Abstract

A biomolecule-to-fluorescent-color (B/F) encoder for optical readout of biomolecular information is proposed. In the B/F encoder, a set of fluorescence wavelengths and their intensity levels are used for coding of a biomolecular signal. A hybridization chain reaction of hairpin DNAs labeled with fluorescent reporters was performed to generate the fluorescence color codes. The fluorescence is modulated via fluorescence resonance energy transfer, which is controlled by DNA structural changes. The results demonstrate that fluorescent color codes can be configured based on two wavelengths and five intensities using the B/F encoder, and the assigned codes can be retrieved via fluorescence measurements.

© 2014 Optical Society of America

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  1. M. Schena, D. Shalon, R. W. Davis, and P. O. Brownt, “Quantitative monitoring of gene expression patterns with a complementary DNA microarray,” Science270, 467–470 (1995).
    [CrossRef] [PubMed]
  2. M. Han, X. Gao, J. Z. Su, and S. Nie, “Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules,” Nat. Biotechnol.19, 631–635 (2001).
    [CrossRef] [PubMed]
  3. C. Lin, Y. Liu, and H. Yan, “Self-Assembled Combinatorial Encoding Nanoarrays for Multiplexed Biosensing,” Nano Lett.7, 507–512 (2007).
    [CrossRef] [PubMed]
  4. Y. Li, Y. T. H. Cu, and D. Luo, “Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobar-codes,” Nat. Biotechnol.23, 885–889 (2005).
    [CrossRef] [PubMed]
  5. C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem.4, 832–839 (2012).
    [CrossRef]
  6. Y. N. Teo and E. T. Kool, “DNA-Multichromophore Systems,” Chem. Rev.1124221–4245 (2012).
    [CrossRef] [PubMed]
  7. K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Med- ley, Z. Cao, J. Li, P. Colon, H. Lin, and W. Tan, “Molecular engineering of DNA: molecular beacons,” Angew. Chem., Int. Ed.48, 856–870 (2009).
    [CrossRef]
  8. T. Nishimura, Y. Ogura, and J. Tanida, “Fluorescence resonance energy transfer-based molecular logic circuit using a DNA scaffold,” Appl. Phys. Lett101, 233703 (2012).
    [CrossRef]
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    [CrossRef] [PubMed]
  10. J. Huang, Y. Wu, Y. Chen, Z. Zhu, X. Yang, C. J. Yang, K. Wang, and W. Tan, “Pyrene-excimer probes based on the hybridization chain reaction for the detection of nucleic acids in complex biological fluids,” Angew. Chem., Int. Ed.50401–404 (2011).
    [CrossRef]
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    [CrossRef] [PubMed]
  12. W. Tang, D. Wang, Y. Xu, N. Li, and F. Liu, “A self-assembled DNA nanostructure-amplified quartz crystal microbalance with dissipation biosensing platform for nucleic acids,” Chem. commun.486678–6680 (2012).
    [CrossRef]
  13. D. A. Chemeris, Y. M. Nikonorov, and V. A. Vakhitov, “Real-time hybridization chain reaction,” Doklady Biochemistry and Biophysics419, 53–55 (2008).
    [CrossRef] [PubMed]
  14. H. M. T. Choi, J. Y. Chang, L. Trinh, J. E. Padilla, S. E. Fraser, and N. A. Pierce, “Programmable in situ amplification for multiplexed imaging of mRNA expression,” Nature biotechnol.28, 1208–1212 (2010).
    [CrossRef]
  15. D. Y. Zhang and G. Seelig, “Dynamic DNA nanotechnology using strand-displacement reactions,” Nat. Chem.3, 103–113 (2011).
    [CrossRef] [PubMed]
  16. R. Roy, S. Hohng, and T. Ha, “A practical guide to single-molecule FRET,” Nature Methods5, 507–516 (2008).
    [CrossRef] [PubMed]
  17. T. Nishimura, Y. Ogura, K. Yamamda, Y. Ohno, and J. Tanida, “Amplification and encoding of biomolecular signals with designed reactions of DNA,” Proceeding of Biomedical Engineering International Conference 2013, D1R3AE (2013).

