A biocatalytic cascade with several output signals—towards biosensors with different levels of confidence

The biocatalytic cascade based on enzyme-catalyzed reactions activated by several biomolecular input signals and producing output signal after each reaction step was developed as an example of a logically reversible information processing system. The model system was designed to mimic the operation of concatenated AND logic gates with optically readable output signals generated at each step of the logic operation. Implications include concurrent bioanalyses and data interpretation for medical diagnostics

Dna Computing Systems Activated By Electrochemically-Triggered Dna Release From A Polymer-Brush-Modified Electrode Array

An array of four independently wired indium tin oxide (ITO) electrodes was used for electrochemically stimulated DNA release and activation of DNA-based Identity, AND and XOR logic gates. Single-stranded DNA molecules were loaded on the mixed poly(N,N-dimethylaminoethyl methacrylate) (PDMAEMA)/poly(methacrylic acid) (PMAA) brush covalently attached to the ITO electrodes. The DNA deposition was performed at pH 5.0 when the polymer brush is positively charged due to protonation of tertiary amino groups in PDMAEMA, thus resulting in electrostatic attraction of the negatively charged DNA. By applying electrolysis at −1.0 V(vs. Ag/AgCl reference) electrochemical oxygen reduction resulted in the consumption of hydrogen ions and local pH increase near the electrode surface. The process resulted in recharging the polymer brush to the negative state due to dissociation of carboxylic groups of PMAA, thus repulsing the negatively charged DNA and releasing it from the electrode surface. The DNA release was performed in various combinations from different electrodes in the array assembly. The released DNA operated as input signals for activation of the Boolean logic gates. The developed system represents a step forward in DNA computing, combining for the first time DNA chemical processes with electronic input signals

Bridging The Two Worlds: A Universal Interface Between Enzymatic And Dna Computing Systems

Molecular computing based on enzymes or nucleic acids has attracted a great deal of attention due to the perspectives of controlling living systems in the way we control electronic computers. Enzyme-based computational systems can respond to a great variety of small molecule inputs. They have the advantage of signal amplification and highly specific recognition. DNA computing systems are most often controlled by oligonucleotide inputs/outputs and are capable of sophisticated computing as well as controlling gene expressions. Here, we developed an interface that enables communication of otherwise incompatible nucleic-acid and enzyme-computational systems. The enzymatic system processes small molecules as inputs and produces NADH as an output. The NADH output triggers electrochemical release of an oligonucleotide, which is accepted by a DNA computational system as an input. This interface is universal because the enzymatic and DNA computing systems are independent of each other in composition and complexity. Interface development: The communication between enzymatic and DNA logic systems was enabled by the development of a corresponding interface

Magnetic Field-Activated Sensing Of Mrna In Living Cells

Detection of specific mRNA in living cells has attracted significant attention in the past decade. Probes that can be easily delivered into cells and activated at the desired time can contribute to understanding translation, trafficking and degradation of mRNA. Here we report a new strategy termed magnetic field-activated binary deoxyribozyme (MaBiDZ) sensor that enables both efficient delivery and temporal control of mRNA sensing by magnetic field. MaBiDZ uses two species of magnetic beads conjugated with different components of a multicomponent deoxyribozyme (DZ) sensor. The DZ sensor is activated only in the presence of a specific target mRNA and when a magnetic field is applied. Here we demonstrate that MaBiDZ sensor can be internalized in live MCF-7 breast cancer cells and activated by a magnetic field to fluorescently report the presence of specific mRNA, which are cancer biomarkers

Nanoreactors Based On Dnazyme-Functionalized Magnetic Nanoparticles Activated By Magnetic Field

A new biomimetic nanoreactor design, MaBiDz, is presented based on a copolymer brush in combination with superparamagnetic nanoparticles. This cellular nanoreactor features two species of magnetic particles, each functionalized with two components of a binary deoxyribozyme system. In the presence of a target mRNA analyte and a magnetic field, the nanoreactor is assembled to form a biocompartment enclosed by the polymeric brush that enables catalytic function of the binary deoxyribozyme with enhanced kinetics. MaBiDz was demonstrated here as a cellular sensor for rapid detection and imaging of a target mRNA biomarker for metastatic breast cancer, and its function shows potential to be expanded as a biomimetic organelle that can downregulate the activity of a target mRNA biomarker

Bioelectronic Interface Connecting Reversible Logic Gates Based On Enzyme And Dna Reactions

