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Articles

Biochemical flip-flop memory systems: essential additions to autonomous biocomputing and biosensing systems

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Pages 722-739 | Received 22 Sep 2013, Accepted 20 Oct 2013, Published online: 02 Jun 2014

References

  • Adamatzky, A., B. De Lacy Costello, L. Bull, S. Stepney, and C. Teuscher, eds. 2005. Unconventional Computing. Frome: Luniver Press.
  • Andreasson, J., and U. Pischel. 2010. “Smart Molecules at Work—Mimicking Advanced Logic Operations.” Chemical Society Reviews 39: 174–188.
  • Andreasson, J., S. D. Straight, T. A. Moore, A. L. Moore, and D. Gust. 2008. “Molecular All-photonic Encoder−Decoder.” Journal of the American Chemical Society 130: 11122–11128.
  • Arugula, M., V. Bocharova, Jan Halámek, Marcos Pita, and E. Katz. 2010. “Enzyme-based Multiplexer and Demultiplexer.” The Journal of Physical Chemistry B 114: 5222–5226.
  • Ashkenazi, G., D. R. Ripoll, N. Lotan, and H. A. Scheraga. 1997. “A Molecular Switch for Biochemical Logic Gates: Conformational Studies.” Biosensors and Bioelectronics 12: 85–95.
  • Baron, R., O. Lioubashevski, E. Katz, T. Niazov, and I. Willner. 2006a. “Two Coupled Enzymes Perform in Parallel the ‘AND’ and ‘InhibAND’ Logic Gate Operations.” Organic and Biomolecular Chemistry 4: 989–991.
  • Baron, R., O. Lioubashevski, E. Katz, T. Niazov, and I. Willner. 2006b. “Logic Gates and Elementary Computing by Enzymes.” The Journal of Physical Chemistry 110: 8548–8553.
  • Baron, R., O. Lioubashevski, E. Katz, T. Niazov, and I. Willner. 2006c. “Elementary Arithmetic Operations by Enzymes: A Model for Metabolic Pathway Based Computing.” Angewandte Chemie 45: 1572–1576 (International Edition).
  • Baron, R., A. Onopriyenko, E. Katz, O. Lioubashevski, I. Willner, S. Wang, and H. Tian. 2006. “An Electrochemical/Photochemical Information Processing System Using a Monolayer-functionalized Electrode.” Chemical Communications 20: 2147–2149.
  • Baytekin, H. T., and E. U. Akkaya. 2000. “A Molecular NAND Gate Based on Watson−Crick Base Pairing.” Organic Letters 2: 1725–1727.
  • Calude, C. S., J. F. Costa, N. Dershowitz, E. Freire, and G. Rozenberg, eds. 2009. Unconventional Computation. Lecture Notes in Computer Science. Vol. 5715. Berlin: Springer.
  • Canary, J. W. 2009. “Redox-triggered Chiroptical Molecular Switches.” Chemical Society Reviews 38: 747–756.
  • Coronado, E., P. Gavina, and S. Tatay. 2009. “Catenanes and Threaded Systems: From Solution to Surfaces.” Chemical Society Reviews 38: 1674–1689.
  • Coskun, A., E. Deniz, and E. U. Akkaya. 2005. “Effective PET and ICT Switching of Boradiazaindacene Emission:  A Unimolecular, Emission-mode, Molecular Half-subtractor with Reconfigurable Logic Gates.” Organic Letters 7: 5187–5189.
  • Credi, A. 2007. “Molecules That Make Decisions.” Angewandte Chemie 46: 5472–5475 (International Edition).
  • Credi, A., V. Balzani, S. J. Langford, and J. F. Stoddart. 1997. “Logic Operations at the Molecular Level. An XOR Gate Based on a Molecular Machine.” Journal of the American Chemical Society 119: 2679–2681.
  • De Ruiter, G., L. Motiei, J. Choudhury, N. Oded, and M. E. Van der Boom. 2010b. “Electrically Addressable Multistate Volatile Memory with Flip-flop and Flip-flap-flop Logic Circuits on a Solid Support.” Angewandte Chemie 49: 4780–4783 (International Edition).
