Construction of a Fuzzy and Boolean Logic Gates Based on DNA

Logic gates are devices that can perform logical operations by transforming a set of inputs into a predictable single detectable output. The hybridization properties, structure, and function of nucleic acids can be used to make DNA‐based logic gates. These devices are important modules in molecular computing and biosensing. The ideal logic gate system should provide a wide selection of logical operations, and be integrable in multiple copies into more complex structures. Here we show the successful construction of a small DNA‐based logic gate complex that produces fluorescent outputs corresponding to the operation of the six Boolean logic gates AND, NAND, OR, NOR, XOR, and XNOR. The logic gate complex is shown to work also when implemented in a three‐dimensional DNA origami box structure, where it controlled the position of the lid in a closed or open position. Implementation of multiple microRNA sensitive DNA locks on one DNA origami box structure enabled fuzzy logical operation that allows biosensing of complex molecular signals. Integrating logic gates with DNA origami systems opens a vast avenue to applications in the fields of nanomedicine for diagnostics and therapeutics.     

Engineering Aptamer Switches for Multifunctional Stimulus-Responsive Nanosystems

Although RNA and DNA are best known for their capacity to encode biological information, it has become increasingly clear over the past few decades that these biomolecules are also capable of performing other complex functions, such as molecular recognition (e.g., aptamers) and catalysis (e.g., ribozymes). Building on these foundations, researchers have begun to exploit the predictable base-pairing properties of RNA and DNA in order to utilize nucleic acids as functional materials that can undergo a molecular “switching” process, performing complex functions such as signaling or controlled payload release in response to external stimuli including light, pH, ligand-binding and other microenvironmental cues. Although this field is still in its infancy, these efforts offer exciting potential for the development of biologically based “smart materials”. Herein, ongoing progress in the use of nucleic acids as an externally controllable switching material is reviewed. The diverse range of mechanisms that can trigger a stimulus response, and strategies for engineering those functionalities into nucleic acid materials are explored. Finally, recent progress is discussed in incorporating aptamer switches into more complex synthetic nucleic acid-based nanostructures and functionalized smart materials.     

Low‐Dimensional Nanomaterials Based on Small Organic Molecules: Preparation and Optoelectronic Properties

This article presents a comprehensive review of recent progress of research dedicated to low‐dimensional nanomaterials constructed from functional low‐molecular‐weight organic compounds, whose optoelectronic properties are fundamentally different from those of their inorganic counterparts. After introducing the development of inorganic and organic macromolecular nanomaterials, we begin with a general review of the construction strategies for achieving both zero‐dimensional (0D) and one‐dimensional (1D) nanostructures from small organic functional molecules. We then provide an overview of the unique optoelectronic properties induced by molecular aggregation in the nanostructures. Special emphasis is put on the luminescent properties that are different from those of the corresponding bulk materials, such as aggregation‐induced enhanced emission, fluorescence narrowing, multicolor emission, and tunable and switchable emissions from doped nanostructures. We conclude with a summary and our personal view of the direction of future development of organic opto‐functional nanomaterials and devices.     

Programmable DNA Nanoindicator‐Based Platform for Large‐Scale Square Root Logic Biocomputing

The prospect of programming molecular computing systems to realize complex autonomous tasks has advanced the design of synthetic biochemical logic circuits. One way to implement digital and analog integrated circuits is to use noncovalent hybridization and strand displacement reactions in cell‐free and enzyme‐free nucleic acid systems. To date, DNA‐based circuits involving tens of logic gates capable of implementing basic and complex logic functions have been demonstrated experimentally. However, most of these circuits are still incapable of realizing complex mathematical operations, such as square root logic operations, which can only be carried out with 4 bit binary numbers. A high‐capacity DNA biocomputing system is demonstrated through the development of a 10 bit square root logic circuit. It can calculate the square root of a 10 bit binary number (within the decimal integer 900) by designing DNA sequences and programming DNA strand displacement reactions. The input signals are optimized through the output feedback to improve performance in more complex logical operations. This study provides a more universal approach for applications in biotechnology and bioengineering.     