It is believed that connecting biomolecular computation elements in complex networks of communicating molecules may eventually lead to a biocomputer that can be used for diagnostics and/or the cure of physiological and genetic disorders. Here, a bioelectronic interface based on biomolecule-modified electrodes has been designed to bridge reversible enzymatic logic gates with reversible DNA-based logic gates. The enzyme-based Fredkin gate with three input and three output signals was connected to the DNA-based Feynman gate with two input and two output signals—both representing logically reversible computing elements. In the reversible Fredkin gate, the routing of two data signals between two output channels was controlled by the control signal (third channel). The two data output signals generated by the Fredkin gate were directed toward two electrochemical flow cells, responding to the output signals by releasing DNA molecules that serve as the input signals for the next Feynman logic gate based on the DNA reacting cascade, producing, in turn, two final output signals. The Feynman gate operated as the controlled NOT gate (CNOT), where one of the input channels controlled a NOT operation on another channel. Both logic gates represented a highly sophisticated combination of input-controlled signal-routing logic operations, resulting in redirecting chemical signals in different channels and performing orchestrated computing processes. The biomolecular reaction cascade responsible for the signal processing was realized by moving the solution from one reacting cell to another, including the reacting flow cells and electrochemical flow cells, which were organized in a specific network mimicking electronic computing circuitries. The designed system represents the first example of high complexity biocomputing processes integrating enzyme and DNA reactions and performing logically reversible signal processing

Pacemaker Activated by an Abiotic Biofuel Cell Operated in Human Serum Solution

International audienceAn "abiotic" biofuel cell composed of catalytic electrodes modified with inorganic nanostructured species was used to activate a pacemaker. The catalytic nanoparticles of various compositions, AuxPty, deposited on carbon black (CB) were prepared and extensively characterized to select the species with selectivity for glucose oxidation and oxygen reduction. Then two kinds of 3D-electrode materials with different morphology, buckypaper composed of carbon nanotubes (ca. 50 nm diameter) and carbon paper made of carbon fibers (ca. 7 mm diameter), were used in a combination with different catalytic species. Finally, Au/CB nanospecies deposited on buckypaper were selected for catalyzing glucose oxidation (composing the biofuel cell anode) and Au60Pt40/CB species deposited on carbon paper were selected for catalyzing oxygen reduction (composing the biofuel cell cathode). The catalytic electrodes were characterized by cyclic voltammetry in an aqueous buffer solution and the polarization function for the biofuel cell was studied in a human serum solution. The open circuit voltage, V-oc, short circuit current density, j(sc), and maximum power produced by the biofuel cell, P-max, were found as 0.35 V, 0.65 mAcm(-2) and 104 mu W, respectively (in human serum at 5.4 mM glucose). The biofuel cell produced the steady state open circuit voltage over 10 hours with its slow decrease over 50 hours originating from the glucose depletion and slow mass-transport within the 3D-electrode. The voltage produced by the biofuel cell was amplified with an energy harvesting circuit and applied to a pacemaker resulting in its proper operation. The present study continues the research line where different implantable (enzyme-based or abiotic) biofuel cells are used for the activation of biomedical electronic devices, e. g., pacemakers

Wireless Information Transmission System Powered by an Abiotic Biofuel Cell Implanted in an Orange

International audienceAn "abiotic" biofuel cell composed of catalytic electrodes modified with inorganic nanoparticles (NPs) deposited on carbon black (CB) was used to activate a wireless information transmission system. The cathode and anode were made of carbon paper modified with Pt-NPs/CB and buckypaper modified with Au80Pt20-NPs/CB, respectively. The cathode/anode pair was implanted in orange pulp extracting power from its content (glucose and fructose in the juice). The open circuit voltage, V-oc, short circuit current density, j(sc), and maximum power produced by the biofuel cell, P-max, were found as 0.36 V, 1.3 mA cm(-2) and 182 mu W, respectively. The voltage produced by the biofuel cell was amplified with an energy harvesting circuit and applied to a wireless transmitter. The present study continues the research line where different implantable biofuel cells are used for activation of electronic devices

Activation of a Biocatalytic Electrode by Removing Glucose Oxidase from the SurfaceApplication to Signal Triggered Drug Release

A biocatalytic electrode activated by pH signals was prepared with a multilayered nanostructured interface including PQQ-dependent glucose dehydrogenase (PQQ-GDH) directly associated with the conducting support and glucose oxidase (GOx) located on the external interface. GOx was immobilized through a pH-signal-cleavable linker composed of an iminobiotin/avidin complex. In the presence of GOx, glucose was intercepted at the external interface and biocatalytically oxidized without current generation, thus keeping the electrode in its nonactive state. When the pH value was lowered from pH 7.5 to 4.5 the iminobiotin/avidin complex was cleaved and GOx was removed from the interface allowing glucose penetration to the electrode surface where it was oxidized by PQQ-GDH yielding a bioelectrocatalytic current, thus switching the electrode to its active state. This process was used to trigger a drug-mimicking release process from another connected electrode. Furthermore, the pH-switchable electrode can be activated by biochemical signals logically processed by biocatalytic systems mimicking various Boolean gates. Therefore, the developed switchable electrode can interface biomolecular computing/sensing systems with drug-release processes