Abstract

We propose a photoactivatable and resettable molecular sensor using DNA probes. The functionality is achieved by reversible change of DNA structure induced via photonic signals. Based on the mechanism, the sensor can detect target molecules at a desired instant and can be returned to its initial state after detection. The experimental results demonstrate that the concentrations of the target molecules are detected correctly and repeatedly according to the light signal.

© 2012 OSA

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  1. K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, 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]
  2. D. P. Bratu, B. J. Cha, M. M. Mhlanga, F. R. Kramer, and S. Tyagi, “Visualizing the distribution and transport of mRNAs in living cells,” Proc. Natl. Acad. Sci.100, 13308–13313 (2003).
    [CrossRef] [PubMed]
  3. H. Asanuma, X. Liang, H. Nishioka, D. Matsunaga, M. Liu, and M. Komiyama, “Synthesis of azobenzene-tethered DNA for reversible photo-regulation of DNA functions: hybridization and transcription,” Nat. Protocols2, 203–212 (2007).
    [CrossRef]
  4. H. Asanuma, T. Ito, T. Yoshida, X. Liang, and M. Komiyama, “Photo-regulation of the formation and dissociation of DNA-duplex by using the cis-trans isomerization of azobenzene,” Angew. Chem. Int. Ed.38, 2393–2395 (1999).
    [CrossRef]
  5. S. Ogasawara and M. Maeda, “Straightforward and reversible photoregulation of hybridization by using a photochromic nucleoside,” Angew. Chem. Int. Ed.47, 8839–8842 (2008).
    [CrossRef]
  6. L. Poon, W. Zandberg, D. Hsiao, Z. Erno, D. Sen, B. D. Gates, and N. R. Branda, “Photothermal release of single-stranded DNA from the surface of gold nanoparticles through controlled denaturating and Au–S bond breaking,” ACS Nano4, 6395–6403 (2010).
    [CrossRef] [PubMed]
  7. X. Liang, H. Nishioka, N. Takenaka, and H. Asanuma, “A DNA nanomachine powered by light irradiation,” ChemBioChem9, 702–705 (2008).
    [CrossRef] [PubMed]
  8. Y. Ogura, T. Nishimura, and J. Tanida, “Self-contained photonically-controlled DNA tweezers,” Appl. Phys. Express2, 025004 (2009).
    [CrossRef]
  9. H. Kang, H. Liu, J. A. Phillips, Z. Cao, Y. Kim, Y. Chen, Z. Yang, J. Li, and W. Tan, “Single-DNA molecule nanomotor regulated by photons,” Nano Lett.9, 2690–2696 (2009).
    [CrossRef] [PubMed]
  10. X. Liang, T. Mochizuki, and H. Asanuma, “A supra-photoswitch involving sandwiched DNA base pairs and azobenzenes for light-driven nanostructures and nanodevices,” Small5, 1761–1768 (2009).
    [CrossRef] [PubMed]
  11. L. Wu, K. Koumoto, and N. Sugimoto, “Reversible stability switching of a hairpin DNA via a photo-responsive linker unit,” Chem. Commun.47, 1915–1917 (2009).
    [CrossRef]
  12. Y. Kim, J. A. Phillipsa, H. Liua, H. Kanga, and W. Tan, “Using photons to manipulate enzyme inhibition by an azobenzene-modified nucleic acid probe,” Proc. Natl. Acad. Sci.106, 6489–6494 (2009).
    [CrossRef] [PubMed]
  13. M. Zhou, X. Liang, T. Mochizuki, and H. Asanuma, “A light-driven DNA nanomachine for the efficient photo-switching of RNA digestion,” Angew. Chem. Int. Ed.49, 2167–2170 (2010).
    [CrossRef]
  14. C. Wang, Z. Zhu, Y. Song, H. Lin, C. J. Yang, and W. Tan, “Caged molecular beacons: controlling nucleic acid hybridization with light,” Chem. Commun.47, 5708–5710 (2011).
    [CrossRef]
  15. T. Nishimura, Y. Ogura, and J. Tanida, “A photonic DNA processor: concept and implementation,” Proc. SPIE8102, 810207 (2011).
    [CrossRef]

