Rapid engineering of versatile molecular logic gates using heterologous genetic transcriptional modules.
Ontology highlight
ABSTRACT:
SUBMITTER: Wang B
PROVIDER: S-EPMC4185417 | biostudies-literature | 2014 Oct
REPOSITORIES: biostudies-literature
Publications
Rapid engineering of versatile molecular logic gates using heterologous genetic transcriptional modules.
Chemical communications (Cambridge, England) 20141001 79
We designed and constructed versatile modular genetic logic gates in bacterial cells. These function as digital logic 1-input Buffer gate, 2-input and 3-input AND gates with one inverted input and integrate multiple chemical input signals in customised logic manners. Such rapidly engineered devices serve to achieve increased sensing signal selectivity. ...[more]
Similar Datasets
Project description:This paper proposes the use of astrocytes to realize Boolean logic gates, through manipulation of the threshold of [Formula: see text] ion flows between the cells based on the input signals. Through wet-lab experiments that engineer the astrocytes cells with pcDNA3.1-hGPR17 genes as well as chemical compounds, we show that both AND and OR gates can be implemented by controlling [Formula: see text] signals that flow through the population. A reinforced learning platform is also presented in the paper to optimize the [Formula: see text] activated level and time slot of input signals [Formula: see text] into the gate. This design platform caters for any size and connectivity of the cell population, by taking into consideration the delay and noise produced from the signalling between the cells. To validate the effectiveness of the reinforced learning platform, a [Formula: see text] signalling simulator was used to simulate the signalling between the astrocyte cells. The results from the simulation show that an optimum value for both the [Formula: see text] activated level and time slot of input signals [Formula: see text] is required to achieve up to 90% accuracy for both the AND and OR gates. Our method can be used as the basis for future Neural-Molecular Computing chips, constructed from engineered astrocyte cells, which can form the basis for a new generation of brain implants.
| S-EPMC7803753 | biostudies-literature
Project description:Modular and orthogonal genetic logic gates are essential for building robust biologically based digital devices to customize cell signalling in synthetic biology. Here we constructed an orthogonal AND gate in Escherichia coli using a novel hetero-regulation module from Pseudomonas syringae. The device comprises two co-activating genes hrpR and hrpS controlled by separate promoter inputs, and a σ(54)-dependent hrpL promoter driving the output. The hrpL promoter is activated only when both genes are expressed, generating digital-like AND integration behaviour. The AND gate is demonstrated to be modular by applying new regulated promoters to the inputs, and connecting the output to a NOT gate module to produce a combinatorial NAND gate. The circuits were assembled using a parts-based engineering approach of quantitative characterization, modelling, followed by construction and testing. The results show that new genetic logic devices can be engineered predictably from novel native orthogonal biological control elements using quantitatively in-context characterized parts.
| S-EPMC3207208 | biostudies-literature
Project description:Small molecule metabolites and their allosterically regulated repressors play an important role in many gene expression and metabolic disorder processes. These natural sensors, though valuable as good logic switches, have rarely been employed without transcription machinery in cells. Here, two pairs of repressors, which function in opposite ways, were cloned, purified and used to control DNA replication in rolling circle amplification (RCA) in vitro. By using metabolites and repressors as inputs, RCA signals as outputs, four basic logic modules were constructed successfully. To achieve various logic computations based on these basic modules, we designed series and parallel strategies of circular templates, which can further assemble these repressor modules in an RCA platform to realize twelve two-input Boolean logic gates and a three-input logic gate. The RCA-output and RCA-assembled platform was proved to be easy and flexible for complex logic processes and might have application potential in molecular computing and synthetic biology.
| S-EPMC5116584 | biostudies-literature
Project description:Molecular logic gates (MLGs) are compounds that can solve Boolean logic operations to give an answer (OUTPUT) upon receiving a stimulus (INPUT). These derivatives can be used as biological sensors and are promising substitutes for the present logic gates. Although MLGs with complex molecular structures have been reported, they often show stability problems. To address this problem, we describe herein six stable pseudo-hemiindigo-derived MLGs capable of solving complex logic operations. MLGs 7, 8, 9, and 10 can solve a complex logic operation connecting 4 logic gates using 2 different wavelengths (445 nm and 400 nm) and the presence of p-TsOH and triethylamine (TEA) as inputs; MLG 11 solves a complex logic operation connecting 3 logic gates and uses 3 inputs, one wavelength of 445 nm and the presence of p-TsOH and TEA; and MLG 12 can only solve one logic operation (INH) and uses only the presence of p-TsOH and TEA as an input. Each operating method of the MLGs was evaluated with several techniques; proton interactions with MLGs were screened with NMR by titrating with p-TsOH, the photochemical properties were examined with absorption ultraviolet-visible (UV-Vis) spectroscopy, and the isomerization dynamics were examined with NMR using the two wavelengths for isomerization (photostationary isomer). The results indicate that the pseudo-hemiindigo-derived MLGs described herein can be applied as multiplexers or data selectors that are necessary for the transient flow of information for biological and computer systems. Finally, to design different MLGs and a system that can treat more information as complex logic gates (demultiplexers), two and three MLGs were mixed in different experiments. In both cases, four inputs were employed (445 nm, 400 nm, p-TsOH and TEA), yielding more outputs. Detailed information about the system dynamics was obtained from NMR experiments.
