Scholarly article on topic 'Interfacing of biocomputing systems with silicon chips: Enzyme logic gates based on field-effect devices'

Interfacing of biocomputing systems with silicon chips: Enzyme logic gates based on field-effect devices Academic research paper on "Materials engineering"

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Procedia Chemistry
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{"enzyme logic gate" / biocomputing / "field-effect device" / biosensor / nanoparticles}

Abstract of research paper on Materials engineering, author of scientific article — Arshak Poghossian, Melina Krämer, Maryam H. Abouzar, Marcos Pita, Evgeny Katz, et al.

Abstract Field-effect capacitive EIS (electrolyte-insulator-semiconductor) sensors functionalised with gold nanoparticles have been used for electronic transduction of biochemical signals processed by enzyme-based AND-Reset / OR-Reset logic gates. The developed enzyme logic system produces pH changes as a result of biochemical reactions activated by different combinations of chemical input signals. The pH-induced charge changes of the nanoparticle shells and/or gate-insulator surface of the EIS transducer result in an electronic signal corresponding to the logic output produced by the enzymes. The logic output signals have been read out by means of capacitance-voltage method.

Academic research paper on topic "Interfacing of biocomputing systems with silicon chips: Enzyme logic gates based on field-effect devices"

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Procedía Chemistry

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Procedía Chemistry 1 (2009) 682-685

www.elsevier.com/locate/procedia

Proceedings of the Eurosensors XXIII conference

Interfacing of biocomputing systems with silicon chips: Enzyme logic gates based on field-effect devices

Arshak Poghossiana,b, Melina Kramera, Maryam H. Abouzara,b, Marcos Pitac, Evgeny Katzc, Michael J. Schoninga,b*

aInstitute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Ginsterweg 1, Jülich 52428, Germany bInstitute of Bio- andNanosystems, Research Centre Jülich GmbH, Jülich 52425, Germany cDepartment of Chemistry and Biomolecular Science, NanoBio Laboratory (NABLAB), Clarkson University, Potsdam, NY 13699-5810, USA

Field-effect capacitive EIS (electrolyte-insulator-semiconductor) sensors functionalised with gold nanoparticles have been used for electronic transduction of biochemical signals processed by enzyme-based AND-Reset / OR-Reset logic gates. The developed enzyme logic system produces pH changes as a result of biochemical reactions activated by different combinations of chemical input signals. The pH-induced charge changes of the nanoparticle shells and/or gate-insulator surface of the EIS transducer result in an electronic signal corresponding to the logic output produced by the enzymes. The logic output signals have been read out by means of capacitance-voltage method.

Keywords: enzyme logic gate; biocomputing; field-effect device; biosensor; nanoparticles

1. Introduction

Unconventional biomolecular computing (biocomputing) using various biomolecules such as proteins, DNA, RNA or bioreceptors for information processing and performing Boolean logic operations is an exciting new research field, which shows great promise, but at the same time faces substantial challenges1-4. Different physical (light, electrical potentials) or chemical (e.g., pH change) signals can be used to switch the state of the molecular systems and activate various logic operations. Recently developed enzyme-based logic gates (AND, OR, XOR, Inhib A, etc.), biocomputing security systems (biomolecular keypad lock) or systems composed of several concatenated logic gates that perform molecular-scale arithmetic operations (half-adder, half-subtractor), pave the way to elementary computing by the use of enzymes5-9. An application of enzymes as active component for biomolecular logic gates is especially intriguing because many biochemical reactions in living cells are catalysed by the presence of specific enzymes. However, the future of these logic elements and biocomputing is strongly connected to the successful transformation of biomolecular logic principles (input) into macroscopically useable

* Corresponding author. Tel.: +49-241-6009-53215; fax: +49-241-6009-53235. E-mail address: m.j.schoening@fz-juelich.de.