2011

C. Wang, Z. Zhu, Y. Song, H. Lin, C. J. Yang, and W. Tan, “Caged molecular beacons: controlling nucleic acid hybridization with light,” Chem. Commun.47, 5708–5710 (2011).
[CrossRef]

T. Nishimura, Y. Ogura, and J. Tanida, “A photonic DNA processor: concept and implementation,” Proc. SPIE8102, 810207 (2011).
[CrossRef]

2010

L. Poon, W. Zandberg, D. Hsiao, Z. Erno, D. Sen, B. D. Gates, and N. R. Branda, “Photothermal release of single-stranded DNA from the surface of gold nanoparticles through controlled denaturating and Au–S bond breaking,” ACS Nano4, 6395–6403 (2010).
[CrossRef] [PubMed]

M. Zhou, X. Liang, T. Mochizuki, and H. Asanuma, “A light-driven DNA nanomachine for the efficient photo-switching of RNA digestion,” Angew. Chem. Int. Ed.49, 2167–2170 (2010).
[CrossRef]

2009

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, 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]

Y. Ogura, T. Nishimura, and J. Tanida, “Self-contained photonically-controlled DNA tweezers,” Appl. Phys. Express2, 025004 (2009).
[CrossRef]

H. Kang, H. Liu, J. A. Phillips, Z. Cao, Y. Kim, Y. Chen, Z. Yang, J. Li, and W. Tan, “Single-DNA molecule nanomotor regulated by photons,” Nano Lett.9, 2690–2696 (2009).
[CrossRef] [PubMed]

X. Liang, T. Mochizuki, and H. Asanuma, “A supra-photoswitch involving sandwiched DNA base pairs and azobenzenes for light-driven nanostructures and nanodevices,” Small5, 1761–1768 (2009).
[CrossRef] [PubMed]

L. Wu, K. Koumoto, and N. Sugimoto, “Reversible stability switching of a hairpin DNA via a photo-responsive linker unit,” Chem. Commun.47, 1915–1917 (2009).
[CrossRef]

Y. Kim, J. A. Phillipsa, H. Liua, H. Kanga, and W. Tan, “Using photons to manipulate enzyme inhibition by an azobenzene-modified nucleic acid probe,” Proc. Natl. Acad. Sci.106, 6489–6494 (2009).
[CrossRef] [PubMed]

2008

S. Ogasawara and M. Maeda, “Straightforward and reversible photoregulation of hybridization by using a photochromic nucleoside,” Angew. Chem. Int. Ed.47, 8839–8842 (2008).
[CrossRef]

X. Liang, H. Nishioka, N. Takenaka, and H. Asanuma, “A DNA nanomachine powered by light irradiation,” ChemBioChem9, 702–705 (2008).
[CrossRef] [PubMed]

2007

H. Asanuma, X. Liang, H. Nishioka, D. Matsunaga, M. Liu, and M. Komiyama, “Synthesis of azobenzene-tethered DNA for reversible photo-regulation of DNA functions: hybridization and transcription,” Nat. Protocols2, 203–212 (2007).
[CrossRef]

2003

D. P. Bratu, B. J. Cha, M. M. Mhlanga, F. R. Kramer, and S. Tyagi, “Visualizing the distribution and transport of mRNAs in living cells,” Proc. Natl. Acad. Sci.100, 13308–13313 (2003).
[CrossRef] [PubMed]

1999

H. Asanuma, T. Ito, T. Yoshida, X. Liang, and M. Komiyama, “Photo-regulation of the formation and dissociation of DNA-duplex by using the cis-trans isomerization of azobenzene,” Angew. Chem. Int. Ed.38, 2393–2395 (1999).
[CrossRef]

Asanuma, H.