2012 (5)

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem.4, 832–839 (2012).
[CrossRef]

Y. N. Teo and E. T. Kool, “DNA-Multichromophore Systems,” Chem. Rev.1124221–4245 (2012).
[CrossRef] [PubMed]

T. Nishimura, Y. Ogura, and J. Tanida, “Fluorescence resonance energy transfer-based molecular logic circuit using a DNA scaffold,” Appl. Phys. Lett101, 233703 (2012).
[CrossRef]

Y. Jiang, B. Li, X. Chen, and A. D. Ellington, “Coupling two different nucleic acid circuits in an enzyme-free amplifier,” Molecules1713211–13220 (2012).
[CrossRef] [PubMed]

W. Tang, D. Wang, Y. Xu, N. Li, and F. Liu, “A self-assembled DNA nanostructure-amplified quartz crystal microbalance with dissipation biosensing platform for nucleic acids,” Chem. commun.486678–6680 (2012).
[CrossRef]

2011 (2)

J. Huang, Y. Wu, Y. Chen, Z. Zhu, X. Yang, C. J. Yang, K. Wang, and W. Tan, “Pyrene-excimer probes based on the hybridization chain reaction for the detection of nucleic acids in complex biological fluids,” Angew. Chem., Int. Ed.50401–404 (2011).
[CrossRef]

D. Y. Zhang and G. Seelig, “Dynamic DNA nanotechnology using strand-displacement reactions,” Nat. Chem.3, 103–113 (2011).
[CrossRef] [PubMed]

2010 (1)

H. M. T. Choi, J. Y. Chang, L. Trinh, J. E. Padilla, S. E. Fraser, and N. A. Pierce, “Programmable in situ amplification for multiplexed imaging of mRNA expression,” Nature biotechnol.28, 1208–1212 (2010).
[CrossRef]

2009 (1)

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Med- ley, Z. Cao, J. Li, P. Colon, H. Lin, and W. Tan, “Molecular engineering of DNA: molecular beacons,” Angew. Chem., Int. Ed.48, 856–870 (2009).
[CrossRef]

2008 (2)

D. A. Chemeris, Y. M. Nikonorov, and V. A. Vakhitov, “Real-time hybridization chain reaction,” Doklady Biochemistry and Biophysics419, 53–55 (2008).
[CrossRef] [PubMed]

R. Roy, S. Hohng, and T. Ha, “A practical guide to single-molecule FRET,” Nature Methods5, 507–516 (2008).
[CrossRef] [PubMed]

2007 (1)

C. Lin, Y. Liu, and H. Yan, “Self-Assembled Combinatorial Encoding Nanoarrays for Multiplexed Biosensing,” Nano Lett.7, 507–512 (2007).
[CrossRef] [PubMed]

2005 (1)

Y. Li, Y. T. H. Cu, and D. Luo, “Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobar-codes,” Nat. Biotechnol.23, 885–889 (2005).
[CrossRef] [PubMed]

2004 (1)

R. M. Dirks and N. A. Pierce, “Triggered amplification by hybridization chain reaction, Proc. Natl. Acad. Sci. USA101, 15275–15278 (2004).
[CrossRef] [PubMed]

2001 (1)

M. Han, X. Gao, J. Z. Su, and S. Nie, “Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules,” Nat. Biotechnol.19, 631–635 (2001).
[CrossRef] [PubMed]

1995 (1)

M. Schena, D. Shalon, R. W. Davis, and P. O. Brownt, “Quantitative monitoring of gene expression patterns with a complementary DNA microarray,” Science270, 467–470 (1995).
[CrossRef] [PubMed]

Brownt, P. O.

M. Schena, D. Shalon, R. W. Davis, and P. O. Brownt, “Quantitative monitoring of gene expression patterns with a complementary DNA microarray,” Science270, 467–470 (1995).
[CrossRef] [PubMed]

Cao, Z.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Med- ley, Z. Cao, J. Li, P. Colon, H. Lin, and W. Tan, “Molecular engineering of DNA: molecular beacons,” Angew. Chem., Int. Ed.48, 856–870 (2009).
[CrossRef]

Chang, J. Y.

H. M. T. Choi, J. Y. Chang, L. Trinh, J. E. Padilla, S. E. Fraser, and N. A. Pierce, “Programmable in situ amplification for multiplexed imaging of mRNA expression,” Nature biotechnol.28, 1208–1212 (2010).
[CrossRef]

Chemeris, D. A.

D. A. Chemeris, Y. M. Nikonorov, and V. A. Vakhitov, “Real-time hybridization chain reaction,” Doklady Biochemistry and Biophysics419, 53–55 (2008).
[CrossRef] [PubMed]

Chen, X.