Phonon‐Assisted Electro‐Optical Switches and Logic Gates Based on Semiconductor Nanostructures

High‐performance nanostructured electro‐optical switches and logic gates are highly desirable as essential building blocks in integrated photonics. In contrast to silicon‐based optoelectronic devices, with their inherent indirect optical bandgap, weak light‐modulation mechanism, and sophisticated device configuration, direct‐bandgap‐semiconductor nanostructures with attractive electro‐optical properties are promising candidates for the construction of nanoscale optical switches for on‐chip photonic integrations. However, previously reported semiconductor‐nanostructure optical switches suffer from serious drawbacks such as high drive voltage, limited operation spectral range, and low modulation depth. High‐efficiency electro‐optical switches based on single CdS nanobelts with low drive voltage, ultra‐high on/off ratio, and broad operation wavelength range, properties resulting from unique electric‐field‐dependent phonon‐assisted optical transitions, are demonstrated. Furthermore, functional NOT, NOR, and NAND optical logic gates are demonstrated based on these switches. These switches and optical logic gates represent an important step toward integrated photonic circuits.     

Beta‐Sheet‐Forming,Self‐Assembled Peptide Nanomaterials towards Optical,Energy, and Healthcare Applications

Peptide self‐assembly is an attractive route for the synthesis of intricate organic nanostructures that possess remarkable structural variety and biocompatibility. Recent studies on peptide‐based, self‐assembled materials have expanded beyond the construction of high‐order architectures; they are now reporting new functional materials that have application in the emerging fields such as artificial photosynthesis and rechargeable batteries. Nevertheless, there have been few reviews particularly concentrating on such versatile, emerging applications. Herein, recent advances in the synthesis of self‐assembled peptide nanomaterials (e.g., cross β‐sheet‐based amyloid nanostructures, peptide amphiphiles) are selectively reviewed and their new applications in diverse, interdisciplinary fields are described, ranging from optics and energy storage/conversion to healthcare. The applications of peptide‐based self‐assembled materials in unconventional fields are also highlighted, such as photoluminescent peptide nanostructures, artificial photosynthetic peptide nanomaterials, and lithium‐ion battery components. The relation of such functional materials to the rapidly progressing biomedical applications of peptide self‐assembly, which include biosensors/chips and regenerative medicine, are discussed. The combination of strategies shown in these applications would further promote the discovery of novel, functional, small materials.     

Self‐Assembled Peptide‐Based Nanomaterials for Biomedical Imaging and Therapy

Peptide‐based materials are one of the most important biomaterials, with diverse structures and functionalities. Over the past few decades, a self‐assembly strategy is introduced to construct peptide‐based nanomaterials, which can form well‐controlled superstructures with high stability and multivalent effect. More recently, peptide‐based functional biomaterials are widely utilized in clinical applications. However, there is no comprehensive review article that summarizes this growing area, from fundamental research to clinic translation. In this review, the recent progress of peptide‐based materials, from molecular building block peptides and self‐assembly driving forces, to biomedical and clinical applications is systematically summarized. Ex situ and in situ constructed nanomaterials based on functional peptides are presented. The advantages of intelligent in situ construction of peptide‐based nanomaterials in vivo are emphasized, including construction strategy, nanostructure modulation, and biomedical effects. This review highlights the importance of self‐assembled peptide nanostructures for nanomedicine and can facilitate further knowledge and understanding of these nanosystems toward clinical translation.     

