Investigating the dynamics of surface-immobilized DNA nanomachines

A Dual-Recognition Fluorescence Enzyme-Linked Immunosorbent Assay for Specific Detection of Intact Lipid Nanoparticles via a Localized Scaffolding Autocatalytic DNA Circuit Amplifier

Lipid nanoparticles (LNPs) are emerging as one of the most promising drug delivery systems. The long-circulating effect of intact LNPs (i-LNPs) is the key to efficacy and toxicity in vivo. However, the significant challenge is specific and sensitive detection of i-LNPs. Herein, a dual-recognition fluorescence enzyme-linked immunosorbent assay (DR-FELISA) was developed to directly isolate and detect i-LNPs by combining dual-recognition separation with a one-step signal amplification strategy. The microplates captured and enriched i-LNPs through antibody-antigen reaction. Dual-chol probes were spontaneously introduced into the lipid bilayer of captured i-LNPs, converting the detection of i-LNPs into the detection of double-cholesterol probes. Finally, the end of the dual-chol probes initiated the localized scaffolding autocatalytic DNA circuits (SADC) system for further signal amplification. The SADC system provides a sensitive and efficient amplifier through localized network structures and self-assembled triggers. Simultaneous recognition of i-LNPs surface PEG-lipid and lipid bilayer structures significantly eliminates interference from biological samples. i-LNPs were detected with high selectivity, ranging from 0.2 to 1.25 mg/mL with a limit of detection of 0.1 mg/mL. Moreover, this method allows the isolation and quantitative analysis of different formulations of i-LNPs in serum samples with a satisfactory recovery rate ranging from 94.8 to 116.3%. Thus, the DR-FELISA method provides an advanced platform for the exclusive and sensitive detection of i-LNPs, providing new insights for the study of the quality and intracorporal process of complex formulations.

Design and Simulation of an Autonomous Molecular Mechanism Using Spatially Localized DNA Computation

As a well-established technique, DNA synthesis offers interesting possibilities for designing multifunctional nanodevices. The micro-processing system of modern semiconductor circuits is dependent on strategies organized on silicon chips to achieve the speedy transmission of substances or information. Similarly, spatially localized structures allow for fixed DNA molecules in close proximity to each other during the synthesis of molecular circuits, thus providing a different strategy that of opening up a remarkable new area of inquiry for researchers. Herein, the Visual DSD (DNA strand displacement) modeling language was used to design and analyze the spatially organized DNA reaction network. The execution rules depend on the hybridization reaction caused by directional complementary nucleotide sequences. A series of DNA strand displacement calculations were organized on the locally coded travel track, and autonomous movement and addressing operations are gradually realized. The DNA nanodevice operates in this manner follows the embedded "molecular program", which improves the reusability and scalability of the same sequence domain in different contexts. Through the communication between various building blocks, the DNA device-carrying the target molecule moves in a controlled manner along the programmed track. In this way, a variety of molecular functional group transport and specific partition storage can be realized. The simulation results of the visual DSD tool provide qualitative and quantitative proof for the operation of the system.

Harnessing DNA Nanotechnology and Chemistry for Applications in Photonics and Electronics

Many photonic and electronic devices rely on nanotechnology and nanofabrication, but DNA-based approaches have yet to make a significant commercial impact in these fields even though DNA molecules are now well-established as versatile building blocks for nanostructures. As we describe here, DNA molecules can be chemically modified with a wide variety of functional groups enabling nanocargoes to be attached at precisely determined locations. DNA nanostructures can also be used as templates for the growth of inorganic structures. Together, these factors enable the use of DNA nanotechnology for the construction of many novel devices and systems. In this topical review, we discuss four case studies of potential applications in photonics and electronics: carbon nanotube transistors, devices for quantum computing, artificial electromagnetic materials, and enzymatic fuel cells. We conclude by speculating about the barriers to the exploitation of these technologies in real-world settings.