M. Zhou, X. Liang, T. Mochizuki, and H. Asanuma, “A light-driven DNA nanomachine for the efficient photo-switching of RNA digestion,” Angew. Chem. Int. Ed.49, 2167–2170 (2010).
[CrossRef]

X. Liang, T. Mochizuki, and H. Asanuma, “A supra-photoswitch involving sandwiched DNA base pairs and azobenzenes for light-driven nanostructures and nanodevices,” Small5, 1761–1768 (2009).
[CrossRef] [PubMed]

X. Liang, H. Nishioka, N. Takenaka, and H. Asanuma, “A DNA nanomachine powered by light irradiation,” ChemBioChem9, 702–705 (2008).
[CrossRef] [PubMed]

H. Asanuma, X. Liang, H. Nishioka, D. Matsunaga, M. Liu, and M. Komiyama, “Synthesis of azobenzene-tethered DNA for reversible photo-regulation of DNA functions: hybridization and transcription,” Nat. Protocols2, 203–212 (2007).
[CrossRef]

H. Asanuma, T. Ito, T. Yoshida, X. Liang, and M. Komiyama, “Photo-regulation of the formation and dissociation of DNA-duplex by using the cis-trans isomerization of azobenzene,” Angew. Chem. Int. Ed.38, 2393–2395 (1999).
[CrossRef]

Branda, N. R.

L. Poon, W. Zandberg, D. Hsiao, Z. Erno, D. Sen, B. D. Gates, and N. R. Branda, “Photothermal release of single-stranded DNA from the surface of gold nanoparticles through controlled denaturating and Au–S bond breaking,” ACS Nano4, 6395–6403 (2010).
[CrossRef] [PubMed]

Bratu, D. P.

D. P. Bratu, B. J. Cha, M. M. Mhlanga, F. R. Kramer, and S. Tyagi, “Visualizing the distribution and transport of mRNAs in living cells,” Proc. Natl. Acad. Sci.100, 13308–13313 (2003).
[CrossRef] [PubMed]

Cao, Z.

H. Kang, H. Liu, J. A. Phillips, Z. Cao, Y. Kim, Y. Chen, Z. Yang, J. Li, and W. Tan, “Single-DNA molecule nanomotor regulated by photons,” Nano Lett.9, 2690–2696 (2009).
[CrossRef] [PubMed]

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, 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]

Cha, B. J.

D. P. Bratu, B. J. Cha, M. M. Mhlanga, F. R. Kramer, and S. Tyagi, “Visualizing the distribution and transport of mRNAs in living cells,” Proc. Natl. Acad. Sci.100, 13308–13313 (2003).
[CrossRef] [PubMed]

Chen, Y.

H. Kang, H. Liu, J. A. Phillips, Z. Cao, Y. Kim, Y. Chen, Z. Yang, J. Li, and W. Tan, “Single-DNA molecule nanomotor regulated by photons,” Nano Lett.9, 2690–2696 (2009).
[CrossRef] [PubMed]

Colon, P.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, 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]

Erno, Z.

L. Poon, W. Zandberg, D. Hsiao, Z. Erno, D. Sen, B. D. Gates, and N. R. Branda, “Photothermal release of single-stranded DNA from the surface of gold nanoparticles through controlled denaturating and Au–S bond breaking,” ACS Nano4, 6395–6403 (2010).
[CrossRef] [PubMed]

Fang, X.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, 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]

Gates, B. D.

L. Poon, W. Zandberg, D. Hsiao, Z. Erno, D. Sen, B. D. Gates, and N. R. Branda, “Photothermal release of single-stranded DNA from the surface of gold nanoparticles through controlled denaturating and Au–S bond breaking,” ACS Nano4, 6395–6403 (2010).
[CrossRef] [PubMed]

Hsiao, D.

L. Poon, W. Zandberg, D. Hsiao, Z. Erno, D. Sen, B. D. Gates, and N. R. Branda, “Photothermal release of single-stranded DNA from the surface of gold nanoparticles through controlled denaturating and Au–S bond breaking,” ACS Nano4, 6395–6403 (2010).
[CrossRef] [PubMed]

Ito, T.