  • De Ruiter, G., and M. E. Van der Boom. 2011. “Sequential Logic and Random Access Memory (RAM): A Molecular Approach.” Journal of Materials Chemistry 21: 17575–17581.
  • De Ruiter, G., E. Tartakovsky, N. Oded, and M. E. Van der Boom. 2010. “Sequential Logic Operations with Surface-confined Polypyridyl Complexes Displaying Molecular Random Access Memory Features.” Angewandte Chemie 49: 169–172 (International Edition).
  • De Silva, A. P., I. M. Dixon, H. Q. N. Gunaratne, T. Gunnlaugsson, P. R. S. Maxwell, and T. E. Rice. 1999. “Integration of Logic Functions and Sequential Operation of Gates at the Molecular-scale.” Journal of the American Chemical Society 121: 1393–1394.
  • De Silva, A. P., H. Q. N. Gunaratne, and G. E. M. Maguire. 1994. “‘Off–On’ Fluorescent Sensors for Physiological Levels of Magnesium Ions Based on Photoinduced Electron Transfer (PET), which also Behave as Photoionic OR Logic Gates.” Journal of the Chemical Society, Chemical Communications 10: 1213–1214.
  • De Silva, A. P., H. Q. N. Gunaratne, and C. P. McCoy. 1993. “A Molecular Photoionic AND Gate Based on Fluorescent Signalling.” Nature 364: 42–44.
  • De Silva, A. P., H. Q. N. Gunaratne, and C. P. McCoy. 1997. “Molecular Photoionic AND Logic Gates with Bright Fluorescence and ‘Off−On’ Digital Action.” Journal of the American Chemical Society 119: 7891–7892.
  • De Silva, A. P., and N. D. McClenaghan. 2002. “Simultaneously Multiply-configurable or Superposed Molecular Logic Systems Composed of ICT (Internal Charge Transfer) Chromophores and Fluorophores Integrated with One- or Two-Ion Receptors.” Chemistry – A European Journal 8: 4935–4945.
  • De Silva, A. P., and S. Uchiyama. 2007. “Molecular Logic and Computing.” Nature Nanotechnology 2: 399–410.
  • De Silva, A. P., S. Uchiyama, T. P. Vance, and B. Wannalerse. 2007. “A Supramolecular Chemistry Basis for Molecular Logic and Computation.” Coordination Chemistry Reviews 251: 1623–1632.
  • De Sousa, M., B. De Castro, S. Abad, M. A. Miranda, and U. Pischel. 2006. “A Molecular Tool Kit for the Variable Design of Logic Operations (NOR, INH, EnNOR).” Chemical Communications 2051–2053.
  • Deonarine, A. S., S. M. Clark, and L. Konermann. 2003. “Implementation of a Multifunctional Logic Gate Based on Folding/Unfolding Transitions of a Protein.” Future Generation Computer Systems 19: 87–97.
  • Elbaz, J., M. Moshe, and I. Willner. 2009. “Coherent Activation of DNA Tweezers: A ‘SET-RESET’ Logic System.” Angewandte Chemie 48: 3834–3837 (International Edition).
  • Elbaz, J., Z.-G. Wang, R. Orbach, and I. Willner. 2009. “pH-Stimulated Concurrent Mechanical Activation of Two DNA ‘Tweezers’. A ‘SET−RESET’ Logic Gate System.” Nano Letters 9: 4510–4514.
  • Ezziane, Z. 2006. DNA Computing: Applications and Challenges. Nanotechnology 17: R27–R39.
  • Flood, A. H., R. J. A. Ramirez, W. Q. Deng, R. P. Muller, W. A. Goddard, and J. F. Stoddart. 2004. “Meccano on the Nanoscale—A Blueprint for Making Some of the World’s Tiniest Machines.” Australian Journal of Chemistry 57: 301–322.
