Enzymatic AND Logic Gates Operated Under Conditions Characteristic of Biomedical Applications

Picking Out Logic Operations in a Naphthalene β-Diketone Derivative by Using Molecular Encapsulation, Controlled Protonation, and DNA Binding

On–off switching and molecular logic in fluorescent molecules are associated with what chemical inputs can do to the structure and dynamics of these molecules. Herein, we report the structure of a naphthalene derivative, the fashion of its binding to β-cyclodextrin and DNA, and the operation of logic possible using protons, cyclodextrin, and DNA as chemical inputs. The compound crystallizes out in a keto-amine form, with intramolecular N−H⋅⋅⋅O bonding. It shows stepwise formation of 1:1 and 1:2 inclusion complexes with β-cyclodextrin. The aminopentenone substituents are encapsulated by β-cyclodextrin, leaving out the naphthalene rings free. The binding constant of the β-cyclodextrin complex is 512 m⁻¹. The pK_a value of the guest molecule is not greatly affected by the complexation. Dual input logic operations, based on various chemical inputs, lead to the possibility of several molecular logic gates, namely NOR, XOR, NAND, and Buffer. Such chemical inputs on the naphthalene derivative are examples of how variable signal outputs based on binding can be derived, which, in turn, are dependent on the size and shape of the molecule.

Majority and minority gates realized in enzyme-biocatalyzed systems integrated with logic networks and interfaced with bioelectronic systems

Biocatalytic reactions operating in parallel and resulting in reduction of NAD(+) or oxidation of NADH were used to mimic 3-input majority and minority logic gates, respectively. The substrates corresponding to the enzyme reactions were used as the input signals. When the input signals were applied at their high concentrations, defined as logic 1 input values, the corresponding biocatalytic reactions were activated, resulting in changes of the NADH concentration defined as the output signal. The NADH concentration changes were dependent on the number of parallel reactions activated by the input signals. The absence of the substrates, meaning their logic 0 input values, kept the reactions mute with no changes in the NADH concentration. In the system mimicking the majority function, the enzyme-biocatalyzed reactions resulted in a higher production of NADH when more than one input signal was applied at the logic 1 value. Another system mimicking the minority function consumed more NADH, thus leaving a smaller residual output signal, when more than one input signal was applied at the logic 1 value. The performance of the majority gate was improved by processing the output signal through a filter system in which another biocatalytic reaction consumed a fraction of the output signal, thus reducing its physical value to zero when the logic 0 value was obtained. The majority gate was integrated with a preceding AND logic gate to illustrate the possibility of complex networks. The output signal, NADH, was also used to activate a process mimicking drug release, thus illustrating the use of the majority gate in decision-making biomedical systems. The 3-input majority gate was also used as a switchable AND/OR gate when one of the input signals was reserved as a command signal, switching the logic operation for processing of the other two inputs. Overall, the designed majority and minority logic gates demonstrate novel functions of biomolecular information processing systems.

Complex logic functions implemented with quantum dot bionanophotonic circuits

We combine quantum dots (QDs) with long-lifetime terbium complexes (Tb), a near-IR Alexa Fluor dye (A647), and self-assembling peptides to demonstrate combinatorial and sequential bionanophotonic logic devices that function by time-gated Förster resonance energy transfer (FRET). Upon excitation, the Tb-QD-A647 FRET-complex produces time-dependent photoluminescent signatures from multi-FRET pathways enabled by the capacitor-like behavior of the Tb. The unique photoluminescent signatures are manipulated by ratiometrically varying dye/Tb inputs and collection time. Fluorescent output is converted into Boolean logic states to create complex arithmetic circuits including the half-adder/half-subtractor, 2:1 multiplexer/1:2 demultiplexer, and a 3-digit, 16-combination keypad lock.

Biocomputing, Biosensing and Bioactuation Based on Enzyme Biocatalyzed Reactions

The focus of this review paper is on the design and implementation of smart ‘Sense-and-Treat’ systems using enzyme-biocatalytic systems. These systems were used to perform biomolecular computing and they were functionally integrated with signal responsive materials aiming towards their biomedical use. Electrode interfaces, functionalized with signal-responsive materials, find applications in biocomputing, biosensing, and, specifically, triggered release of bioactive substances. ‘Sense-and-Treat’ systems require multiple components working together, including biosensors, actuators, and filters, in order to achieve closed-loop and autonomous operation. In general, biochemical logic networks were developed to process single biochemical or chemical inputs as well as multiple inputs, responding to nonphysiological (for concept demonstration purposes) and physiological signals (for injury detection or diagnosis). Actuation of drug-mimicking release was performed using the responsive material iron-cross-linked alginate with entrapped biomolecular species, responding to physical, chemical or biochemical signals.