H. Asanuma, T. Ito, T. Yoshida, X. Liang, and M. Komiyama, “Photo-regulation of the formation and dissociation of DNA-duplex by using the cis-trans isomerization of azobenzene,” Angew. Chem. Int. Ed.38, 2393–2395 (1999).
[CrossRef]

Kang, H.

H. Kang, H. Liu, J. A. Phillips, Z. Cao, Y. Kim, Y. Chen, Z. Yang, J. Li, and W. Tan, “Single-DNA molecule nanomotor regulated by photons,” Nano Lett.9, 2690–2696 (2009).
[CrossRef] [PubMed]

Kanga, H.

Y. Kim, J. A. Phillipsa, H. Liua, H. Kanga, and W. Tan, “Using photons to manipulate enzyme inhibition by an azobenzene-modified nucleic acid probe,” Proc. Natl. Acad. Sci.106, 6489–6494 (2009).
[CrossRef] [PubMed]

Kim, Y.

Y. Kim, J. A. Phillipsa, H. Liua, H. Kanga, and W. Tan, “Using photons to manipulate enzyme inhibition by an azobenzene-modified nucleic acid probe,” Proc. Natl. Acad. Sci.106, 6489–6494 (2009).
[CrossRef] [PubMed]

H. Kang, H. Liu, J. A. Phillips, Z. Cao, Y. Kim, Y. Chen, Z. Yang, J. Li, and W. Tan, “Single-DNA molecule nanomotor regulated by photons,” Nano Lett.9, 2690–2696 (2009).
[CrossRef] [PubMed]

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, 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]

Komiyama, M.

H. Asanuma, X. Liang, H. Nishioka, D. Matsunaga, M. Liu, and M. Komiyama, “Synthesis of azobenzene-tethered DNA for reversible photo-regulation of DNA functions: hybridization and transcription,” Nat. Protocols2, 203–212 (2007).
[CrossRef]

H. Asanuma, T. Ito, T. Yoshida, X. Liang, and M. Komiyama, “Photo-regulation of the formation and dissociation of DNA-duplex by using the cis-trans isomerization of azobenzene,” Angew. Chem. Int. Ed.38, 2393–2395 (1999).
[CrossRef]

Koumoto, K.

L. Wu, K. Koumoto, and N. Sugimoto, “Reversible stability switching of a hairpin DNA via a photo-responsive linker unit,” Chem. Commun.47, 1915–1917 (2009).
[CrossRef]

Kramer, F. R.

D. P. Bratu, B. J. Cha, M. M. Mhlanga, F. R. Kramer, and S. Tyagi, “Visualizing the distribution and transport of mRNAs in living cells,” Proc. Natl. Acad. Sci.100, 13308–13313 (2003).
[CrossRef] [PubMed]

Li, J.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, 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]

H. Kang, H. Liu, J. A. Phillips, Z. Cao, Y. Kim, Y. Chen, Z. Yang, J. Li, and W. Tan, “Single-DNA molecule nanomotor regulated by photons,” Nano Lett.9, 2690–2696 (2009).
[CrossRef] [PubMed]

Li, W.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, 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]

Liang, X.

M. Zhou, X. Liang, T. Mochizuki, and H. Asanuma, “A light-driven DNA nanomachine for the efficient photo-switching of RNA digestion,” Angew. Chem. Int. Ed.49, 2167–2170 (2010).
[CrossRef]

X. Liang, T. Mochizuki, and H. Asanuma, “A supra-photoswitch involving sandwiched DNA base pairs and azobenzenes for light-driven nanostructures and nanodevices,” Small5, 1761–1768 (2009).
[CrossRef] [PubMed]

X. Liang, H. Nishioka, N. Takenaka, and H. Asanuma, “A DNA nanomachine powered by light irradiation,” ChemBioChem9, 702–705 (2008).
[CrossRef] [PubMed]

H. Asanuma, X. Liang, H. Nishioka, D. Matsunaga, M. Liu, and M. Komiyama, “Synthesis of azobenzene-tethered DNA for reversible photo-regulation of DNA functions: hybridization and transcription,” Nat. Protocols2, 203–212 (2007).
[CrossRef]

H. Asanuma, T. Ito, T. Yoshida, X. Liang, and M. Komiyama, “Photo-regulation of the formation and dissociation of DNA-duplex by using the cis-trans isomerization of azobenzene,” Angew. Chem. Int. Ed.38, 2393–2395 (1999).
[CrossRef]

Lin, H.