Y. Jiang, B. Li, X. Chen, and A. D. Ellington, “Coupling two different nucleic acid circuits in an enzyme-free amplifier,” Molecules1713211–13220 (2012).
[CrossRef] [PubMed]

Chen, Y.

J. Huang, Y. Wu, Y. Chen, Z. Zhu, X. Yang, C. J. Yang, K. Wang, and W. Tan, “Pyrene-excimer probes based on the hybridization chain reaction for the detection of nucleic acids in complex biological fluids,” Angew. Chem., Int. Ed.50401–404 (2011).
[CrossRef]

Choi, H. M. T.

H. M. T. Choi, J. Y. Chang, L. Trinh, J. E. Padilla, S. E. Fraser, and N. A. Pierce, “Programmable in situ amplification for multiplexed imaging of mRNA expression,” Nature biotechnol.28, 1208–1212 (2010).
[CrossRef]

Church, G. M.

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem.4, 832–839 (2012).
[CrossRef]

Colon, P.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Med- ley, Z. Cao, J. Li, P. Colon, H. Lin, and W. Tan, “Molecular engineering of DNA: molecular beacons,” Angew. Chem., Int. Ed.48, 856–870 (2009).
[CrossRef]

Cu, Y. T. H.

Y. Li, Y. T. H. Cu, and D. Luo, “Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobar-codes,” Nat. Biotechnol.23, 885–889 (2005).
[CrossRef] [PubMed]

Davis, R. W.

M. Schena, D. Shalon, R. W. Davis, and P. O. Brownt, “Quantitative monitoring of gene expression patterns with a complementary DNA microarray,” Science270, 467–470 (1995).
[CrossRef] [PubMed]

Dirks, R. M.

R. M. Dirks and N. A. Pierce, “Triggered amplification by hybridization chain reaction, Proc. Natl. Acad. Sci. USA101, 15275–15278 (2004).
[CrossRef] [PubMed]

Ellington, A. D.

Y. Jiang, B. Li, X. Chen, and A. D. Ellington, “Coupling two different nucleic acid circuits in an enzyme-free amplifier,” Molecules1713211–13220 (2012).
[CrossRef] [PubMed]

Fang, X.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Med- ley, Z. Cao, J. Li, P. Colon, H. Lin, and W. Tan, “Molecular engineering of DNA: molecular beacons,” Angew. Chem., Int. Ed.48, 856–870 (2009).
[CrossRef]

Fraser, S. E.

H. M. T. Choi, J. Y. Chang, L. Trinh, J. E. Padilla, S. E. Fraser, and N. A. Pierce, “Programmable in situ amplification for multiplexed imaging of mRNA expression,” Nature biotechnol.28, 1208–1212 (2010).
[CrossRef]

Gao, X.

M. Han, X. Gao, J. Z. Su, and S. Nie, “Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules,” Nat. Biotechnol.19, 631–635 (2001).
[CrossRef] [PubMed]

Ha, T.

R. Roy, S. Hohng, and T. Ha, “A practical guide to single-molecule FRET,” Nature Methods5, 507–516 (2008).
[CrossRef] [PubMed]

Han, M.

M. Han, X. Gao, J. Z. Su, and S. Nie, “Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules,” Nat. Biotechnol.19, 631–635 (2001).
[CrossRef] [PubMed]

Hohng, S.

R. Roy, S. Hohng, and T. Ha, “A practical guide to single-molecule FRET,” Nature Methods5, 507–516 (2008).
[CrossRef] [PubMed]

Huang, J.

J. Huang, Y. Wu, Y. Chen, Z. Zhu, X. Yang, C. J. Yang, K. Wang, and W. Tan, “Pyrene-excimer probes based on the hybridization chain reaction for the detection of nucleic acids in complex biological fluids,” Angew. Chem., Int. Ed.50401–404 (2011).
[CrossRef]

Jiang, Y.

Y. Jiang, B. Li, X. Chen, and A. D. Ellington, “Coupling two different nucleic acid circuits in an enzyme-free amplifier,” Molecules1713211–13220 (2012).
[CrossRef] [PubMed]

Jungmann, R.

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem.4, 832–839 (2012).
[CrossRef]

Kim, Y.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Med- ley, Z. Cao, J. Li, P. Colon, H. Lin, and W. Tan, “Molecular engineering of DNA: molecular beacons,” Angew. Chem., Int. Ed.48, 856–870 (2009).
[CrossRef]

Kool, E. T.