Allosteric Nucleic Acid Enzyme: A Versatile Stimuli-Responsive Tool for Molecular Computing and Biosensing Nanodevices

Allostery is a naturally occurring mechanism in which effector binding induces the modulation and fine control of a related biomolecule function. Deoxyribozyme (DNAzyme) with catalytic activity and substrate recognition ability is ideal to be regulated by allosteric strategies. However, the current regulations frequently confront various obstacles, such as severe activity decay, signal leakage, and limited effectors. In this work, a rational regulation strategy for developing versatile effectors-responsive allosteric nucleic acid enzyme (ANAzyme) by introducing an allosteric domain in response to diverse effectors is established. The enzyme-like activity of this re-engineered ANAzyme can be modulated in a more predictable and fine way compared with the previous DNAzyme regulation strategies. Based on the allosteric strategy, the construction of allosterically coregulatory nanodevices and a series of basic logic gates and logic circuits are achieved, demonstrating that the proposed ANAzyme-regulated strategy showed great potential in molecular computing. Given these facts, the rational design of ANAzyme with the allosteric domain presented here can expand the available toolbox to develop a variety of stimuli-responsive allosteric DNA materials, including molecular machines, computing systems, biosensing platforms, and gene-silencing tools.     

Polymetallated porphyrin ultrathin films as transducing elements for molecular devices and logic gates

Meso-tetrapyridylporphyrins peripherally coordinated to four ruthenium complexes, such as [Ru(bpy)2Cl] and [Ru(5-ClPhen)2Cl] (bpy = 2,2'-bipyridine; Phen = 1,10-phenanthroline), provide a versatile class of molecular materials in which the complexes act as co-factors, inducing electronic effects and acting as electron-transfer relays and electron pools or sinks, depending upon their oxidation state. These cationic porphyrins can be assembled into thin films by conventional methods, or into organized layer-by-layer structures by combining with negatively charged tetrasulfonated porphyrins or phthalocyanines. Their electrocatalytic and photoelectrochemical properties have been successfully exploited in chemical sensors. Their usefulness in molecular logic gates are being demonstrated by using modified transparent conducting electrodes in miniaturized flow injection cells. In such designs, the chemical, electrochemical, and light inputs can be readily combined to perform the basic logic functions, such as AND, OR, and NOT, for molecular computing.     

Chemically Modified Silk Proteins

Silks are of central importance as smart natural biomaterials and are attracting increasing attention for their biomimetic potential due to their sophisticated molecular structure, self‐assembly mechanism, impressive mechanical properties, biocompatibility, and biodegradability. The versatility of silk proteins (SP) allows the chemical modification of silk‐based materials with diverse morphologies under harsh conditions. The chemical modification of amino acids within SP enables the expanded generation of new biomaterials and the extension of their potential functional applications. The authors review the current chemical modification strategies and routes for the functionalization of SP.

     

Directed Assembly of Hybrid Nanomaterials and Nanocomposites

Hybrid nanomaterials are molecular or colloidal‐level combinations of organic and inorganic materials, or otherwise strongly dissimilar materials. They are often, though not exclusively, anisotropic in shape. A canonical example is an inorganic nanorod or nanosheet sheathed in, or decorated by, a polymeric or other organic material, where both the inorganic and organic components are important for the properties of the system. Hybrid nanomaterials and nanocomposites have generated strong interest for a broad range of applications due to their functional properties. Generating macroscopic assemblies of hybrid nanomaterials and nanomaterials in nanocomposites with controlled orientation and placement by directed assembly is important for realizing such applications. Here, a survey of critical issues and themes in directed assembly of hybrid nanomaterials and nanocomposites is provided, highlighting recent efforts in this field with particular emphasis on scalable methods.     

Selective Coassembly of Aromatic Amino Acids to Fabricate Hydrogels with Light Irradiation‐Induced Emission for Fluorescent Imprint

Controlling the structural parameters in coassembly is crucial for the fabrication of multicomponent functional materials. Here a proof‐of‐concept study is presented to reveal the α‐substituent effect of aromatic amino acids on their selective coassembly with bipyridine binders. With the assistance of X‐ray scattering technique, it is found that individual packing in the solid state as well as bulky effect brought by α‐substitution determines the occurrence of coassembly. A well‐performed hydrogels based on the complexation between certain aromatic amino acids and bipyridine units are successfully constructed, providing unprecedented smart materials with light irradiation‐triggered luminescence. Such hydrogels without the phase separation and photobleaching during light irradiation are able to behave fluorescent imprint materials. This study provides a suitable protocol in rationally designing amino acid residues of short peptides for fabricating self‐assembled multicomponent materials. In addition, this protocol is useful in screening potential functional materials on account of diverse self‐assembly behavior.     