Biophotonic logic devices based on quantum dots and temporally-staggered Förster energy transfer relays

Integrating photonic inputs/outputs into unimolecular logic devices can provide significantly increased functional complexity and the ability to expand the repertoire of available operations. Here, we build upon a system previously utilized for biosensing to assemble and prototype several increasingly sophisticated biophotonic logic devices that function based upon multistep Förster resonance energy transfer (FRET) relays. The core system combines a central semiconductor quantum dot (QD) nanoplatform with a long-lifetime Tb complex FRET donor and a near-IR organic fluorophore acceptor; the latter acts as two unique inputs for the QD-based device. The Tb complex allows for a form of temporal memory by providing unique access to a time-delayed modality as an alternate output which significantly increases the inherent computing options. Altering the device by controlling the configuration parameters with biologically based self-assembly provides input control while monitoring changes in emission output of all participants, in both a spectral and temporal-dependent manner, gives rise to two input, single output Boolean Logic operations including OR, AND, INHIBIT, XOR, NOR, NAND, along with the possibility of gate transitions. Incorporation of an enzymatic cleavage step provides for a set-reset function that can be implemented repeatedly with the same building blocks and is demonstrated with single input, single output YES and NOT gates. Potential applications for these devices are discussed in the context of their constituent parts and the richness of available signal.

Fabrication of lactate biosensor based on lactate dehydrogenase immobilized on cerium oxide nanoparticles

An electrochemical biosensor was developed to determine lactate that plays an important role in clinical diagnosis, fermentation and food quality analysis. Abnormal concentration of lactate has been related to diseases such as hypoxia, acute heart disorders, lactic acidosis, muscle fatigue and meningitis. Also, lactate concentration in blood helps to evaluate the athletic performance in sports. The main aim of the work is to fabricate NADH/LDH/Nano-CeO2/GCE bio-electrode for sensing lactate in human blood samples. Toward this, CeO2 nanoparticles were synthesized by a hydroxide mediated approach using cerium nitrate hexahydrate (Ce(NO3)3·6H2O) and NaOH as precursors. X-ray diffraction (XRD) and Field Emission Scanning Electron Microscopy (FE-SEM) studies were carried out to determine the structural and morphological characteristics of CeO2 nanoparticles. XRD pattern indicated the formation of highly crystalline CeO2 nanoparticles with face centered cubic structure. The FE-SEM studies revealed the formation of nanospherical particles of size 29.73±2.59 nm. The working electrode was fabricated by immobilizing nicotinamide adenine dinucleotide (NADH) and lactate dehydrogenase (LDH) on GCE surface with CeO2 nanoparticles as an interface. Electrochemical studies were carried out through cyclic voltammetry using a three electrode system with NADH/LDH/NanoCeO2/GCE as a working electrode, Ag/AgCl saturated with 0.1M KCl as a reference electrode and Pt wire as a counter electrode. From the amperometric study, the linearity was found to be in the range of 0.2-2 mM with the response time of less than 4s.

Enzymatic AND logic gate with sigmoid response induced by photochemically controlled oxidation of the output

We report a study of a system which involves an enzymatic cascade realizing an AND logic gate, with an added photochemical processing of the output, allowing the gate's response to be made sigmoid in both inputs. New functional forms are developed for quantifying the kinetics of such systems, specifically designed to model their response in terms of signal and information processing. These theoretical expressions are tested for the studied system, which also allows us to consider aspects of biochemical information processing such as noise transmission properties and control of timing of the chemical and physical steps.

Multianalyte digital enzyme biosensors with built-in Boolean logic

Novel biosensors based on the biocomputing concept digitally process multiple biochemical signals through Boolean logic networks of coupled biomolecular reactions and produce output in the form of a YES/NO response. Compared to traditional single-analyte sensing devices, biocomputing approach enables a high-fidelity multianalyte biosensing, particularly beneficial for biomedical applications.

