Construction of integrated gene logic-chip

Strategies to Reduce Promoter-Independent Transcription of DNA Nanostructures and Strand Displacement Complexes

Bacteriophage RNA polymerases, in particular T7 RNA polymerase (RNAP), are well-characterized and popular enzymes for many RNA applications in biotechnology both in vitro and in cellular settings. These monomeric polymerases are relatively inexpensive and have high transcription rates and processivity to quickly produce large quantities of RNA. T7 RNAP also has high promoter-specificity on double-stranded DNA (dsDNA) such that it only initiates transcription downstream of its 17-base promoter site on dsDNA templates. However, there are many promoter-independent T7 RNAP transcription reactions involving transcription initiation in regions of single-stranded DNA (ssDNA) that have been reported and characterized. These promoter-independent transcription reactions are important to consider when using T7 RNAP transcriptional systems for DNA nanotechnology and DNA computing applications, in which ssDNA domains often stabilize, organize, and functionalize DNA nanostructures and facilitate strand displacement reactions. Here we review the existing literature on promoter-independent transcription by bacteriophage RNA polymerases with a specific focus on T7 RNAP, and provide examples of how promoter-independent reactions can disrupt the functionality of DNA strand displacement circuit components and alter the stability and functionality of DNA-based materials. We then highlight design strategies for DNA nanotechnology applications that can mitigate the effects of promoter-independent T7 RNAP transcription. The design strategies we present should have an immediate impact by increasing the rate of success of using T7 RNAP for applications in DNA nanotechnology and DNA computing.

Organ-Specific Gene Expression Control Using DNA Origami-Based Nanodevices

Nanodevices that function in specific organs or cells are one of the ultimate goals of synthetic biology. The recent progress in DNA nanotechnology such as DNA origami has allowed us to construct nanodevices to deliver a payload (e.g., drug) to the tumor. However, delivery to specific organs remains difficult due to the fragility of the DNA nanostructure and the low targeting capability of the DNA nanostructure. Here, we constructed tough DNA origami that allowed us to encapsulate the DNA origami into lipid-based nanoparticles (LNPs) under harsh conditions (low pH), harnessing organ-specific delivery of the gene of interest (GOI). We found that DNA origami-encapsulated LNPs can increase the functionality of payload GOIs (mRNA and siRNA) inside mouse organs through the contribution from different LNP structures revealed by cryogenic electron microscope (Cryo-EM). These data should be the basis for future organ-specific gene expression control using DNA origami nanodevices.

DNA Origami: From Molecular Folding Art to Drug Delivery Technology

DNA molecules that store genetic information in living creatures can be repurposed as building blocks to construct artificial architectures, ranging from the nanoscale to the microscale. The precise fabrication of self-assembled DNA nanomaterials and their various applications have greatly impacted nanoscience and nanotechnology. More specifically, the DNA origami technique has realized the assembly of various nanostructures featuring rationally predesigned geometries, precise addressability, and versatile programmability, as well as remarkable biocompatibility. These features have elevated DNA origami from academic interest to an emerging class of drug delivery platform for a wide range of diseases. In this minireview, the latest advances in the burgeoning field of DNA-origami-based innovative platforms for regulating biological functions and delivering versatile drugs are presented. Challenges regarding the novel drug vehicle's safety, stability, targeting strategy, and future clinical translation are also discussed.

Size-Selective Capturing of Exosomes Using DNA Tripods

Fractionating and characterizing target samples are fundamental to the analysis of biomolecules. Extracellular vesicles (EVs), containing information regarding the cellular birthplace, are promising targets for biology and medicine. However, the requirement for multiple-step purification in conventional methods hinders analysis of small samples. Here, we apply a DNA origami tripod with a defined aperture of binders (e.g., antibodies against EV biomarkers), which allows us to capture the target molecule. Using exosomes as a model, we show that our tripod nanodevice can capture a specific size range of EVs with cognate biomarkers from a broad distribution of crude EV mixtures. We further demonstrate that the size of captured EVs can be controlled by changing the aperture of the tripods. This simultaneous selection with the size and biomarker approach should simplify the EV purification process and contribute to the precise analysis of target biomolecules from small samples.