Y. N. Teo and E. T. Kool, “DNA-Multichromophore Systems,” Chem. Rev.1124221–4245 (2012).
[CrossRef] [PubMed]

Leifer, A. M.

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem.4, 832–839 (2012).
[CrossRef]

Levner, D.

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem.4, 832–839 (2012).
[CrossRef]

Li, B.

Y. Jiang, B. Li, X. Chen, and A. D. Ellington, “Coupling two different nucleic acid circuits in an enzyme-free amplifier,” Molecules1713211–13220 (2012).
[CrossRef] [PubMed]

Li, C.

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem.4, 832–839 (2012).
[CrossRef]

Li, J.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Med- ley, Z. Cao, J. Li, P. Colon, H. Lin, and W. Tan, “Molecular engineering of DNA: molecular beacons,” Angew. Chem., Int. Ed.48, 856–870 (2009).
[CrossRef]

Li, N.

W. Tang, D. Wang, Y. Xu, N. Li, and F. Liu, “A self-assembled DNA nanostructure-amplified quartz crystal microbalance with dissipation biosensing platform for nucleic acids,” Chem. commun.486678–6680 (2012).
[CrossRef]

Li, W.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Med- ley, Z. Cao, J. Li, P. Colon, H. Lin, and W. Tan, “Molecular engineering of DNA: molecular beacons,” Angew. Chem., Int. Ed.48, 856–870 (2009).
[CrossRef]

Li, Y.

Y. Li, Y. T. H. Cu, and D. Luo, “Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobar-codes,” Nat. Biotechnol.23, 885–889 (2005).
[CrossRef] [PubMed]

Lin, C.

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem.4, 832–839 (2012).
[CrossRef]

C. Lin, Y. Liu, and H. Yan, “Self-Assembled Combinatorial Encoding Nanoarrays for Multiplexed Biosensing,” Nano Lett.7, 507–512 (2007).
[CrossRef] [PubMed]

Lin, H.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Med- ley, Z. Cao, J. Li, P. Colon, H. Lin, and W. Tan, “Molecular engineering of DNA: molecular beacons,” Angew. Chem., Int. Ed.48, 856–870 (2009).
[CrossRef]

Liu, F.

W. Tang, D. Wang, Y. Xu, N. Li, and F. Liu, “A self-assembled DNA nanostructure-amplified quartz crystal microbalance with dissipation biosensing platform for nucleic acids,” Chem. commun.486678–6680 (2012).
[CrossRef]

Liu, Y.

C. Lin, Y. Liu, and H. Yan, “Self-Assembled Combinatorial Encoding Nanoarrays for Multiplexed Biosensing,” Nano Lett.7, 507–512 (2007).
[CrossRef] [PubMed]

Luo, D.

Y. Li, Y. T. H. Cu, and D. Luo, “Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobar-codes,” Nat. Biotechnol.23, 885–889 (2005).
[CrossRef] [PubMed]

Med- ley, C. D.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Med- ley, Z. Cao, J. Li, P. Colon, H. Lin, and W. Tan, “Molecular engineering of DNA: molecular beacons,” Angew. Chem., Int. Ed.48, 856–870 (2009).
[CrossRef]

Nie, S.

M. Han, X. Gao, J. Z. Su, and S. Nie, “Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules,” Nat. Biotechnol.19, 631–635 (2001).
[CrossRef] [PubMed]

Nikonorov, Y. M.

D. A. Chemeris, Y. M. Nikonorov, and V. A. Vakhitov, “Real-time hybridization chain reaction,” Doklady Biochemistry and Biophysics419, 53–55 (2008).
[CrossRef] [PubMed]

Nishimura, T.

T. Nishimura, Y. Ogura, and J. Tanida, “Fluorescence resonance energy transfer-based molecular logic circuit using a DNA scaffold,” Appl. Phys. Lett101, 233703 (2012).
[CrossRef]

T. Nishimura, Y. Ogura, K. Yamamda, Y. Ohno, and J. Tanida, “Amplification and encoding of biomolecular signals with designed reactions of DNA,” Proceeding of Biomedical Engineering International Conference 2013, D1R3AE (2013).

Ogura, Y.