Controlling Dynamic DNA Reactions at the Surface of Single-Walled Carbon Nanotube Electrodes to Design Hybridization Platforms with a Specific Amperometric Readout

Carbon nanotube (CNT)-based electrodes are cheap, highly performing, and robust platforms for the fabrication of electrochemical sensors. Engineering programmable DNA nanotechnologies on the CNT surface can support the construction of new electrochemical DNA sensors providing an amperometric output in response to biomolecular recognition. This is a significant challenge, since it requires gaining control of specific hybridization processes and functional DNA systems at the interface, while limiting DNA physisorption on the electrode surface, which contributes to nonspecific signal. In this study, we provide design rules to program dynamic DNA structures at the surface of single-walled carbon nanotubes electrodes, showing that specific DNA interactions can be monitored through measurement of the current signal provided by redox-tagged DNA strands. We propose the use of pyrene as a backfilling agent to reduce nonspecific adsorption of reporter DNA strands and demonstrate the controlled formation of DNA duplexes on the electrode surface, which we then apply in the design and conduction of programmable DNA strand displacement reactions. Expanding on this aspect, we report the development of novel amperometric hybridization platforms based on artificial DNA structures templated by the small molecule melamine. These platforms enable dynamic strand exchange reactions orthogonal to conventional toehold-mediated strand displacement and may support new strategies in electrochemical sensing of biomolecular targets, combining the physicochemical properties of nanostructured carbon-based materials with programmable nucleic acid hybridization.

Customizable Aptamer Transducer Network Designed for Feed-Forward Coupling

Solution-based biosensors that utilize aptamers have been engineered in a variety of formats to detect a range of analytes for both medical and environmental applications. However, since aptamers have fixed base sequences, incorporation of aptamers into DNA strand displacement networks for feed-forward signal amplification and processing requires significant redesign of downstream DNA reaction networks. We designed a novel aptamer transduction network that releases customizable output domains, which can then be used to initiate downstream strand displacement reaction networks without any sequence redesign of the downstream reaction networks. In our aptamer transducer (AT), aptamer input domains are independent of output domains within the same DNA complex and are reacted with a fuel strand after aptamer-ligand binding. ATs were designed to react with two fluorescent dye-labeled reporter complexes to show the customizability of the output domains, as well as being used as feed-forward inputs to two previously studied catalytic reaction networks, which can be used as amplifiers. Through our study, we show both successful customizability and feed-forward capability of our ATs.

Rapid kinetic fingerprinting of single nucleic acid molecules by a FRET-based dynamic nanosensor

Biofluid-derived cell-free nucleic acids such as microRNAs (miRNAs) and circulating tumor-derived DNAs (ctDNAs) have emerged as promising disease biomarkers. Conventional detection of these biomarkers by digital PCR and next generation sequencing, although highly sensitive, requires time-consuming extraction and amplification steps that also increase the risk of sample loss and cross-contamination. To achieve the direct, rapid, and amplification-free detection of miRNAs and ctDNAs with near-perfect specificity and single-molecule level sensitivity, we herein designed a single-molecule kinetic fingerprinting assay, termed intramolecular single-molecule recognition through equilibrium Poisson sampling (iSiMREPS). iSiMREPS exploits a dynamic DNA nanosensor comprising a surface anchor and a pair of fluorescent detection probes: one probe captures a target molecule onto the surface, while the other transiently interrogates the target to generate kinetic fingerprints by intramolecular single-molecule Förster resonance energy transfer (smFRET) that are recorded by single-molecule fluorescence microscopy and identify the target after kinetic filtering and data analysis. We optimize the sensor design, use formamide to further accelerate the fingerprinting kinetics, and maximize sensitivity by removing non-target-bound probes using toehold-mediated strand displacement to reduce background. We show that iSiMREPS can detect, in as little as 10 s, two distinct, promising cancer biomarkers-miR-141 and a common EGFR exon 19 deletion-reaching a limit of detection (LOD) of ~3 fM and a mutant allele fraction among excess wild-type as low as 1 in 1 million, or 0.0001%. We anticipate that iSiMREPS will find utility in research and clinical diagnostics based on its features of rapid detection, high specificity, sensitivity, and generalizability.

Stoichiometric quantification of spatially dense assemblies with qPAINT

Quantitative PAINT (qPAINT) is a useful method for counting well-separated molecules within nanoscale assemblies. But whether cross-reactivity in densely-packed arrangements perturbs measurements is unknown. Here we establish that qPAINT measurements are robust even when target molecules are separated by as little as 3 nm, sufficiently close that single-stranded DNA binding sites can interact.