Chemically Conjugated Branched Staples for Super-DNA Origami

DNA origami, comprising a long folded DNA scaffold and hundreds of linear DNA staple strands, has been developed to construct various sophisticated structures, smart devices, and drug delivery systems. However, the size and diversity of DNA origami are usually constrained by the length of DNA scaffolds themselves. Herein, we report a new paradigm of scaling up DNA origami assembly by introducing a novel branched staple concept. Owing to their covalent characteristics, the chemically conjugated branched DNA staples we describe here can be directly added to a typical DNA origami assembly system to obtain super-DNA origami with a predefined number of origami tiles in one pot. Compared with the traditional two-step coassembly system (yields <10%), a much greater yield (>80%) was achieved using this one-pot strategy. The diverse superhybrid DNA origami with the combination of different origami tiles can be also efficiently obtained by the hybrid branched staples. Furthermore, the branched staples can be successfully employed as the effective molecular glues to stabilize micrometer-scale, super-DNA origami arrays (e.g., 10 × 10 array of square origami) in high yields, paving the way to bridge the nanoscale precision of DNA origami with the micrometer-scale device engineering. This rationally developed assembly strategy for super-DNA origami based on chemically conjugated branched staples presents a new avenue for the development of multifunctional DNA origami-based materials.

Programming and monitoring surface-confined DNA computing

DNA-based molecular computing has evolved to encompass a diverse range of functions, demonstrating substantial promise for both highly parallel computing and various biomedical applications. Recent advances in DNA computing systems based on surface reactions have demonstrated improved levels of specificity and computational speed compared to their solution-based counterparts that depend on three-dimensional molecular collisions. Herein, computational biomolecular interactions confined by various surfaces such as DNA origamis, nanoparticles, lipid membranes and chips are systematically reviewed, along with their manipulation methodologies. Monitoring techniques and applications for these surface-based computing systems are also described. The advantages and challenges of surface-confined DNA computing are discussed.

A genetic circuit on a single DNA molecule as an autonomous dissipative nanodevice

Realizing genetic circuits on single DNA molecules as self-encoded dissipative nanodevices is a major step toward miniaturization of autonomous biological systems. A circuit operating on a single DNA implies that genetically encoded proteins localize during coupled transcription-translation to DNA, but a single-molecule measurement demonstrating this has remained a challenge. Here, we use a genetically encoded fluorescent reporter system with improved temporal resolution and observe the synthesis of individual proteins tethered to a DNA molecule by transient complexes of RNA polymerase, messenger RNA, and ribosome. Against expectations in dilute cell-free conditions where equilibrium considerations favor dispersion, these nascent proteins linger long enough to regulate cascaded reactions on the same DNA. We rationally design a pulsatile genetic circuit by encoding an activator and repressor in feedback on the same DNA molecule. Driven by the local synthesis of only several proteins per hour and gene, the circuit dynamics exhibit enhanced variability between individual DNA molecules, and fluctuations with a broad power spectrum. Our results demonstrate that co-expressional localization, as a nonequilibrium process, facilitates single-DNA genetic circuits as dissipative nanodevices, with implications for nanobiotechnology applications and artificial cell design.

Modularized synthetic biology enabled intelligent biosensors

Biosensors that sense the concentration of a specified target and produce a specific signal output have become important technology for biological analysis. Recently, intelligent biosensors have received great interest due to their adaptability to meet sophisticated demands. Advances in developing standard modules and carriers in synthetic biology have shed light on intelligent biosensors that can implement advanced analytical processing to better accommodate practical applications. This review focuses on intelligent synthetic biology-enabled biosensors (SBBs). First, we illustrate recent progress in intelligent SBBs with the capability of computation, memory storage, and self-calibration. Then, we discuss emerging applications of SBBs in point-of-care testing (POCT) and wearable monitoring. Finally, future perspectives on intelligent SBBs are proposed.