  • Gheorghe, M. 2005. Molecular Computational Models. Idea Group Publishing.
  • Gunnlaugsson, T., D. A. MacDónaill, and D. Parker. 2000. “Luminescent Molecular Logic Gates: The Two-input Inhibit (INH) Function.” Chemical Communications 93–94.
  • Gunnlaugsson, T., D. A. Mac Dónaill, and D. Parker. 2001. “Lanthanide Macrocyclic Quinolyl Conjugates as Luminescent Molecular-level Devices.” Journal of the American Chemical Society 123: 12866–12876.
  • Guo, X., D. Zhang, and D. Zhu. 2004. “Logic Control of the Fluorescence of a New Dyad, Spiropyran-Perylene Diimide-Spiropyran, with Light, Ferric Ion, and Proton: Construction of a New Three-Input ‘AND’ Logic Gate.” Advanced Materials 16: 125–130.
  • Guo, X., D. Zhang, G. Zhang, and D. Zhu. 2004. “Monomolecular Logic: ‘Half-adder’ Based on Multistate/Multifunctional Photochromic Spiropyrans.” The Journal of Physical Chemistry B 108: 11942–11945.
  • Hoteit, I., N. Kharma, and L. Varin. 2012. “Computational Simulation of a Gene Regulatory Network Implementing an Extendable Synchronous Single-Input Delay Flip-Flop.” BioSystems 109: 57–71.
  • Jiang, G., Y. Song, X. Guo, D. Zhang, and D. Zhu. 2008. “Organic Functional Molecules towards Information Processing and High-density Information Storage.” Advanced Materials 20: 2888–2898.
  • Jimenez, D., R. Martínez-Máñez, F. Sancenón, J. V. Ros-Lis, J. Soto, Ángel Benito, and E. García-Breijo. 2005. “Multi-channel Receptors and their Relation to Guest Chemosensing and Reconfigurable Molecular Logic Gates.” European Journal of Inorganic Chemistry 12: 2393–2403.
  • Kahan, M., B. Gil, R. Adar, and E. Shapiro. 2008. “Towards Molecular Computers that Operate in a Biological Environment.” Physica D: Nonlinear Phenomena 237: 1165–1172.
  • Katz, E., ed. 2012a. Molecular and Supramolecular Information Processing: From Molecular Switches to Logic Systems. Weinheim: Wiley-VCH.
  • Katz, E., ed. 2012b. Biomolecular Information Processing – From Logic Systems to Smart Sensors and Actuators. Weinheim: Wiley-VCH.
  • Katz, E., and K. MacVittie. 2013. “Implanted Biofuel Cells Operating in Vivo – Methods, Applications and Perspectives – Feature Article.” Energy & Environmental Science 6: 2791–2803.
  • Katz, E., and V. Privman. 2010. “Enzyme-based Logic Systems for Information Processing.” Chemical Society Reviews 39: 1835–1857.
  • Katz, E., S. Minko, J. Halámek, K. MacVittie, and K. Yancey. 2013. “Electrode Interfaces Switchable by Physical and Chemical Signals for Biosensing, Biofuel, and Biocomputing Applications.” Analytical and Bioanalytical Chemistry 405: 3659–3672.
  • Krämer, M., M. Pita, J. Zhou, M. Ornatska, A. Poghossian, M. J. Schöning, and E. Katz. 2009. “Coupling of Biocomputing Systems with Electronic Chips: Electronic Interface for Transduction of Biochemical Information.” The Journal of Physical Chemistry C 113: 2573–2579.
  • Leung, K. C.-F., C.-P. Chak, C.-M. Lo, W.-Y. Wong, S. Xuan, and C. H. K. Cheng. 2009. “pH-Controllable Supramolecular Systems.” Chemistry -– An Asian Journal 4: 364–381.
  • Li, Z. X., L. Y. Liao, W. Sun, C. H. Xu, C. Zhang, C. J. Fang, and C. H. Yan. 2008. “Reconfigurable Cascade Circuit in a Photo- and Chemical-switchable Fluorescent Diarylethene Derivative.” The Journal of Physical Chemistry C 112: 5190–5196.
