Programming the dynamics of biochemical reaction networks

Synthesis, Modulation, and Application of Two-Dimensional TMD Heterostructures

Two-dimensional (2D) transition metal dichalcogenide (TMD) heterostructures have attracted a lot of attention due to their rich material diversity and stack geometry, precise controllability of structure and properties, and potential practical applications. These heterostructures not only overcome the inherent limitations of individual materials but also enable the realization of new properties through appropriate combinations, establishing a platform to explore new physical and chemical properties at micro-nano-pico scales. In this review, we systematically summarize the latest research progress in the synthesis, modulation, and application of 2D TMD heterostructures. We first introduce the latest techniques for fabricating 2D TMD heterostructures, examining the rationale, mechanisms, advantages, and disadvantages of each strategy. Furthermore, we emphasize the importance of characteristic modulation in 2D TMD heterostructures and discuss some approaches to achieve novel functionalities. Then, we summarize the representative applications of 2D TMD heterostructures. Finally, we highlight the challenges and future perspectives in the synthesis and device fabrication of 2D TMD heterostructures and provide some feasible solutions.

Recent Advances in DNA Nanomaterials

Applications of DNA-containing nanomaterials (DNA-NMs) in science and technology are currently attracting increasing attention in the fields of medicine, environment, engineering, etc. Such objects have become important for various branches of science and industries due to their outstanding characteristics such as small size, high controllability, clustering actions, and strong permeability. For these reasons, DNA-NMs deserve a review with respect to their recent advancements. On the other hand, precise cluster control, targeted drug distribution in vivo, and cellular micro-nano operation remain as problems. This review summarizes the recent progress in DNA-NMs and their crossover and integration into multiple disciplines (including in vivo/in vitro, microcircles excisions, and plasmid oligomers). We hope that this review will motivate relevant practitioners to generate new research perspectives and boost the advancement of nanomanipulation.

Manipulating Enzymes Properties with DNA Nanostructures

Nucleic acids and proteins are two major classes of biopolymers in living systems. Whereas nucleic acids are characterized by robust molecular recognition properties, essential for the reliable storage and transmission of the genetic information, the variability of structures displayed by proteins and their adaptability to the environment make them ideal functional materials. One of the major goals of DNA nanotechnology-and indeed its initial motivation-is to bridge these two worlds in a rational fashion. Combining the predictable base-pairing rule of DNA with chemical conjugation strategies and modern protein engineering methods has enabled the realization of complex DNA-protein architectures with programmable structural features and intriguing functionalities. In this review, we will focus on a special class of biohybrid structures, characterized by one or many enzyme molecules linked to a DNA scaffold with nanometer-scale precision. After an initial survey of the most important methods for coupling DNA oligomers to proteins, we will report the strategies adopted until now for organizing these conjugates in a predictable spatial arrangement. The major focus of this review will be on the consequences of such manipulations on the binding and kinetic properties of single enzymes and enzyme complexes: an interesting aspect of artificial DNA-enzyme hybrids, often reported in the literature, however, not yet entirely understood and whose full comprehension may open the way to new opportunities in protein science.

Efficient and Layer-Dependent Exciton Pumping across Atomically Thin Organic-Inorganic Type-I Heterostructures

The fundamental light-matter interactions in monolayer transition metal dichalcogenides might be significantly engineered by hybridization with their organic counterparts, enabling intriguing optoelectronic applications. Here, atomically thin organic-inorganic (O-I) heterostructures, comprising monolayer MoSe2 and mono-/few-layer single-crystal pentacene samples, are fabricated. These heterostructures show type-I band alignments, allowing efficient and layer-dependent exciton pumping across the O-I interfaces. The interfacial exciton pumping has much higher efficiency (>86 times) than the photoexcitation process in MoSe2 , although the pentacene layer has much lower optical absorption than MoSe2 . This highly enhanced pumping efficiency is attributed to the high quantum yield in pentacene and the ultrafast energy transfer between the O-I interface. Furthermore, those organic counterparts significantly modulate the bindings of charged excitons in monolayer MoSe2 via their precise dielectric environment engineering. The results open new avenues for exploring fundamental phenomena and novel optoelectronic applications using atomically thin O-I heterostructures.

Continuous variables logic via coupled automata using a DNAzyme cascade with feedback

The concentration of molecules can be changed by chemical reactions and thereby offer a continuous readout. Yet computer architecture is cast in textbooks in terms of binary valued, Boolean variables. To enable reactive chemical systems to compute we show how, using the Cox interpretation of probability theory, one can transcribe the equations of chemical kinetics as a sequence of coupled logic gates operating on continuous variables. It is discussed how the distinct chemical identity of a molecule allows us to create a common language for chemical kinetics and Boolean logic. Specifically, the logic AND operation is shown to be equivalent to a bimolecular process. The logic XOR operation represents chemical processes that take place concurrently. The values of the rate constants enter the logic scheme as inputs. By designing a reaction scheme with a feedback we endow the logic gates with a built in memory because their output then depends on the input and also on the present state of the system. Technically such a logic machine is an automaton. We report an experimental realization of three such coupled automata using a DNAzyme multilayer signaling cascade. A simple model verifies analytically that our experimental scheme provides an integrator generating a power series that is third order in time. The model identifies two parameters that govern the kinetics and shows how the initial concentrations of the substrates are the coefficients in the power series.

Stacking modular DNA circuitry in cascading self-assembly of spherical nucleic acids

Integrated circuitries are successfully built through using the cascaded modular strategy with the assistance of stochastic simulations.

A cascade reaction network mimicking the basic functional steps of adaptive immune response

Biological systems use complex ‘information-processing cores’ composed of molecular networks to coordinate their external environment and internal states. An example of this is the acquired, or adaptive, immune system (AIS), which is composed of both humoral and cell-mediated components. Here we report the step-by-step construction of a prototype mimic of the AIS that we call an adaptive immune response simulator (AIRS). DNA and enzymes are used as simple artificial analogues of the components of the AIS to create a system that responds to specific molecular stimuli in vitro. We show that this network of reactions can function in a manner that is superficially similar to the most basic responses of the vertebrate AIS, including reaction sequences that mimic both humoral and cellular responses. As such, AIRS provides guidelines for the design and engineering of artificial reaction networks and molecular devices.

A cascade reaction network has been created that can function in a manner that is superficially similar to the most basic steps of the vertebrate adaptive immune response. This reaction network uses DNA and enzymes as simple artificial analogues of the components of the acquired immune system.

Real-time monitoring of enzyme-free strand displacement cascades by colorimetric assays

The enzyme-free toehold-mediated strand displacement reaction has shown potential for building programmable DNA circuits, biosensors, molecular machines and chemical reaction networks. Here we report a simple colorimetric method using gold nanoparticles as signal generators for the real-time detection of the product of the strand displacement cascade. During the process the assembled gold nanoparticles can be separated, resulting in a color change of the solution. This assay can also be applied in complex mixtures, fetal bovine serum, and to detect single-base mismatches. These results suggest that this method could be of general utility to monitor more complex enzyme-free strand displacement reaction-based programmable systems or for further low-cost diagnostic applications.