Evaluating the effect of two-dimensional molecular layout on DNA origami-based transporters

Cellular transport systems are sophisticated and efficient. Hence, one of the ultimate goals of nanotechnology is to design artificial transport systems rationally. However, the design principle has been elusive, because how motor layout affects motile activity has not been established, partially owing to the difficulty in achieving a precise layout of the motile elements. Here, we employed a DNA origami platform to evaluate the two-dimensional (2D) layout effect of kinesin motor proteins on transporter motility. We succeeded in accelerating the integration speed of the protein of interest (POI) to the DNA origami transporter by up to 700 times by introducing a positively charged poly-lysine tag (Lys-tag) into the POI (kinesin motor protein). This Lys-tag approach allowed us to construct and purify a transporter with high motor density, allowing a precise evaluation on the 2D layout effect. Our single-molecule imaging showed that the densely packed layout of kinesin decreased the run length of the transporter, although its velocity was moderately affected. These results indicate that steric hindrance is a critical parameter to be considered in the design of transport systems.

Recent Advances in DNA Origami-Engineered Nanomaterials and Applications

DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.

Functionalizing DNA origami to investigate and interact with biological systems

DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophysical studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromolecular cargos. Here, we review methods developed to functionalize, purify, and characterize DNA origami nanostructures. We identify remaining challenges, such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.

Three-dimensional electron ptychography of organic-inorganic hybrid nanostructures

Three dimensional scaffolded DNA origami with inorganic nanoparticles has been used to create tailored multidimensional nanostructures. However, the image contrast of DNA is poorer than those of the heavy nanoparticles in conventional transmission electron microscopy at high defocus so that the biological and non-biological components in 3D scaffolds cannot be simultaneously resolved using tomography of samples in a native state. We demonstrate the use of electron ptychography to recover high contrast phase information from all components in a DNA origami scaffold without staining. We further quantitatively evaluate the enhancement of contrast in comparison with conventional transmission electron microscopy. In addition, We show that for ptychography post-reconstruction focusing simplifies the workflow and reduces electron dose and beam damage.

The authors demonstrate electron ptychographic computed tomography by simultaneously recording high contrast data from both the organic- and inorganic components in a 3D DNA-origami framework hybrid nanostructure.

Oscillatory movement of a dynein-microtubule complex crosslinked with DNA origami

Bending of cilia and flagella occurs when axonemal dynein molecules on one side of the axoneme produce force and move toward the microtubule (MT) minus end. These dyneins are then pulled back when the axoneme bends in the other direction, meaning oscillatory back and forth movement of dynein during repetitive bending of cilia/flagella. There are various factors that may regulate the dynein activity, e.g. the nexin-dynein regulatory complex, radial spokes, and central apparatus. In order to understand the basic mechanism of dynein’s oscillatory movement, we constructed a simple model system composed of MTs, outer-arm dyneins, and crosslinks between the MTs made of DNA origami. Electron microscopy (EM) showed pairs of parallel MTs crossbridged by patches of regularly arranged dynein molecules bound in two different orientations, depending on which of the MTs their tails bind to. The oppositely oriented dyneins are expected to produce opposing forces when the pair of MTs have the same polarity. Optical trapping experiments showed that the dynein-MT-DNA-origami complex actually oscillates back and forth after photolysis of caged ATP. Intriguingly, the complex, when held at one end, showed repetitive bending motions. The results show that a simple system composed of ensembles of oppositely oriented dyneins, MTs, and inter-MT crosslinkers, without any additional regulatory structures, has an intrinsic ability to cause oscillation and repetitive bending motions.

