Reusable molecular sensor based on photonic activation control of DNA probes

doi:10.1364/BOE.3.000920

Reusable molecular sensor based on photonic activation control of DNA probes

Takahiro Nishimura, Yusuke Ogura, and Jun Tanida »View Author Affiliations

Biomedical Optics Express, Vol. 3, Issue 5, pp. 920-926 (2012)
http://dx.doi.org/10.1364/BOE.3.000920

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Abstract
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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.

OCIS Codes
(350.5130) Other areas of optics : Photochemistry
(280.1415) Remote sensing and sensors : Biological sensing and sensors
(170.2655) Medical optics and biotechnology : Functional monitoring and imaging

ToC Category:
Biosensors and Molecular Diagnostics

History
Original Manuscript: March 14, 2012
Revised Manuscript: April 3, 2012
Manuscript Accepted: April 4, 2012
Published: April 11, 2012

Citation
Takahiro Nishimura, Yusuke Ogura, and Jun Tanida, "Reusable molecular sensor based on photonic activation control of DNA probes," Biomed. Opt. Express 3, 920-926 (2012)
http://www.opticsinfobase.org/boe/abstract.cfm?URI=boe-3-5-920

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References

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

Asanuma, H.
Branda, N. R.
Bratu, D. P.
Cao, Z.
Cha, B. J.
Chen, Y.
Colon, P.
Erno, Z.
Fang, X.
Gates, B. D.
Hsiao, D.
Ito, T.
Kang, H.
Kanga, H.
Kim, Y.
Komiyama, M.
Koumoto, K.
Kramer, F. R.
Li, J.
Li, W.
Liang, X.
Lin, H.
Liu, H.
Liu, M.
Liua, H.
Maeda, M.
Matsunaga, D.
Medley, C. D.
Mhlanga, M. M.
Mochizuki, T.
Nishimura, T.
Nishioka, H.
Ogasawara, S.
Ogura, Y.
Phillips, J. A.
Phillipsa, J. A.
Poon, L.
Sen, D.
Song, Y.
Sugimoto, N.
Takenaka, N.
Tan, W.
Tang, Z.
Tanida, J.
Tyagi, S.
Wang, C.
Wang, K.
Wu, L.
Wu, Y.
Yang, C. J.
Yang, Z.
Yoshida, T.
Zandberg, W.
Zhou, M.
Zhu, Z.

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). [CrossRef]
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]
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]

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). [CrossRef] [PubMed]

Proc. SPIE

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

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]

2011, Wang, Chem. Commun.
2011, Nishimura, Proc. SPIE
2010, Poon, ACS Nano
2010, Zhou, Angew. Chem. Int. Ed.
2009, Wang, Angew. Chem. Int. Ed.
2009, Ogura, Appl. Phys. Express
2009, Kang, Nano Lett.
2009, Liang, Small
2009, Wu, Chem. Commun.
2009, Kim, Proc. Natl. Acad. Sci.
2008, Ogasawara, Angew. Chem. Int. Ed.
2008, Liang, ChemBioChem
2007, Asanuma, Nat. Protocols
2003, Bratu, Proc. Natl. Acad. Sci.
1999, Asanuma, Angew. Chem. Int. Ed.

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