Asymmetric Fullerene Nanosurfactant: Interface Engineering for Automatic Molecular Alignments

Since the molecular self‐assembly of nanomaterials is sensitive to their surface properties, the molecular packing structure on the surface is essential to build the desired chemical and physical properties of nanomaterials. Here, a new nanosurfactant is proposed for the automatic construction of macroscopic surface alignment layer for liquid crystal (LC) molecules. An asymmetric nanosurfactant (C₆₀NS) consisted of mesogenic cyanobiphenyl moieties with flexible alkyl chains and a [60]fullerene nanoatom is newly designed and precisely synthesized. The C₆₀NS directly introduced in the anisotropic LC medium is self‐assembled into the monolayered protrusions on the surface because of its amphiphilic nature originated by asymmetrically programmed structural motif of LC‐favoring moieties and LC‐repelling groups. The monolayered protrusions constructed by the phase‐separation and self‐assembly of asymmetric C₆₀NS nanosurfactant in the anisotropic LC media amplify and transfer the molecular orientational order from surface to bulk, and finally create the automatic vertical molecular alignment on the macroscopic length scale. The asymmetric C₆₀NS nanosurfactant and its self‐assembly described herein can offer the direct guideline of interface engineering for the automatic molecular alignments.     

Engineering Protein Nanoparticles Out from Components of the Human Microbiome

Nanoscale protein materials are highly convenient as vehicles for targeted drug delivery because of their structural and functional versatility. Selective binding to specific cell surface receptors and penetration into target cells require the use of targeting peptides. Such homing stretches should be incorporated to larger proteins that do not interact with body components, to prevent undesired drug release into nontarget organs. Because of their low interactivity with human body components and their tolerated immunogenicity, proteins derived from the human microbiome are appealing and fully biocompatible building blocks for the biofabrication of nonreactive, inert protein materials within the nanoscale. Several phage and phage‐like bacterial proteins with natural structural roles are produced in Escherichia coli as polyhistidine‐tagged recombinant proteins, looking for their organization as discrete, nanoscale particulate materials. While all of them self‐assemble in a variety of sizes, the stability of the resulting constructs at 37 °C is found to be severely compromised. However, the fine adjustment of temperature and Zn²⁺ concentration allows the formation of robust nanomaterials, fully stable in complex media and under physiological conditions. Then, microbiome‐derived proteins show promise for the regulatable construction of scaffold protein nanomaterials, which can be tailored and strengthened by simple physicochemical approaches.     

Simple and universal platform for logic gate operations based on molecular beacon probes

A new platform technology is herein described with which to construct molecular logic gates by employing the hairpin-structured molecular beacon probe as a basic work unit. In this logic gate operation system, single-stranded DNA is used as the input to induce a conformational change in a molecular beacon probe through a sequence-specific interaction. The fluorescent signal resulting from the opening of the molecular beacon probe is then used as the output readout. Importantly, because the logic gates are based on DNA, thus permitting input/output homogeneity to be preserved, their wiring into multi-level circuits can be achieved by combining separately operated logic gates or by designing the DNA output of one gate as the input to the other. With this novel strategy, a complete set of two-input logic gates is successfully constructed at the molecular level, including OR, AND, XOR, INHIBIT, NOR, NAND, XNOR, and IMPLICATION. The logic gates developed herein can be reversibly operated to perform the set-reset function by applying an additional input or a removal strand. Together, these results introduce a new platform technology for logic gate operation that enables the higher-order circuits required for complex communication between various computational elements.     

