Z. & Nie, S.

Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules. _Nat. Biotechnol._ 19, 631–635 (2001). Article  CAS  Google Scholar  * Fulton, R.J., McDade, R.L., Smith, P.L.,

Kienker, L.J. & Kettman, J.R. Advanced multiplexed analysis with the FlowMetrix(TM) system. _Clin. Chem._ 43, 1749–1756 (1997). Article  CAS  Google Scholar  * Steemers, F.J., Ferguson,

J.A. & Walt, D.R. Screening unlabeled DNA targets with randomly ordered fiber-optic gene arrays. _Nat. Biotechnol._ 18, 91–94 (2000). Article  CAS  Google Scholar  * Braeckmans, K., De

Smedt, S.C., Leblans, M., Pauwels, R. & Demeester, J. Encoding microcarriers: Present and future technologies. _Nat. Rev. Drug Discov._ 1, 447–456 (2002). Article  CAS  Google Scholar  *

Duggan, D., Bittner, M., Chen, Y., Meltzer, P. & Trent, J. Expression profiling using cDNA microarrays. _Nat. Genet._ 21, 10–14 (1999). Article  CAS  Google Scholar  * DeRisi, J. et al.

Use of a cDNA microarray to analyse gene expression patterns in human cancer. _Nat. Genet._ 14, 457–460 (1996). Article  CAS  Google Scholar  * Schena, M., Shalon, D., Davis, R. &

Brown, P. Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray. _Science_ 270, 467–470 (1995). Article  CAS  Google Scholar  * Cheung, V.G. et al. Making

and reading microarrays. _Nat. Genet._ 21, 15–19 (1999). Article  CAS  Google Scholar  * Cunin, F. et al. Biomolecular screening with encoded porous-silicon photonic crystals. _Nat. Mater._

1, 39–41 (2002). Article  CAS  Google Scholar  * Wang, J., Liu, G.D. & Rivas, G. Encoded beads for electrochemical identification. _Anal. Chem._ 75, 4667–4671 (2003). Article  CAS 

Google Scholar  * Chan, W.C. et al. Luminescent quantum dots for multiplexed biological detection and imaging. _Curr. Opin. Biotechnol._ 13, 40–46 (2002). Article  CAS  Google Scholar  *

Nicewarner-Pena, S.R. et al. Submicrometer metallic barcodes. _Science_ 294, 137–141 (2001). Article  CAS  Google Scholar  * Nam, J.M., Thaxton, C.S. & Mirkin, C.A. Nanoparticle-based

bio-bar codes for the ultrasensitive detection of proteins. _Science_ 301, 1884–1886 (2003). Article  CAS  Google Scholar  * Li, Y. et al. Controlled assembly of dendrimer-like DNA. _Nat.

Mater._ 3, 38–42 (2004). Article  CAS  Google Scholar  * Luo, D. The road from biology to materials. _Mater. Today_ 6, 38–43 (2003). Article  CAS  Google Scholar  * Ried, T., Baldini, A.,

Rand, T.C. & Ward, D.C. Simultaneous visualization of 7 different DNA probes by _in situ_ hybridization using combinatorial fluorescence and digital imaging microscopy. _Proc. Natl.

Acad. Sci. USA_ 89, 1388–1392 (1992). Article  CAS  Google Scholar  * Taton, T., Mirkin, C. & Letsinger, R. Scanometric DNA array detection with nanoparticle probes. _Science_ 289,

1757–1760 (2000). Article  CAS  Google Scholar  * Sjostedt, A., Eriksson, U., Berglund, L. & Tarnvik, A. Detection of _Francisella tularensis_ in ulcers of patients with tularemia by

PCR. _J. Clin. Microbiol._ 35, 1045–1048 (1997). Article  CAS  Google Scholar  * Sanchez, A. et al. Detection and molecular characterization of Ebola viruses causing disease in human and

nonhuman primates. _J. Infect. Dis._ 179, S164–S169 (1999). Article  CAS  Google Scholar  * Poon, L.L. et al. Detection of SARS coronavirus in patients with severe acute respiratory syndrome

by conventional and real-time quantitative reverse transcription-PCR assays. _Clin. Chem._ 50, 67–72 (2004). Article  CAS  Google Scholar  * Fuja, T., Hou, S. & Bryant, P. A multiplex

microsphere bead assay for comparative RNA expression analysis using flow cytometry. _J. Biotechnol._ 108, 193–205 (2004). Article  CAS  Google Scholar  * Vignali, D.A. Multiplexed

particle-based flow cytometric assays. _J. Immunol. Methods_ 243, 243–255 (2000). Article  CAS  Google Scholar  * Wang, J. et al. Adsorption and detection of DNA dendrimers at carbon

electrodes. _Electroanal._ 10, 553–556 (1998). Article  CAS  Google Scholar  * Wang, J., Jiang, M., Nilsen, T. & Getts, R. Dendritic nucleic acid probes for DNA biosensors. _J. Am. Chem.