T. Nishimura, Y. Ogura, and J. Tanida, “Fluorescence resonance energy transfer-based molecular logic circuit using a DNA scaffold,” Appl. Phys. Lett101, 233703 (2012).
[CrossRef]

T. Nishimura, Y. Ogura, K. Yamamda, Y. Ohno, and J. Tanida, “Amplification and encoding of biomolecular signals with designed reactions of DNA,” Proceeding of Biomedical Engineering International Conference 2013, D1R3AE (2013).

Ohno, Y.

T. Nishimura, Y. Ogura, K. Yamamda, Y. Ohno, and J. Tanida, “Amplification and encoding of biomolecular signals with designed reactions of DNA,” Proceeding of Biomedical Engineering International Conference 2013, D1R3AE (2013).

Padilla, J. E.

H. M. T. Choi, J. Y. Chang, L. Trinh, J. E. Padilla, S. E. Fraser, and N. A. Pierce, “Programmable in situ amplification for multiplexed imaging of mRNA expression,” Nature biotechnol.28, 1208–1212 (2010).
[CrossRef]

Pierce, N. A.

H. M. T. Choi, J. Y. Chang, L. Trinh, J. E. Padilla, S. E. Fraser, and N. A. Pierce, “Programmable in situ amplification for multiplexed imaging of mRNA expression,” Nature biotechnol.28, 1208–1212 (2010).
[CrossRef]

R. M. Dirks and N. A. Pierce, “Triggered amplification by hybridization chain reaction, Proc. Natl. Acad. Sci. USA101, 15275–15278 (2004).
[CrossRef] [PubMed]

Roy, R.

R. Roy, S. Hohng, and T. Ha, “A practical guide to single-molecule FRET,” Nature Methods5, 507–516 (2008).
[CrossRef] [PubMed]

Schena, M.

M. Schena, D. Shalon, R. W. Davis, and P. O. Brownt, “Quantitative monitoring of gene expression patterns with a complementary DNA microarray,” Science270, 467–470 (1995).
[CrossRef] [PubMed]

Seelig, G.

D. Y. Zhang and G. Seelig, “Dynamic DNA nanotechnology using strand-displacement reactions,” Nat. Chem.3, 103–113 (2011).
[CrossRef] [PubMed]

Shalon, D.

M. Schena, D. Shalon, R. W. Davis, and P. O. Brownt, “Quantitative monitoring of gene expression patterns with a complementary DNA microarray,” Science270, 467–470 (1995).
[CrossRef] [PubMed]

Shih, W. M.

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem.4, 832–839 (2012).
[CrossRef]

Su, J. Z.

M. Han, X. Gao, J. Z. Su, and S. Nie, “Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules,” Nat. Biotechnol.19, 631–635 (2001).
[CrossRef] [PubMed]

Tan, W.

J. Huang, Y. Wu, Y. Chen, Z. Zhu, X. Yang, C. J. Yang, K. Wang, and W. Tan, “Pyrene-excimer probes based on the hybridization chain reaction for the detection of nucleic acids in complex biological fluids,” Angew. Chem., Int. Ed.50401–404 (2011).
[CrossRef]

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Med- ley, Z. Cao, J. Li, P. Colon, H. Lin, and W. Tan, “Molecular engineering of DNA: molecular beacons,” Angew. Chem., Int. Ed.48, 856–870 (2009).
[CrossRef]

Tang, W.

W. Tang, D. Wang, Y. Xu, N. Li, and F. Liu, “A self-assembled DNA nanostructure-amplified quartz crystal microbalance with dissipation biosensing platform for nucleic acids,” Chem. commun.486678–6680 (2012).
[CrossRef]

Tang, Z.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Med- ley, Z. Cao, J. Li, P. Colon, H. Lin, and W. Tan, “Molecular engineering of DNA: molecular beacons,” Angew. Chem., Int. Ed.48, 856–870 (2009).
[CrossRef]

Tanida, J.

T. Nishimura, Y. Ogura, and J. Tanida, “Fluorescence resonance energy transfer-based molecular logic circuit using a DNA scaffold,” Appl. Phys. Lett101, 233703 (2012).
[CrossRef]

T. Nishimura, Y. Ogura, K. Yamamda, Y. Ohno, and J. Tanida, “Amplification and encoding of biomolecular signals with designed reactions of DNA,” Proceeding of Biomedical Engineering International Conference 2013, D1R3AE (2013).

Teo, Y. N.

Y. N. Teo and E. T. Kool, “DNA-Multichromophore Systems,” Chem. Rev.1124221–4245 (2012).
[CrossRef] [PubMed]

Trinh, L.