Nucleic Acid Nanostructures for Chemical and Biological Sensing

The nanoscale features of DNA have made it a useful molecule for bottom‐up construction of nanomaterials, for example, two‐ and three‐dimensional lattices, nanomachines, and nanodevices. One of the emerging applications of such DNA‐based nanostructures is in chemical and biological sensing, where they have proven to be cost‐effective, sensitive and have shown promise as point‐of‐care diagnostic tools. DNA is an ideal molecule for sensing not only because of its specificity but also because it is robust and can function under a broad range of biologically relevant temperatures and conditions. DNA nanostructure‐based sensors provide biocompatibility and highly specific detection based on the molecular recognition properties of DNA. They can be used for the detection of single nucleotide polymorphism and to sense pH both in solution and in cells. They have also been used to detect clinically relevant tumor biomarkers. In this review, recent advances in DNA‐based biosensors for pH, nucleic acids, tumor biomarkers and cancer cell detection are introduced. Some challenges that lie ahead for such biosensors to effectively compete with established technologies are also discussed.     

Gaseous Nanocarving‐Mediated Carbon Framework with Spontaneous Metal Assembly for Structure‐Tunable Metal/Carbon Nanofibers

Vapor phase carbon (C)‐reduction‐based syntheses of C nanotubes and graphene, which are highly functional solid C nanomaterials, have received extensive attention in the field of materials science. This study suggests a revolutionary method for precisely controlling the C structures by oxidizing solid C nanomaterials into gaseous products in the opposite manner of the conventional approach. This gaseous nanocarving enables the modulation of inherent metal assembly in metal/C hybrid nanomaterials because of the promoted C oxidation at the metal/C interface, which produces inner pores inside C nanomaterials. This phenomenon is revealed by investigating the aspects of structure formation with selective C oxidation in the metal/C nanofibers, and density functional theory calculation. Interestingly, the tendency of C oxidation and calculated oxygen binding energy at the metal surface plane is coincident with the order Co > Ni > Cu > Pt. The customizable control of the structural factors of metal/C nanomaterials through thermodynamic‐calculation‐derived processing parameters is reported for the first time in this work. This approach can open a new class of gas–solid reaction‐based synthetic routes that dramatically broaden the structure‐design range of metal/C hybrid nanomaterials. It represents an advancement toward overcoming the limitations of intrinsic activities in various applications.     

Performing Logical Operations with Stimuli‐Responsive Building Blocks

Chemical logic gates can be fabricated by synthesizing molecules that have the ability to detect external stimuli (e.g., temperature or pH) and provide logical outputs. It is, however, challenging to fabricate a system that consists of many logic gates using this method: complex molecules can be difficult to synthesize and these logic gates typically cannot be integrated together. Here, we fabricated different types of logic gates by assembling a combination of different types of stimuli‐responsive hydrogels that change their size under the influence of one type of stimulus. Importantly, the preparation of these stimuli‐responsive hydrogels is widely reported and technically simple. Through designing the geometry of the systems, we fabricated the YES, NOT, OR, AND, NOR, and NAND gates. Although the hydrogels respond to different types of stimuli, their outputs are the same: a change in size of the hydrogel. Hence, we show that the logic gates can be integrated easily (e.g., by connecting an AND gate to an OR gate). In addition, we fabricated a standalone system with the size of a normal drug tablet (i.e., a “smart tablet”) that can analyze (or diagnose) different stimuli and control the release of a chemical (or drug) via the logic gates.     

智能混凝土与结构

智能混凝土是通过将极少量具有某种特殊功能的材料复合于传统的混凝土材料中形成的具有多功能特性或某一种特殊功能特性的新型土木工程结构材料。与其他智能材料相比,智能混凝土是多功能本征性智能材料,可从本质上提高工程结构的性能。自感知混凝土(纳米混凝土、碳纤维混凝土)、自阻尼混凝土和自愈合混凝土等是智能混凝土研究的热点。总结了近年来作者在智能混凝土的制备、性能、机理,以及智能混凝土结构等方面的研究成果,并指出需进一步研究的问题。