Improving linking interface between collagen-based hydrogels and bone-like substrates

Regenerative medicine requires the use of heterogeneous scaffolds when the tissue that needs to be repaired presents a gradient in its properties and cannot be replaced by a homogeneous graft. Then, an intimate contact between the different layers is critical to guarantee the optimal performance of the construct. This work presents a procedure that allows the immobilization of collagen-based hydrogels by self-assembly onto any desired substrate, by means of a pentafluorophenyl methacrylate (PFM) coating obtained by plasma enhanced chemical vapor deposition and a collagen monolayer. The latter is attached onto the PFM-coated substrate thanks to its high reactivity towards amines and it will act as anchoring point for the subsequent collagen fibrillation and hydrogel formation. The interaction between collagen and PFM-coated substrates has been evaluated using the quartz crystal microbalance with dissipation (QCM-D) technique. In addition, QCM-D has been used to design and monitor the collagen fibril formation process. A correlation between QCM-D data and optical microscopy has been established, and fibril formation has been confirmed by atomic force microscopy (AFM).

DNA-based communication in populations of synthetic protocells

Developing molecular communication platforms based on orthogonal communication channels is a crucial step towards engineering artificial multicellular systems. Here, we present a general and scalable platform entitled 'biomolecular implementation of protocellular communication' (BIO-PC) to engineer distributed multichannel molecular communication between populations of non-lipid semipermeable microcapsules. Our method leverages the modularity and scalability of enzyme-free DNA strand-displacement circuits to develop protocellular consortia that can sense, process and respond to DNA-based messages. We engineer a rich variety of biochemical communication devices capable of cascaded amplification, bidirectional communication and distributed computational operations. Encapsulating DNA strand-displacement circuits further allows their use in concentrated serum where non-compartmentalized DNA circuits cannot operate. BIO-PC enables reliable execution of distributed DNA-based molecular programs in biologically relevant environments and opens new directions in DNA computing and minimal cell technology.

Tunable DNA Hybridization Enables Spatially and Temporally Controlled Surface-Anchoring of Biomolecular Cargo

The controlled immobilization of biomolecules onto surfaces is relevant in biosensing and cell biological research. Spatial control is achieved by surface-tethering molecules in micro- or nanoscale patterns. Yet, there is an increasing demand for temporal control over how long biomolecular cargo stays immobilized until released into the medium. Here, we present a DNA hybridization-based approach to reversibly anchor biomolecular cargo onto micropatterned surfaces. Cargo is linked to a DNA oligonucleotide that hybridizes to a sequence-complementary, surface-tethered strand. The cargo is released from the substrate by the addition of an oligonucleotide that disrupts the duplex interaction via toehold-mediated strand displacement. The unbound tether strand can be reloaded. The generic strategy is implemented with small-molecule or protein cargo, varying DNA sequences, and multiple surface patterning routes. The approach may be used as a tool in biological research to switch membrane proteins from a locally fixed to a free state, or in biosensing to shed biomolecular receptors to regenerate the sensor surface.

A DNA-nanoparticle actuator enabling optical monitoring of nanoscale movements induced by an electric field

Merging biological and non-biological matter to fabricate nanoscale assemblies with controllable motion and function is of great interest due to its potential application, for example, in diagnostics and biosensing. Here, we have constructed a DNA-based bionanoactuator that interfaces with biological and non-biological matter via an electric field in a reversibly controllable fashion. The read-out of the actuator is based on motion-induced changes in the plasmon resonance of a gold nanoparticle immobilized to a gold surface by single stranded DNA. The motion of the gold nanoparticle and thus the conformational changes of the DNA under varying electric field were analyzed by dark field spectroscopy. After this basic characterization, another actuator was built utilizing hairpin-DNA coated gold nanoparticles, where the hairpin-DNA induced discrete transitions between two specific open-loop and folded-loop states. These two states and the transition dynamics between them were clearly visible in the actuator behavior. The demonstrated nanoactuator concept could be readily extended to inspection of conformational changes of other biomolecules as well. Besides, this concept enables other possibilities in applications like surface-enhanced Raman spectroscopy and fluorescence enhancement, since the specific wavelength of the plasmon resonance of the actuator can be tuned by the external voltage.