C. Wang, Z. Zhu, Y. Song, H. Lin, C. J. Yang, and W. Tan, “Caged molecular beacons: controlling nucleic acid hybridization with light,” Chem. Commun.47, 5708–5710 (2011).
[CrossRef]

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, 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, H.

H. Kang, H. Liu, J. A. Phillips, Z. Cao, Y. Kim, Y. Chen, Z. Yang, J. Li, and W. Tan, “Single-DNA molecule nanomotor regulated by photons,” Nano Lett.9, 2690–2696 (2009).
[CrossRef] [PubMed]

Liu, M.

H. Asanuma, X. Liang, H. Nishioka, D. Matsunaga, M. Liu, and M. Komiyama, “Synthesis of azobenzene-tethered DNA for reversible photo-regulation of DNA functions: hybridization and transcription,” Nat. Protocols2, 203–212 (2007).
[CrossRef]

Liua, H.

Y. Kim, J. A. Phillipsa, H. Liua, H. Kanga, and W. Tan, “Using photons to manipulate enzyme inhibition by an azobenzene-modified nucleic acid probe,” Proc. Natl. Acad. Sci.106, 6489–6494 (2009).
[CrossRef] [PubMed]

Maeda, M.

S. Ogasawara and M. Maeda, “Straightforward and reversible photoregulation of hybridization by using a photochromic nucleoside,” Angew. Chem. Int. Ed.47, 8839–8842 (2008).
[CrossRef]

Matsunaga, D.

H. Asanuma, X. Liang, H. Nishioka, D. Matsunaga, M. Liu, and M. Komiyama, “Synthesis of azobenzene-tethered DNA for reversible photo-regulation of DNA functions: hybridization and transcription,” Nat. Protocols2, 203–212 (2007).
[CrossRef]

Medley, C. D.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, 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]

Mhlanga, M. M.

D. P. Bratu, B. J. Cha, M. M. Mhlanga, F. R. Kramer, and S. Tyagi, “Visualizing the distribution and transport of mRNAs in living cells,” Proc. Natl. Acad. Sci.100, 13308–13313 (2003).
[CrossRef] [PubMed]

Mochizuki, T.

M. Zhou, X. Liang, T. Mochizuki, and H. Asanuma, “A light-driven DNA nanomachine for the efficient photo-switching of RNA digestion,” Angew. Chem. Int. Ed.49, 2167–2170 (2010).
[CrossRef]

X. Liang, T. Mochizuki, and H. Asanuma, “A supra-photoswitch involving sandwiched DNA base pairs and azobenzenes for light-driven nanostructures and nanodevices,” Small5, 1761–1768 (2009).
[CrossRef] [PubMed]

Nishimura, T.

T. Nishimura, Y. Ogura, and J. Tanida, “A photonic DNA processor: concept and implementation,” Proc. SPIE8102, 810207 (2011).
[CrossRef]

Y. Ogura, T. Nishimura, and J. Tanida, “Self-contained photonically-controlled DNA tweezers,” Appl. Phys. Express2, 025004 (2009).
[CrossRef]

Nishioka, H.

X. Liang, H. Nishioka, N. Takenaka, and H. Asanuma, “A DNA nanomachine powered by light irradiation,” ChemBioChem9, 702–705 (2008).
[CrossRef] [PubMed]

H. Asanuma, X. Liang, H. Nishioka, D. Matsunaga, M. Liu, and M. Komiyama, “Synthesis of azobenzene-tethered DNA for reversible photo-regulation of DNA functions: hybridization and transcription,” Nat. Protocols2, 203–212 (2007).
[CrossRef]

Ogasawara, S.