Abstract

1876-6196/09/$- See front matter © 2009 Published by Elsevier B.V. doi:10.1016/j.proche.2009.07.170

effects (output), their integration with electronic chips as well as the possibility of external addressing and switching the catalytic activity of enzymes "on" or "off' from the macroscopic level in order to control their complex functionality (e.g., by using inhibitors or via pH and temperature changes). Therefore, recently, an electrically wired enzyme system assembled on a macroelectrode surface that performs various logic operations depending on the applied potential has been realised10-11. In addition, first preliminary results demonstrating the possibility of coupling enzyme logic gates with a field-effect capacitive EIS (electrolyte-insulator-semiconductor) sensor have been reported12.

In the presented work, enzyme-based AND-Reset / OR-Reset logic gates have been realised using a capacitive EIS sensor functionalised with pH-responsive Au nanoparticles (NPs) as transducer and enzymes as biochemical input. The mechanism of biochemical signal transduction will be discussed.

2. Experimental

For the realisation of enzyme-based AND-Reset / OR-Reset logic gates, capacitive Al-Si-SiO2 (p-Si, p=1-10 Qcm; 30 nm thermally grown SiO2; 300 nm Al as rear-side contact layer) structures with chip sizes of 10 x 10 mm2 have been fabricated. After the cleaning, the SiO2 surface was modified with thiol groups by reacting with 10% 3-mercaptoprpyl-trimethoxysilane (MPTMS) solution in dry toluene for 1 hour at 60 °C. The silanised surface was reacted overnight with a dispersion of Au NPs to yield a self-assembled monolayer of NPs on the surface, which was then reacted with an aqueous solution of 3-mercaptopropionic acid (MPA) to generate a thiolated shell containing carboxylic groups. For the measurements, the EIS sensor was mounted into a home-made measuring cell, sealed by an O-ring and contacted on its front side by the electrolyte and a reference electrode, and on its rear side by a gold-plated pin.

Fig. 1 shows the structure of the EIS sensor functionalised with pH-responsive Au NPs (a) and the schematic of the enzyme-based OR-Reset logic gate (b). The OR-Reset logic gate composes of three enzymes (glucose oxidase, esterase, and urease) added into the solution containing particular analytes of glucose, ethyl butyrate, and urea. The enzymatic part of the system is responsible for sensing of the chemical signals and their logic treatment. The absence of the respective enzymes was considered as the input signal 0, while addition of enzymes was used as the input signal 1. The OR operation was activated by glucose oxidase (GOx) or/and esterase (input signals 1,0, 0,1, or 1,1), yielding to lower pH values upon the biochemical reactions catalysed by the enzymes in a non-buffered solution. To complete the reversible cycle, the Reset operation (returning the pH to the initial value) is activated by the addition of the enzyme urease. As a result, the pH-induced charge changes of the nanoparticle shells and/or gate-insulator surface of the EIS transducer generate an electronic signal corresponding to the logic output produced by the enzymes.

Fig. 1. Structure of an EIS sensor functionalised with Au nanoparticles (a) and schematic of an enzyme-based OR-Reset logic gate (b).

The AND logic gate (not shown) was realised by adding the enzymes glucose oxidase and invertase into the solution containing sucrose and dissolved oxygen. The hydrolytic conversion of sucrose to glucose and fructose catalysed by invertase was followed by glucose oxidation catalysed by glucose oxidase. These biochemical chain reactions (input signal 1,1) result in the formation of gluconic acid, thus lowering the pH value of the solution.

The respective pH changes have been read out by means of capacitance-voltage (C-V) method13 using an impedance analyser (Zahner Elektrik). The C-V measurements have been performed at a frequency of 120 Hz. For the measurements, the EIS sensor was mounted into a home-made measuring cell, sealed by an O-ring and contacted on its front side by the electrolyte and a reference electrode, and on its rear side by a gold-plated pin. The contact area of the EIS sensor with the solution is determined by the diameter of the O-ring and was about 0.5 cm2. For operation, a DC polarisation voltage is applied via the reference electrode (conventional Ag/AgCl electrode, Metrohm), and a small AC voltage (20 mV) is applied to the system in order to measure the capacitance of the sensor.

