Enzyme-based logic systems for information processing

Abstract

In this critical review we review enzymatic systems which involve biocatalytic reactions utilized for information processing (biocomputing). Extensive ongoing research in biocomputing, mimicking Boolean logic gates has been motivated by potential applications in biotechnology and medicine. Furthermore, novel sensor concepts have been contemplated with multiple inputs processed biochemically before the final output is coupled to transducing "smart-material" electrodes and other systems. These applications have warranted recent emphasis on networking of biocomputing gates. First few-gate networks have been experimentally realized, including coupling, for instance, to signal-responsive electrodes for signal readout. In order to achieve scalable, stable network design and functioning, considerations of noise propagation and control have been initiated as a new research direction. Optimization of single enzyme-based gates for avoiding analog noise amplification has been explored, as were certain network-optimization concepts. We review and exemplify these developments, as well as offer an outlook for possible future research foci. The latter include design and uses of non-Boolean network elements, e.g., filters, as well as other developments motivated by potential novel sensor and biotechnology applications (136 references).

Taking baby steps in molecular logic-based computation

“…The Krebs cycle of early biochemistry classes is a reminder to us that the product from one enzyme can serve as the substrate for the next enzyme. Since enzyme-based logic 80 is well-developed, 30 this path can be used to cascade enzymes to produce biomolecular logic arrays. For example, Willner, Katz and their colleagues combine acetylcholine esterase, choline oxidase, microperoxidase and glucose dehydrogenase to achieve the minimized gate array shown in Figure 7.…”

“…These logic signatures of 6 and 7 are manifested 25 experimentally by observing the fluorescence intensities of the tagged objects with a microscope after gentle exposure to the 'high' and 'low' levels of H + (Figures 5a and 5b respectively). The YES gate shows strong emission only in acidic solution (beads E and I) whereas the PASS 1 gate glows constantly 30 whatever the pH (beads A, C and G), i.e. the two gates are clearly distinguishable even though they are both displaying the same coloured fluorescence.…”

Kinetic Model for a Threshold Filter in an Enzymatic System for Bioanalytical and Biocomputing Applications

“…[1][2][3][4][5][6][7][8][9][10][11][12][13][14] Such multi-input reaction cascades are used in biosensing, biomolecular computing, and decision making devices and setups utilizing (bio)chemical processes with well-defined responses. [15][16][17][18][19][20] These systems require experimental design and theoretical understanding [21][22][23] of chemical and biochemical reactions that allow signal response modification and control.…”

“…Multi-step and multi-input signal processing has been studied as potentially enabling biomolecular computing, [5][6][7][8][9]45 i.e., information processing involving cascades of (bio)chemical reactions rather than being solely based on electronics. Biomolecular computing is a sub-field of unconventional computing, [46][47][48] and it requires a "toolbox" of logic elements in order to build a binary network.…”

“…Various binary logic gates have been demonstrated, including AND, OR, NAND, NOR, CNOT, XOR, INHIBIT, etc. [6][7][8][9] Such gates were also connected in small networks, [24][25][26][27][28][29] some if which carried out simple computational 49,50 and information storage 51,52 steps. to have a well-defined (practically zero slope) pre-threshold region for low inputs, and to preserve the sensitivity (the slope of the output curve) for large inputs.…”