S. Ogasawara and M. Maeda, “Straightforward and reversible photoregulation of hybridization by using a photochromic nucleoside,” Angew. Chem. Int. Ed.47, 8839–8842 (2008).
[CrossRef]

Ogura, Y.

T. Nishimura, Y. Ogura, and J. Tanida, “A photonic DNA processor: concept and implementation,” Proc. SPIE8102, 810207 (2011).
[CrossRef]

Y. Ogura, T. Nishimura, and J. Tanida, “Self-contained photonically-controlled DNA tweezers,” Appl. Phys. Express2, 025004 (2009).
[CrossRef]

Phillips, J. A.

H. Kang, H. Liu, J. A. Phillips, Z. Cao, Y. Kim, Y. Chen, Z. Yang, J. Li, and W. Tan, “Single-DNA molecule nanomotor regulated by photons,” Nano Lett.9, 2690–2696 (2009).
[CrossRef] [PubMed]

Phillipsa, J. A.

Y. Kim, J. A. Phillipsa, H. Liua, H. Kanga, and W. Tan, “Using photons to manipulate enzyme inhibition by an azobenzene-modified nucleic acid probe,” Proc. Natl. Acad. Sci.106, 6489–6494 (2009).
[CrossRef] [PubMed]

Poon, L.

L. Poon, W. Zandberg, D. Hsiao, Z. Erno, D. Sen, B. D. Gates, and N. R. Branda, “Photothermal release of single-stranded DNA from the surface of gold nanoparticles through controlled denaturating and Au–S bond breaking,” ACS Nano4, 6395–6403 (2010).
[CrossRef] [PubMed]

Sen, D.

L. Poon, W. Zandberg, D. Hsiao, Z. Erno, D. Sen, B. D. Gates, and N. R. Branda, “Photothermal release of single-stranded DNA from the surface of gold nanoparticles through controlled denaturating and Au–S bond breaking,” ACS Nano4, 6395–6403 (2010).
[CrossRef] [PubMed]

Song, Y.

C. Wang, Z. Zhu, Y. Song, H. Lin, C. J. Yang, and W. Tan, “Caged molecular beacons: controlling nucleic acid hybridization with light,” Chem. Commun.47, 5708–5710 (2011).
[CrossRef]

Sugimoto, N.

L. Wu, K. Koumoto, and N. Sugimoto, “Reversible stability switching of a hairpin DNA via a photo-responsive linker unit,” Chem. Commun.47, 1915–1917 (2009).
[CrossRef]

Takenaka, N.

X. Liang, H. Nishioka, N. Takenaka, and H. Asanuma, “A DNA nanomachine powered by light irradiation,” ChemBioChem9, 702–705 (2008).
[CrossRef] [PubMed]

Tan, W.

C. Wang, Z. Zhu, Y. Song, H. Lin, C. J. Yang, and W. Tan, “Caged molecular beacons: controlling nucleic acid hybridization with light,” Chem. Commun.47, 5708–5710 (2011).
[CrossRef]

Y. Kim, J. A. Phillipsa, H. Liua, H. Kanga, and W. Tan, “Using photons to manipulate enzyme inhibition by an azobenzene-modified nucleic acid probe,” Proc. Natl. Acad. Sci.106, 6489–6494 (2009).
[CrossRef] [PubMed]

H. Kang, H. Liu, J. A. Phillips, Z. Cao, Y. Kim, Y. Chen, Z. Yang, J. Li, and W. Tan, “Single-DNA molecule nanomotor regulated by photons,” Nano Lett.9, 2690–2696 (2009).
[CrossRef] [PubMed]

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, 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, Z.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, 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, “A photonic DNA processor: concept and implementation,” Proc. SPIE8102, 810207 (2011).
[CrossRef]

Y. Ogura, T. Nishimura, and J. Tanida, “Self-contained photonically-controlled DNA tweezers,” Appl. Phys. Express2, 025004 (2009).
[CrossRef]

Tyagi, S.