DNA nanotechnology-empowered finite state machines

A finite state machine (FSM, or automaton) is an abstract machine that can switch among a finite number of states in response to temporally ordered inputs, which allows storage and processing of information in an order-sensitive manner. In recent decades, DNA molecules have been actively exploited to develop information storage and nanoengineering materials, which hold great promise for smart nanodevices and nanorobotics under the framework of FSM. In this review, we summarize recent progress in utilizing DNA self-assembly and DNA nanostructures to implement FSMs. We describe basic principles for representative DNA FSM prototypes and highlight their advantages and potential in diverse applications. The challenges in this field and future directions have also been discussed.

A localized DNA finite-state machine with temporal resolution

The identity and timing of environmental stimulus play a pivotal role in living organisms in programming their signaling networks and developing specific phenotypes. The ability to unveil history-dependent signals will advance our understanding of temporally regulated biological processes. Here, we have developed a two-input, five-state DNA finite-state machine (FSM) to sense and record the temporally ordered inputs. The spatial organization of the processing units on DNA origami enables facile modulation of the energy landscape of DNA strand displacement reactions, allowing precise control of the reactions along predefined paths for different input orders. The use of spatial constraints brings about a simple, modular design for the FSM with a minimum set of orthogonal components and confers minimized leaky reactions and fast kinetics. The FSM demonstrates the capability of sensing the temporal orders of two microRNAs, highlighting its potential for temporally resolved biosensing and smart therapeutics.

Revisiting the Glass Treatment for Single-Molecule Analysis of ncRNA Function

Single-molecule imaging is a powerful method for unveiling precise molecular mechanisms. Particularly, single-molecule analysis with total internal reflection fluorescence (TIRF ) microscopy has been successfully applied to the characterization of molecular mechanisms in ncRNA studies. Tracing interactions at the single-molecule level have elucidated the intermediate states of the reaction, which are hidden by ensemble averaging in combinational biochemical approaches, and clarified the key steps of the interaction. However, applying a single-molecule technique to ncRNA analysis still remains a challenge, requiring laborious trial and error to identify a suitable glass surface passivation method. In this chapter, we revisit the major glass surface passivation methods using polyethylene glycol (PEG) treatment and summarize a detailed protocol for single-molecule analysis of the dicing process of Dcr-2, which may apply piRNA studies in the future.

DNA origami-based protein networks: from basic construction to emerging applications

Natural living systems are driven by delicate protein networks whose functions are precisely controlled by many parameters, such as number, distance, orientation, and position. Focusing on regulation rather than just imitation, the construction of artificial protein networks is important in many research areas, including biomedicine, synthetic biology and chemical biology. DNA origami, sophisticated nanostructures with rational design, can offer predictable, programmable, and addressable scaffolds for protein assembly with nanometer precision. Recently, many interdisciplinary efforts have achieved the precise construction of DNA origami-based protein networks, and their emerging application in many areas. To inspire more fantastic research and applications, herein we highlight the applicability and potentiality of DNA origami-based protein networks. After a brief introduction to the development and features of DNA origami, some important factors for the precise construction of DNA origami-based protein networks are discussed, including protein-DNA conjugation methods, networks with different patterns and the controllable parameters in the networks. The discussion then focuses on the emerging application of DNA origami-based protein networks in several areas, including enzymatic reaction regulation, sensing, bionics, biophysics, and biomedicine. Finally, current challenges and opportunities in this research field are discussed.

A strategy for programming the regulation of in vitro transcription with application in molecular circuits

In vitro transcription is a convenient platform for fabricating nanodevices and has been used for assembling synthetic networks. However, it remains challenging to regulate synthetic cell-free in vitro transcription by multiple stimuli in a simple and programmable way. We proposed a strategy to regulate in vitro transcription by controlling the transcription templates' promoter domain via variable DNA inputs. To demonstrate the utility of this strategy, various logic circuits and cascading circuits were implemented. With the advantage of simplicity, modularity, programmability, and extensibility, the proposed strategy has potential in biocomputing, bioanalytical, and therapeutic applications.

