Project description:DNA is commonly employed as a substrate for the building of artificial logic networks due to its excellent biocompatibility and programmability. Till now, DNA logic circuits are rapidly evolving to accomplish advanced operations. Nonetheless, nowadays, most DNA circuits remain to be disposable and lack of field programmability and thereby limits their practicability. Herein, inspired by the Configurable Logic Block (CLB), the CLB-based erasable field-programmable DNA circuit that uses clip strands as its operation-controlling signals is presented. It enables users to realize diverse functions with limited hardware. CLB-based basic logic gates (OR and AND) are first constructed and demonstrated their erasability and field programmability. Furthermore, by adding the appropriate operation-controlling strands, multiple rounds of programming are achieved among five different logic operations on a two-layer circuit. Subsequently, a circuit is successfully built to implement two fundamental binary calculators: half-adder and half-subtractor, proving that the design can imitate silicon-based binary circuits. Finally, a comprehensive CLB-based circuit is built that enables multiple rounds of switch among seven different logic operations including half-adding and half-subtracting. Overall, the CLB-based erasable field-programmable circuit immensely enhances their practicability. It is believed that design can be widely used in DNA logic networks due to its efficiency and convenience.
Project description:The specific inventory of molecules on diseased cell surfaces (e.g., cancer cells) provides clinicians an opportunity for accurate diagnosis and intervention. With the discovery of panels of cancer markers, carrying out analyses of multiple cell-surface markers is conceivable. As a trial to accomplish this, we have recently designed a DNA-based device that is capable of performing autonomous logic-based analysis of two or three cancer cell-surface markers. Combining the specific target-recognition properties of DNA aptamers with toehold-mediated strand displacement reactions, multicellular marker-based cancer analysis can be realized based on modular AND, OR, and NOT Boolean logic gates. Specifically, we report here a general approach for assembling these modular logic gates to execute programmable and higher-order profiling of multiple coexisting cell-surface markers, including several found on cancer cells, with the capacity to report a diagnostic signal and/or deliver targeted photodynamic therapy. The success of this strategy demonstrates the potential of DNA nanotechnology in facilitating targeted disease diagnosis and effective therapy.
Project description:Thermoelectric devices (TEDs) show great potential for waste heat energy recycling and sensing. However, existing TEDs cannot be self-adapted to the complex quadratic surface, leading to significant heat loss and restricting their working scenario. Here, surface-conformable origami-TEDs (o-TEGs) are developed through programmable crease-designed origami substrates and the screen-printing TE legs. Compared with "π" structured TEDs, the origami design (with heat conductive materials) changed the heat-transferring direction of the laminated TE legs, resulting in an enhancement in enlarging ΔT/THot and Vout by 5.02 and 3.51 times. Four o-TEDs with different creases designs are fabricated to verify the heat recycling ability on plane and central quadratic surfaces. Demonstrating a high Vout density (up to 0.98 -2 at ΔT of 50 K) and good surface conformability, o-TEDs are further used in thermal touch panels attached to multiple surfaces, allowing information to be wirelessly transferred on a remote display via finger-writing.
Project description:The catalytic DNA circuits play a critical role in engineered biological systems and molecular information processing. Actually, some of the natural or synthetic DNA circuits were triggered by covalent modifications, where conformational changes were induced to facilitate complex DNA engineering functions and signal transmissions. However, most of the reported artificial catalytic DNA circuits were regulated by the toehold-mediated reaction. Therefore, it is significant to propose a strategy to regulate the catalytic DNA circuit not only by the toehold-mediated mechanism, but also by involving the conformational changes induced by the covalent modification. In this study, we developed the catalytic DNA logic circuits regulated by DNAzyme. Here, a regulation strategy based on the covalent modification was proposed to control the DNA circuit, combing two reaction mechanisms: DNAzyme digestion and entropy-driven strand displacement. The DNAzyme and DNA catalyst can participate into the reactions alternatively, thus realizing the cascading catalytic circuits. Using the DNAzyme regulation, a series of logic gates (YES, OR and AND) were constructed. In addition, a two-layer cascading circuit and a feedback self-catalysis circuit were also established. The proposed DNAzyme-regulated strategy shows great potentials as a reliable and feasible method for constructing more complex catalytic DNA circuits.
Project description:Mechanosensing systems are ubiquitous in nature and control many functions from cell spreading to wound healing. Biologic systems typically rely on supramolecular transformations and secondary reporter systems to sense weak forces. By contrast, synthetic mechanosensitive materials often use covalent transformations of chromophores, serving both as force sensor and reporter, which hinders orthogonal engineering of their sensitivity, response and modularity. Here, we introduce FRET-based, rationally tunable DNA tension probes into macroscopic 3D all-DNA hydrogels to prepare mechanofluorescent materials with programmable sacrificial bonds and stress relaxation. This design addresses current limitations of mechanochromic system by offering spatiotemporal resolution, as well as quantitative and modular force sensing in soft hydrogels. The programmable force probe design further grants temporal control over the recovery of the mechanofluorescence during stress relaxation, enabling reversible and irreversible strain sensing. We show proof-of-concept applications to study strain fields in composites and to visualize freezing-induced strain patterns in homogeneous hydrogels.