Analysis of biomarkers characteristic of porcine liver injury--from biomolecular logic gates to an animal model

A biocatalytic cascade for the analysis of the simultaneous increase in the concentration of two biomarkers characteristic of liver injury (alanine transaminase, ALT, and lactate dehydrogenase, LDH) was tested on real samples acquired from an animal model (domestic pigs, Sus scrofa domesticus) suffering from traumatic liver injury. A two-step reaction biocatalyzed in the presence of both enzyme-biomarkers resulted in the oxidation of NADH followed by optical absorbance measurements. A simple qualitative, YES/NO, test allowed for distinction between animals with and without the presence of liver injury with the probability of 92%. These data represent the first demonstration of applying binary logic systems for the analysis of real biomedical samples.

Electrochemically controlled assembly and logic gates operations of gold nanoparticle arrays

The reversible assembly of β-cyclodextrin-functionalized gold NPs (β-CD Au NPs) is studied on mixed self-assembled monolayer (SAM), formed by coadsorption of redox-active ferrocenylalkylthiols and n-alkanethiols on gold surfaces. The surface coverage and spatial distribution of the β-CD Au NPs monolayer on the gold substrate are tuned by the self-assembled monolayer composition. The binding and release of β-CD Au NPs to and from the SAMs modified surface are followed by surface plasmon resonance (SPR) spectroscopy. The redox state of the tethered ferrocene in binary SAMs controls the formation of the supramolecular interaction between ferrocene moieties and β-CD-capped Au NPs. As a result, the potential-induced uptake and release of β-CD Au NPs to and from the surface is accomplished. The competitive binding of β-CD Au NPs with guest molecules in solution shifted the equilibrium of the complexation-decomplexation process involving the supramolecular interaction with the Fc-functionalized surface. The dual controlled assembly of β-CD Au NPs on the surface enabled to use two stimuli as inputs for logic gate activation; the coupling between the localized surface plasmon, associated with the Au NP, and the surface plasmon wave, associated with the thin metal surface, is implemented as readout signal for "AND" logic gate operations.

A self-powered "sense-act-treat" system that is based on a biofuel cell and controlled by boolean logic

Bio-logic-al: an autonomous, integrated "sense-act-treat" system that is based on an enzymatic biofuel cell has been developed. The system couples a biocomputing logic-detection method with a drug-release system to provide a logic-activated therapeutic intervention in response to a simulated abnormal physiological state, without the need for an external power source, control electronics, or microelectromechanical actuators.

Biomolecular filters for improved separation of output signals in enzyme logic systems applied to biomedical analysis

Biomolecular logic systems processing biochemical input signals and producing "digital" outputs in the form of YES/NO were developed for analysis of physiological conditions characteristic of liver injury, soft tissue injury, and abdominal trauma. Injury biomarkers were used as input signals for activating the logic systems. Their normal physiological concentrations were defined as logic-0 level, while their pathologically elevated concentrations were defined as logic-1 values. Since the input concentrations applied as logic 0 and 1 values were not sufficiently different, the output signals being at low and high values (0, 1 outputs) were separated with a short gap making their discrimination difficult. Coupled enzymatic reactions functioning as a biomolecular signal processing system with a built-in filter property were developed. The filter process involves a partial back-conversion of the optical-output-signal-yielding product, but only at its low concentrations, thus allowing the proper discrimination between 0 and 1 output values.

Enzyme-based NAND gate for rapid electrochemical screening of traumatic brain injury in serum

We report on the development of a rapid enzyme logic gate-based electrochemical assay for the assessment of traumatic brain injury (TBI). The concept harnesses a biocatalytic cascade that emulates the functionality of a Boolean NAND gate in order to process relevant physiological parameters in the biochemical domain. The enzymatic backbone ensures that a high-fidelity diagnosis of traumatic brain injury can be tendered in a rapid fashion when the concentrations of key serum-based biomarkers reach pathological levels. The excitatory neurotransmitter glutamate and the enzyme lactate dehydrogenase were used here as clinically-relevant input TBI biomarkers, in connection to the low-potential detection of the NADH product in the presence of methylene green at a glassy carbon electrode. A systematic optimization of the gate and the entire protocol has resulted in the effective discrimination between the physiological and pathological logic levels. Owing to its robust design, the enzyme-based logic gate mitigates potential interferences from both physiological and electroactive sources and is able to perform direct measurements in human serum samples. Granted further detailed clinical validation, this proof-of-concept study demonstrates the potential of the electrochemical assay to aid in the rapid and decentralized diagnosis of TBI.