[Analysis and Discovery of Functional Biomolecules Using a Combination of Fluorescence Microscopy and Micro- and Nano-devices for Single-molecule Detection]

The author has developed several methodological approaches that use nanophotonic and microfluidic devices to accelerate pharmaceutical research and development. Here, the author describes two of these approaches and provides practical examples. The first is a nanophotonic approach to break the concentration limit of diffusing fluorophore-labeled molecules in single-molecule imaging. Although single-molecule imaging is highly useful in characterizing the kinetics of biomolecular interactions, it requires nanomolar concentrations of labeled molecules in solution. Zero-mode waveguides are nanophotonic structures that reduce the illumination volume by more than three orders of magnitude relative to conventional fluorescence microscopy, thereby allowing single-molecule investigations at micromolar to millimolar concentrations of fluorescent molecules i.e., under near-physiological conditions. The second approach is microfluidic microdroplet-based, allowing the discovery of novel biomolecules with the desired activities. Microfluidics allows the ultrarapid production of monodisperse microdroplets such as water-in-oil microdroplets. Each microdroplet serves as a nano/picoliter-volume test tube, which increases assay sensitivity by increasing the effective concentration of molecules and decreasing the time required to reach detection thresholds. I hope you find this review helpful in your research.

Recent Advances in Liposome-Based Molecular Robots

A molecular robot is a microorganism-imitating micro robot that is designed from the molecular level and constructed by bottom-up approaches. As with conventional robots, molecular robots consist of three essential robotics elements: control of intelligent systems, sensors, and actuators, all integrated into a single micro compartment. Due to recent developments in microfluidic technologies, DNA nanotechnologies, synthetic biology, and molecular engineering, these individual parts have been developed, with the final picture beginning to come together. In this review, we describe recent developments of these sensors, actuators, and intelligence systems that can be applied to liposome-based molecular robots. First, we explain liposome generation for the compartments of molecular robots. Next, we discuss the emergence of robotics functions by using and functionalizing liposomal membranes. Then, we discuss actuators and intelligence via the encapsulation of chemicals into liposomes. Finally, the future vision and the challenges of molecular robots are described.

DNA density-dependent uptake of DNA origami-based two-or three-dimensional nanostructures by immune cells

DNA nanostructures are expected to be applied for targeted drug delivery to immune cells. However, the structural properties of DNA nanostructures required for the delivery have not fully been elucidated. In this study, we focused on the DNA density that can be important for the their recognition and uptake by immune cells. To examine this, DNA nanostructures with almost identical molecular weights and structural flexibility, but with different shapes and DNA densities, were designed using DNA origami technology. We compared the following five types of DNA nanostructures, all of which consisted of ten DNA helices using an identical circular, single-stranded scaffold and staples. Rec180 had a rectangular-shaped, almost flat structure. Rec90, Rec50 and Rec0 were bent forms of Rec180 at the center by 90, 50 or 0 degrees, respectively. Rec50/50 has two bends of 50 degrees each so that the both ends stick together to form a triangular prism shape. The fluctuation, or flexibility, of these DNA nanostructures under solution conditions was estimated using CanDo software. The DNA density estimated from the average distance between any two of the ten DNA helices in the DNA nanostructures was different among them; Rec50, Rec0 and Rec50/50 had a higher density than Rec180 and Rec90. Agarose gel electrophoresis and atomic force microscopy showed that all of the nanostructures were prepared with high yield. Flow cytometry analysis revealed that the uptake of DNA nanostructures by murine macrophage-like RAW264.7 cells was higher for those with higher DNA density than those with low density. There was a positive correlation between the density and cellular uptake. These results indicate that DNA nanostructures with high DNA density are suitable for delivery to immune cells.