D. P. Bratu, B. J. Cha, M. M. Mhlanga, F. R. Kramer, and S. Tyagi, “Visualizing the distribution and transport of mRNAs in living cells,” Proc. Natl. Acad. Sci.100, 13308–13313 (2003).
[CrossRef] [PubMed]

Wang, C.

C. Wang, Z. Zhu, Y. Song, H. Lin, C. J. Yang, and W. Tan, “Caged molecular beacons: controlling nucleic acid hybridization with light,” Chem. Commun.47, 5708–5710 (2011).
[CrossRef]

Wang, K.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, 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, L.

L. Wu, K. Koumoto, and N. Sugimoto, “Reversible stability switching of a hairpin DNA via a photo-responsive linker unit,” Chem. Commun.47, 1915–1917 (2009).
[CrossRef]

Wu, Y.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, 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]

Yang, C. J.

C. Wang, Z. Zhu, Y. Song, H. Lin, C. J. Yang, and W. Tan, “Caged molecular beacons: controlling nucleic acid hybridization with light,” Chem. Commun.47, 5708–5710 (2011).
[CrossRef]

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, 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).
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Yang, Z.

H. Kang, H. Liu, J. A. Phillips, Z. Cao, Y. Kim, Y. Chen, Z. Yang, J. Li, and W. Tan, “Single-DNA molecule nanomotor regulated by photons,” Nano Lett.9, 2690–2696 (2009).
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Yoshida, T.

H. Asanuma, T. Ito, T. Yoshida, X. Liang, and M. Komiyama, “Photo-regulation of the formation and dissociation of DNA-duplex by using the cis-trans isomerization of azobenzene,” Angew. Chem. Int. Ed.38, 2393–2395 (1999).
[CrossRef]

Zandberg, W.

L. Poon, W. Zandberg, D. Hsiao, Z. Erno, D. Sen, B. D. Gates, and N. R. Branda, “Photothermal release of single-stranded DNA from the surface of gold nanoparticles through controlled denaturating and Au–S bond breaking,” ACS Nano4, 6395–6403 (2010).
[CrossRef] [PubMed]

Zhou, M.

M. Zhou, X. Liang, T. Mochizuki, and H. Asanuma, “A light-driven DNA nanomachine for the efficient photo-switching of RNA digestion,” Angew. Chem. Int. Ed.49, 2167–2170 (2010).
[CrossRef]

Zhu, Z.

C. Wang, Z. Zhu, Y. Song, H. Lin, C. J. Yang, and W. Tan, “Caged molecular beacons: controlling nucleic acid hybridization with light,” Chem. Commun.47, 5708–5710 (2011).
[CrossRef]

ACS Nano

L. Poon, W. Zandberg, D. Hsiao, Z. Erno, D. Sen, B. D. Gates, and N. R. Branda, “Photothermal release of single-stranded DNA from the surface of gold nanoparticles through controlled denaturating and Au–S bond breaking,” ACS Nano4, 6395–6403 (2010).
[CrossRef] [PubMed]

Angew. Chem. Int. Ed.

K. Wang, Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, 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]

H. Asanuma, T. Ito, T. Yoshida, X. Liang, and M. Komiyama, “Photo-regulation of the formation and dissociation of DNA-duplex by using the cis-trans isomerization of azobenzene,” Angew. Chem. Int. Ed.38, 2393–2395 (1999).
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S. Ogasawara and M. Maeda, “Straightforward and reversible photoregulation of hybridization by using a photochromic nucleoside,” Angew. Chem. Int. Ed.47, 8839–8842 (2008).
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M. Zhou, X. Liang, T. Mochizuki, and H. Asanuma, “A light-driven DNA nanomachine for the efficient photo-switching of RNA digestion,” Angew. Chem. Int. Ed.49, 2167–2170 (2010).
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Appl. Phys. Express

Y. Ogura, T. Nishimura, and J. Tanida, “Self-contained photonically-controlled DNA tweezers,” Appl. Phys. Express2, 025004 (2009).
[CrossRef]

Chem. Commun.

