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Development of a DNA sensor using a molecular logic gate

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Abstract

This communication reports the increase in fluorescence resonance energy transfer (FRET) efficiency between two laser dyes in the presence of deoxyribonucleic acid (DNA). Two types of molecular logic gates have been designed where DNA acts as input signal and fluorescence intensity of different bands are taken as output signal. Use of these logic gates as a DNA sensor has been demonstrated.

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References

  1. de Silva, P.A., Gunaratne, N.H.Q., Mccoy, C.P.: A molecular photoionic and gate based on fluorescent signaling. Nature 364, 42–44 (1993)

    Article  ADS  Google Scholar 

  2. Margulies, D., Melman, G., Shanzer, A.: A molecular full-adder and full-subtractor, an additional step toward a moleculator. J. Am. Chem. Soc. 128, 4865–4871 (2006)

    Article  Google Scholar 

  3. Pischel, U.: Chemical approaches to molecular logic elements for addition and subtraction. Angew. Chem. Int. Ed. 46, 4026–4040 (2007)

    Article  Google Scholar 

  4. Bozdemir, O.A., Sozmen, F., Büyükcakir, O., Guliyev, R., Cakmak, Y., Akkaya, E.U.: Reaction-based sensing of fluoride ions using built-in triggers for intramolecular charge transfer (ICT) and photoinduced electron transfer (PET). Org. Lett. 12, 1400–1403 (2010)

    Article  Google Scholar 

  5. Andreasson, J., Straight, S.D., Bandyopadhyay, S., Mitchell, R.H., Moore, T.A., Moore, A.L., Gust, D.: Molecular 2:1 digital multiplexer. Angew. Chem. Int. Ed. 46, 958–961 (2007)

    Article  Google Scholar 

  6. Amelia, M., Baroncini, M., Credi, A.: A simple unimolecular multiplexer/demultiplexer. Angew. Chem. Int. Ed. 47, 6240–6243 (2008)

    Article  Google Scholar 

  7. Perez-Inestrosa, E., Montenegro, J.M., Collado, D., Suau, R.: Molecular 1:2 demultiplexer. Chem. Commun. A 9, 1085–1087 (2008)

    Article  Google Scholar 

  8. Andreasson, J., Straight, S.D., Moore, T.A., Moore, A.L., Gust, D.: Molecular all-photonic encoder-decoder. J. Am. Chem. Soc. 130, 11122–11128 (2008)

    Article  Google Scholar 

  9. Ceroni, P., Bergamini, G., Balzani, V.: Old molecules, new concepts: [Ru(bpy)3]2+ as a molecular encoder-decoder. Angew. Chem. Int. Ed. 48, 8516–8518 (2009)

    Article  Google Scholar 

  10. Margulies, D., Felder, C.E., Melman, G., Shanzer, A.: A molecular keypad lock: a photochemical device capable of authorizing password entries. J. Am. Chem. Soc. 129, 347–354 (2007)

    Article  Google Scholar 

  11. Strack, G., Ornatska, M., Pita, M., Katz, E.: Biocomputing security system: concatenated enzyme-based logic gates operating as a biomolecular keypad lock. J. Am. Chem. Soc. 130, 4234–4235 (2008)

    Article  Google Scholar 

  12. Sun, W., Zhou, C., Xu, C.H., Fang, C.J., Zhang, C., Li, Z.X., Yan, C.H.: A fluorescent-switch-based computing platform in defending information risk. Chem. Eur. J. 14, 6342–6351 (2008)

    Article  Google Scholar 

  13. Suresh, M., Ghosh, A., Das, A.: A simple chemosensor for Hg2 +  and Cu2 +  that works as a molecular keypad lock. Chem. Commun. 3906–3908 (2008)

  14. Andreasson, J. Straight, S.D., Moore, T.A., Moore, A.L., Gust, D.: An all-photonic molecular keypad lock. Chem. Eur. J. 15, 3936–3939 (2009)

    Article  Google Scholar 

  15. Bozdemir, O.A., Guliyev, R., Büyükcakir, O., Selcuk, S., Kolemen, S., Gulseren, G., Nalbantoglu, T., Boyaci, H., Akkaya, E.U.: Selective manipulation of ICT and PET processes in styryl-bodipy derivatives: applications in molecular logic and fluorescence sensing of metal ions. J. Am. Chem. Soc. 132, 8029–8036 (2010)

    Article  Google Scholar 

  16. Hayes, J.P.: Introduction to Digital Logic Design. Addison-Wesley Publishing Company, Reading (1993)

    Google Scholar 

  17. de Silva, P.A., Uchiyama, S.N.: Molecular logic and computing. Nanotechnology 2, 399–410 (2007)

    Google Scholar 

  18. Szacizowski, K.: Digital information processing in molecular systems. Chem. Rev. 108, 3481–3548 (2008)

    Article  Google Scholar 

  19. Andreasson, J., Pischel, U.: Smart molecules at work—mimicking advanced logic operations. Rev. Chem. Soc. 39, 174–188 (2010)