Extrusion of RNA from a DNA-Origami-Based Nanofactory

Cells often spatially organize biomolecules to regulate biological interactions. Synthetic mimicry of complex spatial organization may provide a route to similar levels of control for artificial systems. As a proof-of-principle, we constructed an RNA-extruding nanofactory using a DNA-origami barrel with an outer diameter of 60 nm as a chassis for integrated rolling-circle transcription and processing of RNA through spatial organization of DNA templates, RNA polymerases, and RNA endonucleases. The incorporation efficiency of molecular components was quantified to be roughly 50% on designed sites within the DNA-origami chassis. Each integrated nanofactory with RNA-producing units, composed of DNA templates and RNA polymerases, produced 100 copies of target RNA in 30 min on average. Further integration of RNA endonucleases that cleave rolling-circle transcripts from concatemers into monomers resulted in 30% processing efficiency. Disabling spatial organization of molecular components on DNA origami resulted in suppression of RNA production as well as processing.

Near-Atomic Fabrication with Nucleic Acids

Nucleic acids hold great promise for bottom-up construction of nanostructures via programmable self-assembly. Especially, the emerging of advanced sequence design principles and the maturation of chemical synthesis of nucleic acids together have led to the rapid development of structural DNA/RNA nanotechnology. Diverse nucleic acids-based nano objects and patterns have been constructed with near-atomic resolutions and with controllable sizes and geometries. The monodispersed distribution of objects, the up-to-submillimeter scalability of patterns, and the excellent feasibility of carrying other materials with spatial and temporal resolutions have made DNA/RNA assemblies extremely unique in molecular engineering. In this review, we summarize recent advances in nucleic acids-based (mainly DNA-based) near-atomic fabrication by focusing on state-of-the-art design techniques, toolkits for DNA/RNA nanoengineering, and related applications in a range of areas.

Proximity-induced caspase-9 activation on a DNA origami-based synthetic apoptosome

Living cells regulate key cellular processes by spatial organisation of catalytically active proteins in higher-order signalling complexes. These act as organising centres to facilitate proximity-induced activation and inhibition of multiple intrinsically weakly associating signalling components, which makes elucidation of the underlying protein-protein interactions challenging. Here we show that DNA origami nanostructures provide a programmable molecular platform for the systematic analysis of signalling proteins by engineering a synthetic DNA origami-based version of the apoptosome, a multi-protein complex that regulates apoptosis by co-localizing multiple caspase-9 monomers. Tethering of both wildtype and inactive caspase-9 variants to a DNA origami platform demonstrates that enzymatic activity is induced by proximity-driven dimerization with half-of-sites reactivity, and additionally, reveals a multivalent activity enhancement in oligomers of three and four enzymes. Our results offer fundamental insights in caspase-9 activity regulation and demonstrate that DNA origami-based protein assembly platforms have the potential to inform the function of other multi-enzyme complexes involved in inflammation, innate immunity and cell death.

Protein adaptors assemble functional proteins on DNA scaffolds

DNA is an attractive molecular building block to construct nanoscale structures for a variety of applications. In addition to their structure and function, modification the DNA nanostructures by other molecules opens almost unlimited possibilities for producing functional DNA-based architectures. Among the molecules to functionalize DNA nanostructures, proteins are one of the most attractive candidates due to their vast functional variations. DNA nanostructures loaded with various types of proteins hold promise for applications in the life and material sciences. When loading proteins of interest on DNA nanostructures, the nanostructures by themselves act as scaffolds to specifically control the location and number of protein molecules. The methods to arrange proteins of interest on DNA scaffolds at high yields while retaining their activity are still the most demanding task in constructing usable protein-modified DNA nanostructures. Here, we provide an overview of the existing methods applied for assembling proteins of interest on DNA scaffolds. The assembling methods were categorized into two main classes, noncovalent and covalent conjugation, with both showing pros and cons. The recent advance of DNA-binding adaptor mediated assembly of proteins on the DNA scaffolds is highlighted and discussed in connection with the future perspectives of protein assembled DNA nanoarchitectures.