Soc._ 120, 8281–8282 (1998). Article  CAS  Google Scholar  * Nilsen, T., Grayzel, J. & Prensky, W. Dendritic nucleic acid structures. _J. Theor. Biol._ 187, 273–284 (1997). Article  CAS

  Google Scholar  * Capaldi, S., Getts, R.C. & Jayasena, S.D. Signal amplification through nucleotide extension and excision on a dendritic DNA platform. _Nucleic Acids Res._ 28, e21

(2000). Article  CAS  Google Scholar  * Lowe, M., Spiro, A., Zhang, Y. & Getts, R. Multiplexed, particle-based detection of DNA using flow cytometry with 3DNA dendrimers for signal

amplification. _Cytom_ Part A 60A, 135–144 (2004). Article  CAS  Google Scholar  * Shchepinov, M., Mir, K., Elder, J., Frank-Kamenetskii, M. & Southern, E. Oligonucleotide dendrimers:

stable nano-structures. _Nucleic Acids Res._ 27, 3035–3041 (1999). Article  CAS  Google Scholar  * Shchepinov, M., Udalova, I., Bridgman, A. & Southern, E. Oligonucleotide dendrimers:

synthesis and use as polylabelled DNA probes. _Nucleic Acids Res._ 25, 4447–4454 (1997). Article  CAS  Google Scholar  Download references ACKNOWLEDGEMENTS We wish to acknowledge the Cornell

Center for Advanced Technology and the Cornell Center for Vertebrate Genomics for financial support. This material is based upon work supported in part by the Science and Technology Center

Program of the National Science Foundation under agreement no. ECS-9876771. We thank Yung-Fu Chang for providing pathogen genomic DNA (_Mycobacterium avium_ subsp. _paratuberculosis_) and

Carol Bayles for technical support on microscopy. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Department of Biological and Environmental Engineering, Cornell University, Ithaca,

14853-5701, New York, USA Yougen Li, Yen Thi Hong Cu & Dan Luo Authors * Yougen Li View author publications You can also search for this author inPubMed Google Scholar * Yen Thi Hong Cu

View author publications You can also search for this author inPubMed Google Scholar * Dan Luo View author publications You can also search for this author inPubMed Google Scholar

CORRESPONDING AUTHOR Correspondence to Dan Luo. ETHICS DECLARATIONS COMPETING INTERESTS A patent for similar technology is being filed, the value of which may be increased by this

publication. SUPPLEMENTARY INFORMATION SUPPLEMENTARY FIG. 1 Evaluation of nanobarcodes with agarose gel electrophoresis. (PDF 745 kb) SUPPLEMENTARY FIG. 2 Schematic drawing of nanobarcode

denaturation (without showing fluorescence dyes). (PDF 96 kb) SUPPLEMENTARY FIG. 3 DNA nanobarcode quantitative decoding based on microbead populations. (PDF 42 kb) SUPPLEMENTARY FIG. 4

Statistics multiplexed DNA detection using flow cytometry. (PDF 55 kb) SUPPLEMENTARY TABLE 1 Building oligonucleotides (PDF 47 kb) SUPPLEMENTARY TABLE 2 Capture probes, report probes and

target DNA (PDF 47 kb) SUPPLEMENTARY TABLE 3 Y-DNA building blocks (PDF 43 kb) SUPPLEMENTARY TABLE 4 DNA nanobarcodes (PDF 40 kb) SUPPLEMENTARY TABLE 5 Code library (PDF 45 kb) SUPPLEMENTARY

NOTE 1 (PDF 66 KB) SUPPLEMENTARY NOTE 2 (PDF 42 KB) RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Li, Y., Cu, Y. & Luo, D. Multiplexed detection

of pathogen DNA with DNA-based fluorescence nanobarcodes. _Nat Biotechnol_ 23, 885–889 (2005). https://doi.org/10.1038/nbt1106 Download citation * Received: 22 February 2005 * Accepted: 05

May 2005 * Published: 01 July 2005 * Issue Date: 01 July 2005 * DOI: https://doi.org/10.1038/nbt1106 SHARE THIS ARTICLE Anyone you share the following link with will be able to read this

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