Towards a Bioelectronic Computer: A Theoretical Study of a Multi-Layer Biomolecular Computing System That Can Process Electronic Inputs

DNA molecular machines have great potential for use in computing systems. Since Adleman originally introduced the concept of DNA computing through his use of DNA strands to solve a Hamiltonian path problem, a range of DNA-based computing elements have been developed, including logic gates, neural networks, finite state machines (FSMs) and non-deterministic universal Turing machines. DNA molecular machines can be controlled using electrical signals and the state of DNA nanodevices can be measured using electrochemical means. However, to the best of our knowledge there has as yet been no demonstration of a fully integrated biomolecular computing system that has multiple levels of information processing capacity, can accept electronic inputs and is capable of independent operation. Here we address the question of how such a system could work. We present simulation results showing that such an integrated hybrid system could convert electrical impulses into biomolecular signals, perform logical operations and take a decision, storing its history. We also illustrate theoretically how the system might be able to control an autonomous robot navigating through a maze. Our results suggest that a system of the proposed type is technically possible but for practical applications significant advances would be required to increase its speed.

Characterizing Surface-Immobilized DNA Structures and Devices Using a Quartz Crystal Microbalance with Dissipation Monitoring (QCM-D)

A quartz crystal microbalance with dissipation monitoring can be used to study the mass and structure of surface-immobilized layers of molecules, in real time. Here we describe the use of the technique to study DNA structures and devices.

A spatially localized architecture for fast and modular DNA computing

Cells use spatial constraints to control and accelerate the flow of information in enzyme cascades and signalling networks. Synthetic silicon-based circuitry similarly relies on spatial constraints to process information. Here, we show that spatial organization can be a similarly powerful design principle for overcoming limitations of speed and modularity in engineered molecular circuits. We create logic gates and signal transmission lines by spatially arranging reactive DNA hairpins on a DNA origami. Signal propagation is demonstrated across transmission lines of different lengths and orientations and logic gates are modularly combined into circuits that establish the universality of our approach. Because reactions preferentially occur between neighbours, identical DNA hairpins can be reused across circuits. Co-localization of circuit elements decreases computation time from hours to minutes compared to circuits with diffusible components. Detailed computational models enable predictive circuit design. We anticipate our approach will motivate using spatial constraints for future molecular control circuit designs.

An experimental study of the putative mechanism of a synthetic autonomous rotary DNA nanomotor

DNA has been used to construct a wide variety of nanoscale molecular devices. Inspiration for such synthetic molecular machines is frequently drawn from protein motors, which are naturally occurring and ubiquitous. However, despite the fact that rotary motors such as ATP synthase and the bacterial flagellar motor play extremely important roles in nature, very few rotary devices have been constructed using DNA. This paper describes an experimental study of the putative mechanism of a rotary DNA nanomotor, which is based on strand displacement, the phenomenon that powers many synthetic linear DNA motors. Unlike other examples of rotary DNA machines, the device described here is designed to be capable of autonomous operation after it is triggered. The experimental results are consistent with operation of the motor as expected, and future work on an enhanced motor design may allow rotation to be observed at the single-molecule level. The rotary motor concept presented here has potential applications in molecular processing, DNA computing, biosensing and photonics.

Exploiting molecular motors as nanomachines: the mechanisms of de novo and re-engineered cytoskeletal motors

Cytoskeletal molecular motors provide exciting proof that nanoscale transporters can be highly efficient, moving for microns along filamentous tracks by hydrolyzing ATP to fuel nanometer-size steps. For nanotechnology, such conversion of chemical energy into productive work serves as an enticing platform for re-purposing and re-engineering. It also provides a roadmap for successful molecular mechanisms that can be mimicked to create de novo molecular motors for nanotechnology applications. Here we focus specifically on how the mechanisms of molecular motors are being re-engineered for greater control over their transport parameters. We then discuss mechanistic work to create fully synthetic motors de novo and conclude with future directions in creating novel motor systems.