Project description:Accurate identification and isolation of target cells are crucial for precision diagnosis and treatment. DNA aptamer-based logic devices provide a distinct advantage in this context, as they can logically analyze multiple cell surface markers with high efficiency. However, the susceptibility of natural DNA (D-DNA) to degradation can compromise the sensitivity and specificity of these devices, potentially leading to false-positive and false-negative results, particularly in complex biological environments. To address this issue, dual- and triple-aptamer-based cell-surface logic devices are designed and developed using mirror-image L-DNA, a chiral molecule of D-DNA with high biostability. These devices allow for simultaneous analysis of multiple cell surface proteins, achieving greater specificity in cell identification and isolation than D-DNA-based logic devices. The L-DNA probes realized 98.7% and 70.5% sensitivities in FBS buffer with dual- and triple-aptamer-based logic devices for target cell identification, while D-DNA probes only showed 27.9% and 0.1%. It is believed that the high stability of L-DNA and the high efficiency of the devices for labeling cell subpopulations will have broad applications in the life sciences, biomedical engineering, and personalized medicine.
Project description:We describe a self-assembling DNA-based nanosystem for interrogating molecular interactions. The nanosystem contains a rigid supporting dumbbell-shaped frame, a cylindrical central core, and a mobile ring that is coaxial with the core. Motion of the ring is influenced by several control elements whose force-generating capability is based on the transition of single-stranded DNA to double-stranded DNA. These forces can be directed to act in opposition to adhesive forces between the ring and the frame thereby providing a mechanism for molecular detection and interrogation at the ring-frame interface. As proof of principle we use this system to evaluate base stacking adhesion and demonstrate detection of a soluble nucleic acid viral genome mimic.
Project description:Molecular logic gates are information processing devices that can respond to environmental signals and produce a readable output in response through Boolean logic operations. Molecules with these properties have been used to build smart sensors and therapeutic agents. In this work, dual enzyme-responsive molecular AND logic gate is developed with the intention to discriminate various combinations of enzyme level and/or activity. A resorufin-based sensor is substituted with self-immolative tyrosinase recognition site, 3-hydroxy benzyl group. The Hydroxyl group is protected with acetyl moiety which decreases the affinity of the enzyme. When both tyrosinase and esterase are present in the solution, the acetyl group is removed by the latter enzyme, allowing the former to recognise the ligand. Oxidation of the ligand by tyrosinase triggers self-immolative cleavage of the substitution, leading to almost 70 fold enhancement in fluorescence. When single enzyme is applied, there is no significant change in the emission intensity overall, an AND logic gate is constructed. Selectivity and Michaelis-Menten kinetics of the sensor is analysed. Smart molecular probes can contribute to the research on the development of biosensors that can discriminate diseases having characteristic combinations of enzyme activities.
Project description:DNA has become the biomolecule of choice for molecular computation that may one day complement conventional silicon-based processors. In general, DNA computation is conducted in individual tubes, is slow in generating chemical outputs in response to chemical inputs and requires fluorescence readout. Here, we introduce a new paradigm for DNA computation where the chemical input is processed and transduced into a mechanical output using dynamic DNA-based motors operating far from equilibrium. We show that DNA-based motors with onboard logic (DMOLs) can perform Boolean functions (NOT, YES, AND and OR) with 15 min readout times. Because DMOLs are micrometre-sized, massive arrays of DMOLs that are identical or uniquely encoded by size and refractive index can be multiplexed and perform motor-to-motor communication on the same chip. Finally, DMOL computational outputs can be detected using a conventional smartphone camera, thus transducing chemical information into the electronic domain in a facile manner, suggesting potential applications.
Project description:Mechanical computing promises to integrate semiconductor-based digital logic in several applications, but it needs straightforward programmable devices for changing computing rules in situ. A methodology based on strain-governed, bistable soft shells that process digital information by interchanging their internal/external surfaces is proposed. This bistable behavior, explained via model-based design, safeguards robustness by working only once for each input pulse. Thus, these shells are leveraged to create a buffer and a NOT gate that lead to six fundamental gates (AND, OR, NAND, NOR, XOR, and XNOR). All these functions are integrated into a unique programmable device, making mechanically integrated circuits more adaptable with rule-changeable logic operations. This design ensures continuous processes and general applicability to multiple types of signals (a pressurized fluid can replace mechanical driving signals is shown). It also empowers more complex logic functions suitable for expanded applications, such as the half and full adders is addressed.