C. Wang, Z. Zhu, Y. Song, H. Lin, C. J. Yang, and W. Tan, “Caged molecular beacons: controlling nucleic acid hybridization with light,” Chem. Commun.47, 5708–5710 (2011).
[CrossRef]

L. Wu, K. Koumoto, and N. Sugimoto, “Reversible stability switching of a hairpin DNA via a photo-responsive linker unit,” Chem. Commun.47, 1915–1917 (2009).
[CrossRef]

ChemBioChem

X. Liang, H. Nishioka, N. Takenaka, and H. Asanuma, “A DNA nanomachine powered by light irradiation,” ChemBioChem9, 702–705 (2008).
[CrossRef] [PubMed]

Nano Lett.

H. Kang, H. Liu, J. A. Phillips, Z. Cao, Y. Kim, Y. Chen, Z. Yang, J. Li, and W. Tan, “Single-DNA molecule nanomotor regulated by photons,” Nano Lett.9, 2690–2696 (2009).
[CrossRef] [PubMed]

Nat. Protocols

H. Asanuma, X. Liang, H. Nishioka, D. Matsunaga, M. Liu, and M. Komiyama, “Synthesis of azobenzene-tethered DNA for reversible photo-regulation of DNA functions: hybridization and transcription,” Nat. Protocols2, 203–212 (2007).
[CrossRef]

Proc. Natl. Acad. Sci.

Y. Kim, J. A. Phillipsa, H. Liua, H. Kanga, and W. Tan, “Using photons to manipulate enzyme inhibition by an azobenzene-modified nucleic acid probe,” Proc. Natl. Acad. Sci.106, 6489–6494 (2009).
[CrossRef] [PubMed]

D. P. Bratu, B. J. Cha, M. M. Mhlanga, F. R. Kramer, and S. Tyagi, “Visualizing the distribution and transport of mRNAs in living cells,” Proc. Natl. Acad. Sci.100, 13308–13313 (2003).
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Proc. SPIE

T. Nishimura, Y. Ogura, and J. Tanida, “A photonic DNA processor: concept and implementation,” Proc. SPIE8102, 810207 (2011).
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Small

X. Liang, T. Mochizuki, and H. Asanuma, “A supra-photoswitch involving sandwiched DNA base pairs and azobenzenes for light-driven nanostructures and nanodevices,” Small5, 1761–1768 (2009).
[CrossRef] [PubMed]

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Figures (5)

Fig. 1
Fig. 1

(A) Schematic illustration of photonic activation of recognition function of the DNA using azobenzene-tethered hairpin DNA. (B) Schematic illustration of a photonically controlled molecular sensor. Purple squares represent the azobenzene positions. (C) Sequence and modification of the DNA strands used in this study. Here symbol x refers to the position of the azobenzene.

Fig. 2
Fig. 2

Time course of temperature control for one cycle. Light irradiation can be carried out at 80 °C for 2 min.

Fig. 3
Fig. 3

(A) Fluorescence emission spectra measured at the initial state (a), the on-state (b) and the off-state (c). (B) FRET ratio in light irradiation (a) and no light irradiation (b) under the temperature control. The sample concentrations of the sensor and the target were 1 μM in a phosphte buffer (NaCl 1 M, MgCl2 1 mM).

Fig. 4
Fig. 4

(A) Measurement result for different concentrations of the target, 0, 0.1, 0.2, 0.3, 0.4, and 0.5 μM with 0.5 μM of the sensor. (B) FRET ratio during a repeated operation. The sample concentrations of the sensor and the target were 1 μM in a phosphate buffer (NaCl 1 M, MgCl2 1 mM).

Fig. 5
Fig. 5

Results of the tracking of concentration when the target molecule (A) increased from 0.1 μM to 0.3 μM and (B) decreased from 0.4 μM to 0.2 μM. The concentration of the sensor was 0.5 μM.

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