  • Li, L., M.-X. Yu, F. Y. Li, T. Yi, and C. H. Huang. 2007. “INHIBIT Logic Gate Based on Spiropyran Sensitized Semiconductor Electrode.” Colloids and Surfaces A: Physicochemical and Engineering Aspects 304: 49–53.
  • Li, Z., M. A. Rosenbaum, A. Venkataraman, T. K. Tam, E. Katz, and L. T. Angenent. 2011. “Bacteria-Based AND Logic Gate: A Decision-making and Self-powered Biosensor.” Chemical Communications 47: 3060–3062.
  • Loeb, S. J. 2007. “Rotaxanes as Ligands: From Molecules to Materials.” Chemical Society Reviews 36: 226–235.
  • Luxami, V., and S. Kumar. 2008. “Molecular Half-subtractor Based on 3,3′-Bis(1H-Benzimidazolyl-2-Yl)[1,1′]Binaphthalenyl-2,2′-Diol.” New Journal of Chemistry 32: 2074–2079.
  • MacVittie, K., J. Halámek, and E. Katz. 2012a. “Enzyme-based D-flip-flop Memory System.” Chemical Communications 48: 11742–11744.
  • Macvittie, K., J. Halámek, and E. Katz. 2012b. “Enzyme-based T-flip-flop Memory System.” International Journal of Unconventional Computing 8: 383–389.
  • Manesh, K. M., J. Halámek, M. Pita, J. Zhou, T. K. Tam, P. Santhosh, M.-C. Chuang, J. R. Windmiller, D. Abidin, E. Katz, and J. Wang. 2009. “Enzyme Logic Gates for the Digital Analysis of Physiological Level upon Injury.” Biosensors and Bioelectronics 24: 3569–3574.
  • Mano, M. M., and C. R. Kime. 2000. Logic and Computer Design Fundamentals. Upper Saddle River, NJ: Prentice Hall.
  • Margulies, D., C. E. Felder, G. Melman, and A. Shanzer. 2007. “A Molecular Keypad Lock:  A Photochemical Device Capable of Authorizing Password Entries.” Journal of the American Chemical Society 129: 347–354.
  • Matsuda, K., and M. Irie. 2004. “Diarylethene as a Photoswitching Unit.” Journal of Photochemistry and Photobiology C: Photochemistry Reviews 5: 169–182.
  • Motornov, M., J. Zhou, M. Pita, V. Gopishetty, I. Tokarev, E. Katz, and S. Minko. 2008. “‘Chemical Transformers’ from Nanoparticle Ensembles Operated with Logic.” Nano Letters 8: 2993–2997.
  • Motornov, M., J. Zhou, M. Pita, I. Tokarev, V. Gopishetty, E. Katz, and S. Minko. 2009. “An Integrated Multifunctional Nanosystem from Command Nanoparticles and Enzymes.” Small 5: 817–820.
  • Nijhuis, C. A., B. J. Ravoo, J. Huskens, and D. N. Reinhoudt. 2007. “Electrochemically Controlled Supramolecular Systems.” Coordination Chemistry Reviews 251: 1761–1780.
  • Pérez-Inestrosa, E., J. M. Montenegro, D. Collado, and R. Suau. 2008. “A Molecular 1 : 2 Demultiplexer.” Chemical Communications 9: 1085–1087.
  • Pérez-Inestrosa, E., J.-M. Montenegro, D. Collado, R. Suau, and J. Casado. 2007. “Molecules with Multiple Light-Emissive Electronic Excited States as a Strategy toward Molecular Reversible Logic Gates.” Journal of Physical Chemistry C 111: 6904–6909.
  • Periyasamy, G., J.-P. Collin, J.-P. Sauvage, R. D. Levine, and F. Remacle. 2009. “Electrochemically Driven Sequential Machines: An Implementation of Copper Rotaxanes.” Chemistry – A European Journal 15: 1310–1313.