    Article  Google Scholar 

  20. Liu, H., Zhou, Y., Yang, Y., Wang, W., Qu, L., Chen, C., Liu, D., Zhang, D., Zhu, D.: Photo-pH dually modulated fluorescence switch based on DNA spatial nanodevice. J. Phys. Chem. B 112, 6893 (2008)

    Article  Google Scholar 

  21. Margulies, D., Hamilton, A.D.: Digital analysis of protein properties by an ensemble of DNA quadruplexes. J. Am. Chem. Soc. 131, 9142 (2009)

    Article  Google Scholar 

  22. Strack, G., Ornatska, M., Pita, M., Katz, E.: Biocomputing security system: concatenated enzyme-based logic gates operating as a biomolecular keypad lock. J. Am. Chem. Soc. 130, 4234–4235 (2008)

    Article  Google Scholar 

  23. Pais, V.F., Remón, P., Collado, D., Andréasson, J., Inestrosa, E.P., Pischel, U.: OFF-ON-OFF fluorescence switch with T-Latch function. Org. Lett. 13, 5572–5575 (2011)

    Article  Google Scholar 

  24. Kumar, M., Kumar, R., Bhalla, V.: Optical chemosensor for Ag+, Fe3+, and cysteine: information processing at molecular level. Org. Lett. 13, 366–369 (2011)

    Article  MATH  Google Scholar 

  25. Wang, J., Katz, E.: Digital biosensors with built-in logic for biomedical applications—biosensors based on a biocomputing concept. Anal. Bioanal. Chem. 398, 1591–1603 (2010)

    Article  Google Scholar 

  26. Fujimoto, K., Shimizu, H., Inouye, M.: Unambiguous detection of target DNAs by excimer-monomer switching molecular beacons. J. Org. Chem. 69, 3271–3275 (2004)

    Article  Google Scholar 

  27. Clelland, C.T. , Risca, V., Bancroft, C.: Hiding messages in DNA microdots. Nature 399, 533–534 (1999)

    Article  ADS  Google Scholar 

  28. Mao, C., LaBean, T.H., Reif, J.H., Seeman, N.C.: Logical computation using self assembly of DNA triple cross-over molecules. Nature 407, 493–496 (2000)

    Article  ADS  Google Scholar 

  29. Tanaka, K., Okamoto, A., Saito, I.: Public-key system using DNA as a one-way function for key distribution. Biosystems 81, 25–29 (2005)

    Article  Google Scholar 

  30. Seth, D., Chakrabarty, D., Chakraborty, A., Sarkar, N.S.: Study of energy transfer from 7-amino coumarin donors to rhodamine 6G acceptor in non-aqueous reverse micelles. Chem. Phys. Lett. 401, 546–552 (2005)

    Article  ADS  Google Scholar 

  31. Förster, T.H.: Experimentelle und theoretische Untersuchung des Zwischenmolekularen übergangs von Elektrinenanregungsenergie. Z. Naturforsch. 4A, 321–327 (1949)

    ADS  Google Scholar 

  32. Hussain, S.A., Chakraborty, S., Bhattacharjee, D., Schoonheydt, R.A.: Fluorescence resonance energy transfer between organic dyes adsorbed onto nano-clay and Langmuir–Blodgett (LB) films. Spectrochim. Acta, Part A 75, 664–670 (2010)

    Article  ADS  Google Scholar 

  33. Förster, T.H.: Modern Quantum Chemistry, Istanbul Lectures, Part III: Action of Light and Organic Crystals. Academic Press, New York (1965)

    Google Scholar 

  34. Malicka, J., Gryczynski, I., Lakowicz, J.R.: DNA hybridization assays using metal-enhanced fluorescence. Biochem. Biophys. Res. Commun. 306, 213–218 (2003)

    Article  Google Scholar 

  35. Mathur, N., Aneja, A., Bhatnagar, P.K., Mathur, P.C.: A new FRET-based sensitive DNA sensor for medical diagnostics using PNA probe and water-soluble blue light emitting polymer. J. Sens. 2008, 1–6 (2008)

    Article  Google Scholar 

  36. Watson, J.D., Crick, F.H.C.: A structure for deoxyribose nucleic acid. Nature 171, 737–738 (1953)

    Article  ADS  Google Scholar 

  37. Wang, S., Gaylord, B.S., Bazan, G.C.: Fluorescein provides a resonance gate for FRET from conjugated polymers to DNA intercalated dyes. J. Am. Chem. Soc. 126, 5446–5451 (2004)

    Article  Google Scholar 

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Acknowledgements

The author SAH is grateful to DST, CSIR, and DAE for financial support to carry out this research work through DST Fast-Track project Ref. No. SE/FTP/PS-54/2007, CSIR project Ref. 03(1146)/09/EMR-II, and DAE Young Scientist Research Award (No. 2009/20/37/8/BRNS/3328).

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Correspondence to Syed Arshad Hussain.

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Bhattacharjee, D., Dey, D., Chakraborty, S. et al. Development of a DNA sensor using a molecular logic gate. J Biol Phys 39, 387–394 (2013). https://doi.org/10.1007/s10867-012-9295-3

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  • DOI: https://doi.org/10.1007/s10867-012-9295-3

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