3. Results and discussion

Before the AND-Reset / OR-Reset logic gate experiments, the pH sensitivity of the bare and functionalised EIS sensors has been proven in standard buffer solutions of pH 3 to pH 9. The EIS sensors with a SiO2 gate-insulator showed a pH sensitivity of about 38-42 mV/pH that is in good accordance to values typically reported for a SiO2 layer14. A slightly higher pH sensitivity of 46 mV/pH was found for EIS sensors functionalised with the pH-responsive Au NPs.

Fig. 2 shows typical C-V curves for the Au-NPs functionalised EIS sensor recorded by OR and Reset operations. The OR gate was realised by addition of GOx or/and esterase (input signals 1,0, 0,1, or 1,1) into the solution containing glucose, ethyl butyrate and urea, resulting in the formation of acids (gluconic acid, butyric acid or both), thus lowering the pH from the initial value of about pH 7 to the final value of pH 3.8-4. The addition of the enzyme urease increases the pH value of the solution to about pH 8.1-8.4 (Reset function). As a result of these enzymatic reactions, C-V curves of the EIS sensor shift along the voltage axis. The potential shifts by different chemical input combinations are depicted in Fig. 2(c). The observed potential shifts for both AND-Reset (not shown) and OR-Reset logic gates could originate from charge changes associated with the protonation/deprotonation of both the carboxylic groups of pH-responsive shells on the immobilised Au NPs as well as the active sites on the transducer surface not-covered with Au NPs.

Potential {V) 1 2 3 4 5

Input combination

Fig. 2. Capacitance-voltage curves for the Au-NPs functionalised EIS sensor by OR and Reset operations (a), zoomed capacitance-voltage curves in the depletion range (b), and corresponding potential shifts induced via different chemical input combinations (0,0, 0,1 or 1,1) (c).

References

1. Pischel U. Chemical approaches to molecular logic elements for addition and substraction. Angew Chem Int Ed 2007;46:4026-40.

2. Szacilowski K. Digital information processing in molecular systems. Chem Rev 2008;108:3481-548.

3. Shapiro E, Gil B. RNA computing in a living cell. Science 2008;322:387-8.

4. Win MN, Smolke CD. Higher-order cellular information processing with synthetic RNA devices. Science 2008;322:456-60.

5. Baron R, Lioubashevski O, Katz E, Niazov T, Willner I. Logic gates and elementary computing by enzymes. J Phys Chem A 2006;110:8548-53.

6. Baron R, Lioubashevski O, Katz E, Niazov T, Willner I. Elementary arithmetic operations by enzymes: A model for metabolic pathway based computing. Angew Chem Int Ed 2006;45:1572-6.

7. Strack G, Pita M, Ornatska M, Katz E. Boolean logic gates using enzymes as input signals. ChemBioChem 2008;9:1260-6.

8. Pita M, Krämer M, Zhou J, Poghossian A, Schöning MJ, Fernandez VM, Katz E. Optoelectronic properties of nanostructured ensembles controlled by biomolecular logic systems. ACSNano 2008;2:2160-6.

9. 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 2008;130:4234-5.

10. Pita M, Minko S, Katz E. Enzyme-based logic systems and their applications for novel multi-signal-responsive materials. J Mater Sci: Mater Med 2009;20:457-62.

11. Pita M, Katz E. Logic gates based on electrically wired surface-reconstituted enzymes. J Am Chem Soc 2008;130:36-7.

12. Krämer M, Pita M., Zhou J, Ornatska M, Poghossian A, Schöning MJ, Katz E. Coupling of biocomputing systems with electronic chips: Electronic interface for transduction of biochemical information. J Phys Chem C 2009;113:2573-9.

13. Poghossian A, Abouzar MH, Amberger F, Mayer D, Han Y, Ingebrandt S, et al. Field-effect sensors with charged macromolecules: Characterisation by capacitance-voltage, constant-capacitance, impedance spectroscopy and atomic-force microscopy methods. Biosens. Bioelectron. 2007;22:2100-7.

14. Poghossian A, Schöning MJ. Silicon-based chemical and biological field-effect sensors. In: Grimes CA, Dickey EC, Pishko MV, editors. Encyclopedia of Sensors, Stevenson Ranch (USA): American Scientific Publishers; 2006, p. 463-533.