  • Pischel, U. 2007. “Chemical Approaches to Molecular Logic Elements for Addition and Subtraction.” Angewandte Chemie 46: 4026–4040 (International Edition).
  • Pischel, U., and J. Andréasson. 2010. “A Simplicity-guided Approach toward Molecular Set–Reset Memories.” New Journal of Chemistry 34: 2701–2703.
  • Pischel, U., and B. Heller. 2008. “Molecular Logic Devices (Half-Subtractor, Comparator, Complementary Output Circuit) by Controlling Photoinduced Charge Transfer Processes.” New Journal of Chemistry 32: 395–400.
  • Pita, M., M. Krämer, J. Zhou, A. Poghossian, M. Schöning, V. M. Fernández, and E. Katz. 2008. “Optoelectronic Properties of Nanostructured Ensembles Controlled by Biomolecular Logic Systems.” ACS Nano 2: 2160–2166.
  • Pita, M., S. Minko, and E. Katz. 2009. “Enzyme-based Logic Systems and Their Applications for Novel Multi-signal-responsive Materials.” Journal of Materials Science: Materials in Medicine 20: 457–462.
  • Pita, M., G. Strack, K. MacVittie, J. Zhou, and E. Katz. 2009. “Set−Reset Flip-Flop Memory Based on Enzyme Reactions: Toward Memory Systems Controlled by Biochemical Pathways.” The Journal of Physical Chemistry B 113: 16071–16076.
  • Pita, M., T. K. Tam, S. Minko, and E. Katz. 2009. “Dual Magnetobiochemical Logic Control of Electrochemical Processes Based on Local Interfacial pH Changes.” ACS Applied Materials & Interfaces 1: 1166–1168.
  • Pita, M., J. Zhou, K. M. Manesh, J. Halámek, E. Katz, and J. Wang. 2009. “Enzyme Logic Gates for Assessing Physiological Conditions during an Injury: Towards Digital Sensors and Actuators.” Sensors and Actuators B: Chemical 139: 631–636.
  • Polsky, R., J. C. Harper, D. R. Wheeler, and S. M. Brozik. 2008. “Multifunctional Electrode Arrays: Towards a Universal Detection Platform.” Electroanalysis 20: 671–679.
  • Privman, M., T. K. Tam, M. Pita, and E. Katz. 2009. “Switchable Electrode Controlled by Enzyme Logic Network System: Approaching Physiologically Regulated Bioelectronics.” Journal of the American Chemical Society 131: 1314–1321.
  • Puntoriero, F., F. Nastasi, T. Bura, R. Ziessel, S. Campagna, and A. Giannetto. 2011. “Molecular Logics: A Mixed Bodipy–Bipyridine Dye Behaving as a Concealable Molecular Switch.” New Journal of Chemistry 35: 948–952.
  • Qian, J. H., X. H. Qian, Y. F. Xu, and S. Y. Zhang. 2008. “Multiple Molecular Logic Functions and Molecular Calculations Facilitated by Surfactant’s Versatility.” Chemical Communications 13: 4141–4143.
  • Remón, P., M. Bälter, S. Li, J. Andréasson, and U. Pischel. 2011. “An All-photonic Molecule-based D Flip-flop.” Journal of the American Chemical Society 133: 20742–20745.
  • Saha, S., and J. F. Stoddart. 2006. “Photo-Driven Molecular Devices.” Chemical Society Reviews 36: 77–92.
  • Shiva, S. G. 1998. Introduction to Logic Design. 2nd ed. New York: Marcel Dekker.
  • Simpson, M. L., G. S. Sayler, J. T. Fleming, and B. Applegate. 2001. “Whole-cell Biocomputing.” Trends in Biotechnology 19: 317–323.
  • Sivan, S., and N. Lotan. 1999. “A Biochemical Logic Gate Using an Enzyme and its Inhibitor. 1. The Inhibitor as Switching Element.” Biotechnology Progress 15: 964–970.