Osmotic-engine-driven liposomes in microfluidic channels

Self-propelled underwater microrobots that locomote without external sources of energy have potential application as drug carriers and probes in narrow spaces. In this study, we focused on an osmotic engine model, which is a migration mechanism, and applied it as a negative chemotaxis mechanism to induce liposome displacement. First, we confirmed the osmotic flow across the lipid bilayer and calculated the osmotic flow velocity to be 8.5 fL min-1 μm-2 when a salt concentration difference was applied to the lipid bilayer. Next, we designed and fabricated a microchannel that can trap a giant liposome and apply a salt concentration difference to the front and rear of the liposome. Then, we demonstrated the movement of the liposome by flowing it to the microchannel. The liposome successfully moved in the direction of the lower ion concentration at a speed of 0.6 μm min-1 owing to the osmotic pressure difference. Finally, we visualized the inner flow in the liposome by encapsulating microbeads in the liposome and observed the movement of the microbeads to verify that an osmotic flow was generated on the liposome. As a result, we observed the circulation of the microbeads in the liposome when the concentration difference was applied to the front and rear of the liposome, suggesting that the movement of the liposome was driven by the osmotic flow generated by the osmotic pressure difference. These results indicate that the osmotic-pressure-based migration mechanism has the potential to be utilized as the actuator of molecular robots.

Aptamer-based regulation of transcription circuits

We propose synthetic DNA/RNA transcription circuits based on specific aptamer recognition. By mimicking transcription factor regulation, combined with specific enzyme/DNA aptamer binding, multiple biomolecules including DNA, RNA, polymerase, restriction enzymes and methylase were used as regulators. In addition, multi-level cascading networks and methylation-switch circuits were also established. This regulation strategy has the potential to expand the toolkit of in vitro synthetic biology.

Biomedical Applications of DNA-Based Molecular Devices

Strict Watson-Crick base pairing and availability by automated synthesis have allowed deoxyribonucleic acid (DNA) molecules to be used as engineerable building blocks for constructing versatile nanostructures. In recent decades, with the development of DNA nanotechnology, a range of DNA-based dynamic molecular devices with sophisticated nanostructures have been designed and constructed. Featuring programmability and biocompatibility, the applications of DNA-based nanodevices have been extensively focused on the interfaces of biological systems. This review summarizes the recent progress in the design of DNA devices exhibiting programmable functions for biomedical applications. In vitro and in vivo applications of DNA-based nanodevices in cellular imaging and systemic drug delivery are highlighted. The challenges and open opportunities are also discussed.

Programmable RNA-based systems for sensing and diagnostic applications

The emerging field of RNA nanotechnology harnesses the versatility of RNA molecules to generate nature-inspired systems with programmable structure and functionality. Such methodology has therefore gained appeal in the fields of biosensing and diagnostics, where specific molecular recognition and advanced input/output processing are demanded. The use of RNA modules and components allows for achieving diversity in structure and function, for processing information with molecular precision, and for programming dynamic operations on the grounds of predictable non-covalent interactions. When RNA nanotechnology meets bioanalytical chemistry, sensing of target molecules can be performed by harnessing programmable interactions of RNA modules, advanced field-ready biosensors can be manufactured by interfacing RNA-based devices with supporting portable platforms, and RNA sensors can be engineered to be genetically encoded allowing for real-time imaging of biomolecules in living cells. In this article, we report recent advances in RNA-based sensing technologies and discuss current trends in RNA nanotechnology-enabled biomedical diagnostics. In particular, we describe programmable sensors that leverage modular designs comprising dynamic aptamer-based units, synthetic RNA nanodevices able to perform target-responsive regulation of gene expression, and paper-based sensors incorporating artificial RNA networks. Graphical Abstract ᅟ.