H. M. T. Choi, J. Y. Chang, L. Trinh, J. E. Padilla, S. E. Fraser, and N. A. Pierce, “Programmable in situ amplification for multiplexed imaging of mRNA expression,” Nature biotechnol.28, 1208–1212 (2010).
[CrossRef]

Vakhitov, V. A.

D. A. Chemeris, Y. M. Nikonorov, and V. A. Vakhitov, “Real-time hybridization chain reaction,” Doklady Biochemistry and Biophysics419, 53–55 (2008).
[CrossRef] [PubMed]

Wang, D.

W. Tang, D. Wang, Y. Xu, N. Li, and F. Liu, “A self-assembled DNA nanostructure-amplified quartz crystal microbalance with dissipation biosensing platform for nucleic acids,” Chem. commun.486678–6680 (2012).
[CrossRef]

Wang, K.

J. Huang, Y. Wu, Y. Chen, Z. Zhu, X. Yang, C. J. Yang, K. Wang, and W. Tan, “Pyrene-excimer probes based on the hybridization chain reaction for the detection of nucleic acids in complex biological fluids,” Angew. Chem., Int. Ed.50401–404 (2011).
[CrossRef]

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Med- ley, Z. Cao, J. Li, P. Colon, H. Lin, and W. Tan, “Molecular engineering of DNA: molecular beacons,” Angew. Chem., Int. Ed.48, 856–870 (2009).
[CrossRef]

Wu, Y.

J. Huang, Y. Wu, Y. Chen, Z. Zhu, X. Yang, C. J. Yang, K. Wang, and W. Tan, “Pyrene-excimer probes based on the hybridization chain reaction for the detection of nucleic acids in complex biological fluids,” Angew. Chem., Int. Ed.50401–404 (2011).
[CrossRef]

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Med- ley, Z. Cao, J. Li, P. Colon, H. Lin, and W. Tan, “Molecular engineering of DNA: molecular beacons,” Angew. Chem., Int. Ed.48, 856–870 (2009).
[CrossRef]

Xu, Y.

W. Tang, D. Wang, Y. Xu, N. Li, and F. Liu, “A self-assembled DNA nanostructure-amplified quartz crystal microbalance with dissipation biosensing platform for nucleic acids,” Chem. commun.486678–6680 (2012).
[CrossRef]

Yamamda, K.

T. Nishimura, Y. Ogura, K. Yamamda, Y. Ohno, and J. Tanida, “Amplification and encoding of biomolecular signals with designed reactions of DNA,” Proceeding of Biomedical Engineering International Conference 2013, D1R3AE (2013).

Yan, H.

C. Lin, Y. Liu, and H. Yan, “Self-Assembled Combinatorial Encoding Nanoarrays for Multiplexed Biosensing,” Nano Lett.7, 507–512 (2007).
[CrossRef] [PubMed]

Yang, C. J.

J. Huang, Y. Wu, Y. Chen, Z. Zhu, X. Yang, C. J. Yang, K. Wang, and W. Tan, “Pyrene-excimer probes based on the hybridization chain reaction for the detection of nucleic acids in complex biological fluids,” Angew. Chem., Int. Ed.50401–404 (2011).
[CrossRef]

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Figures (5)

Fig. 1
Fig. 1

Schematic illustrations of (a) a biomolecule-to-fluorescent-color (B/F) encoder, and (b) a multiple B/F encoder system.

Fig. 2
Fig. 2

Schematic illustrations of (a) amplification and (b) modulation of fluorescence in a B/F encoder. (c) Sequences and modifications of the DNA strands used in this study.

Fig. 3
Fig. 3

(a) Normalized fluorescence spectra of TMR in HCR for RTMR values of 0.2, 0.4, 0.6, 0.8, and 1. (b) RTMR vs. the normalized 580 nm fluorescence intensity.

Fig. 4
Fig. 4

Fluorescence images of the 25 samples listed in Table 1.

Fig. 5
Fig. 5

Fluorescence spectra for each sample: (a) FAM (470 nm excitation) and (b) TMR (550 nm excitation). (c) Normalized peak emission intensities. (d) Concentration ratios vs. peak intensities.

Tables (1)

Tables Icon

Table 1 Concentration ratios for 25 samples.

Equations (2)

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R x = [ H 1 x ] [ H 1 all ] ,
N = m n 1 .

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