  • Sivan, S., S. Tuchman, and N. Lotan. 2003. “A Biochemical Logic Gate Using an Enzyme and its Inhibitor.” Part II: The Logic Gate. Biosystems 70: 21–33.
  • Stojanovic, M. N., D. Stefanovic, T. LaBean, and H. Yan. 2005. “Computing with Nucleic Acids.” In Bioelectronics, edited by I. Willner and E. Katz, 427–455. Weinheim: Wiley-VCH.
  • Strack, G., M. Pita, M. Ornatska, and E. Katz. 2008. “Boolean Logic Gates that Use Enzymes as Input Signals.” ChemBioChem 9: 1260–1266.
  • Straight, S. D., P. A. Liddell, Y. Terazono, T. A. Moore, A. L. Moore, and D. Gust. 2007. “All-Photonic Molecular XOR and NOR Logic Gates Based on Photochemical Control of Fluorescence in a Fulgimide–Porphyrin–Dithienylethene Triad.” Advanced Functional Materials 17: 777–785.
  • Sun, W., C. H. Xu, Z. Zhu, C. J. Fang, and C. H. Yan. 2008. “Chemical-driven Reconfigurable Arithmetic Functionalities within a Fluorescent Tetrathiafulvalene Derivative.” The Journal of Physical Chemistry C 112: 16973–16983.
  • Sun, W., Y.-R. Zheng, C.-H. Xu, C.-J. Fang, and C.-H. Yan. 2007. “Fluorescence-based Reconfigurable and Resettable Molecular Arithmetic Mode.” Journal of Physical Chemistry C 111: 11706–11711.
  • Szacilowski, K. 2008. “Digital Information Processing in Molecular Systems.” Chemical Reviews 108: 3481–3548.
  • Thanopulos, I., P. Kral, M. Shapiro, and E. Paspalakis. 2009. “Optical Control of Molecular Switches.” Journal of Modern Optics 56: 1–18.
  • Tokarev, I., V. Gopishetty, J. Zhou, M. Pita, M. Motornov, E. Katz, and S. Minko. 2009. “Stimuli-Responsive Hydrogel Membranes Coupled with Biocatalytic Processes.” ACS Applied Materials & Interfaces 1: 532–536.
  • Turfan, B., and E. U. Akkaya. 2002. “Modulation of Boradiazaindacene Emission by Cation-mediated Oxidative PET.” Organic Letters 4: 2857–2859.
  • Unger, R., and J. Moult. 2006. “Towards Computing with Proteins.” Proteins: Structure, Function, and Bioinformatics 63: 53–64.
  • Venturi, M., V. Balzani, R. Ballardini, A. Credi, and M. T. Gandolfi. 2004. International Journal of Photoenergy 6: 1–10.
  • Wang, Z.-G., J. Elbaz, F. Remacle, R. D. Levine, and I. Willner. 2010. “All-DNA Finite-state Automata with Finite Memory.” Proceedings of the National Academy of Sciences 107: 21996–22001.
  • Win, M. N., and C. D. Smolke. 2008. “Higher-order Cellular Information Processing with Synthetic RNA Devices.” Science 322: 456–460.
  • Zhou, J., T. K. Tam, M. Pita, M. Ornatska, S. Minko, and E. Katz. 2009. “Bioelectrocatalytic System Coupled with Enzyme-based Biocomputing Ensembles Performing Boolean Logic Operations: Approaching “Smart” Physiologically Controlled Biointerfaces.” ACS Applied Materials & Interfaces 1: 144–149.
  • Zhou, Y., H. Wu, L. Qu, D. Zhang, and D. Zhu. 2006. “A New Redox-resettable Molecule-based Half-adder with Tetrathiafulvalene.” The Journal of Physical Chemistry B 110: 15676–15679.
  • Zong, G., L. Xian, and G. Lu. 2007. “L-Arginine Bearing an Anthrylmethyl Group: Fluorescent Molecular NAND Logic Gate with H+ and ATP as Inputs.” Tetrahedron Letters 48: 3891–3894.

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