| S-EPMC9034006 | biostudies-literature
Project description:One limit on developing complex synthetic gene circuits is the lack of basic components such as transcriptional logic gates that can process combinatorial inputs. Here, we propose a strategy to construct such components based on reusable designs and convergent reengineering of well-studied natural systems. We demonstrated the strategy using variants of the transcription factor (TF) LacI and operator Olac that form specifically interacting pairs. Guided by a mathematical model derived from existing quantitative knowledge, rational designs of transcriptional NAND, NOR and NOT gates have been realized. The NAND gates have been designed based on direct protein-protein interactions in coupling with DNA looping. We demonstrated that the designs are reusable: a multiplex of logic devices can be readily created using the same designs but different combinations of sequence variants. The designed logic gates are combinable to form compound circuits: a demonstration logic circuit containing all three types of designed logic gates has been synthesized, and the circuit truthfully reproduces the pre-designed input-output logic relations.
| S-EPMC2925522 | biostudies-literature
Project description:The widespread natural ability of RNA to sense small molecules and regulate genes has become an important tool for synthetic biology in applications as diverse as environmental sensing and metabolic engineering. Previous work in RNA synthetic biology has engineered RNA mechanisms that independently regulate multiple targets and integrate regulatory signals. However, intracellular regulatory networks built with these systems have required proteins to propagate regulatory signals. In this work, we remove this requirement and expand the RNA synthetic biology toolkit by engineering three unique features of the plasmid pT181 antisense-RNA-mediated transcription attenuation mechanism. First, because the antisense RNA mechanism relies on RNA-RNA interactions, we show how the specificity of the natural system can be engineered to create variants that independently regulate multiple targets in the same cell. Second, because the pT181 mechanism controls transcription, we show how independently acting variants can be configured in tandem to integrate regulatory signals and perform genetic logic. Finally, because both the input and output of the attenuator is RNA, we show how these variants can be configured to directly propagate RNA regulatory signals by constructing an RNA-meditated transcriptional cascade. The combination of these three features within a single RNA-based regulatory mechanism has the potential to simplify the design and construction of genetic networks by directly propagating signals as RNA molecules.
| S-EPMC3102349 | biostudies-literature
Project description:The ever-growing demand for faster and more efficient data transfer and processing has brought optical computation strategies to the forefront of research in next-generation computing. Here, we report a universal computing approach with the chirality degree of freedom. By exploiting the crystal symmetry-enabled well-known chiral selection rules, we demonstrate the viability of the concept in bulk silica crystals and atomically thin semiconductors and create ultrafast (<100-fs) all-optical chirality logic gates (XNOR, NOR, AND, XOR, OR, and NAND) and a half adder. We also validate the unique advantages of chirality gates by realizing multiple gates with simultaneous operation in a single device and electrical control. Our first demonstrations of logic gates using chiral selection rules suggest that optical chirality could provide a powerful degree of freedom for future optical computing.
| S-EPMC9733934 | biostudies-literature
Project description:A nucleic acid-based constitutional dynamic network (CDN) is introduced as a single computational module that, in the presence of different sets of inputs, operates a variety of logic gates including a half adder, 2 : 1 multiplexer and 1 : 2 demultiplexer, a ternary multiplication matrix and a cascaded logic circuit. The CDN-based computational module leads to four logically equivalent outputs for each of the logic operations. Beyond the significance of the four logically equivalent outputs in establishing reliable and robust readout signals of the computational module, each of the outputs may be fanned out, in the presence of different inputs, to a set of different logic circuits. In addition, the ability to intercommunicate constitutional dynamic networks (CDNs) and to construct DNA-based CDNs of higher complexity provides versatile means to design computing circuits of enhanced complexity.
| S-EPMC8179666 | biostudies-literature
Project description:Genetic programs function to integrate environmental sensors, implement signal processing algorithms and control expression dynamics. These programs consist of integrated genetic circuits that individually implement operations ranging from digital logic to dynamic circuits, and they have been used in various cellular engineering applications, including the implementation of process control in metabolic networks and the coordination of spatial differentiation in artificial tissues. A key limitation is that the circuits are based on biochemical interactions occurring in the confined volume of the cell, so the size of programs has been limited to a few circuits. Here we apply part mining and directed evolution to build a set of transcriptional AND gates in Escherichia coli. Each AND gate integrates two promoter inputs and controls one promoter output. This allows the gates to be layered by having the output promoter of an upstream circuit serve as the input promoter for a downstream circuit. Each gate consists of a transcription factor that requires a second chaperone protein to activate the output promoter. Multiple activator-chaperone pairs are identified from type?III secretion pathways in different strains of bacteria. Directed evolution is applied to increase the dynamic range and orthogonality of the circuits. These gates are connected in different permutations to form programs, the largest of which is a 4-input AND gate that consists of 3 circuits that integrate 4 inducible systems, thus requiring 11 regulatory proteins. Measuring the performance of individual gates is sufficient to capture the behaviour of the complete program. Errors in the output due to delays (faults), a common problem for layered circuits, are not observed. This work demonstrates the successful layering of orthogonal logic gates, a design strategy that could enable the construction of large, integrated circuits in single cells.
| S-EPMC3904217 | biostudies-literature
Project description:Individual molecules have been demonstrated to exhibit promising applications as functional components in the fabrication of computing nanocircuits. Based on their advantage in chemical tailorability, many molecular devices with advanced electronic functions have been developed, which can be further modulated by the introduction of external stimuli. Here, orthogonally modulated molecular transport junctions are achieved via chemically fabricated nanogaps functionalized with dithienylethene units bearing organometallic ruthenium fragments. The addressable and stepwise control of molecular isomerization can be repeatedly and reversibly completed with a judicious use of the orthogonal optical and electrochemical stimuli to reach the controllable switching of conductivity between two distinct states. These photo-/electro-cooperative nanodevices can be applied as resettable electronic logic gates for Boolean computing, such as a two-input OR and a three-input AND-OR. The proof-of-concept of such logic gates demonstrates the possibility to develop multifunctional molecular devices by rational chemical design.
| S-EPMC3896775 | biostudies-literature