Multiplexed aptasensors and amplified DNA sensors using functionalized graphene oxide: application for logic gate operations

Enzyme-Programmed Self-Assembly of Nanoparticles

Nanoparticles are a hot topic in the field of nanomaterial research due to their excellent physical and chemical properties. In recent years, DNA-directed nanoparticle self-assembly technology has been widely applied to the development of numerous complex nanoparticle superstructures. Due to the inherent stability and surface electric repulsion of nanoparticles, it is difficult to make nanoparticle superstructures respond to molecular signals in the external environment. In fact, enzyme-programmed molecular systems are developed to allow diverse functions, including logical operations, signal amplification, and dynamic assembly control. Therefore, combining enzyme-controlled DNA systems may endow nanoparticle assembly systems with more flexibility in program design, allowing them to respond to a variety of external signals. In this review, we summarize the basic principles of enzyme-controlled DNA/nanoparticle self-assembly and introduce its applications in heavy metal detection, gene expression, proteins inside living cells, cancer cell therapy, and drug delivery. With the continuous development of new nanoparticle materials and the increasing functionality of enzyme DNA circuits, enzyme-directed DNA/nanoparticle self-assembled probe technology is expected to see significant future development.

Upgraded and Light-Up Biosensing Platform: Entropy-Driven Catalysis Circuit Manipulates the Configuration Transformation of Novel DNA Silver Nanoclusters on the Graphene Oxide Surface

To tackle the predicament of the traditional turn-off mechanism, exploring an activated turn-on system remains an intriguing and crucial objective in biosensing fields. Herein, a dark DNA Ag nanocluster (NC) with hairpin-structured DNA containing a six-base cytosine loop (6C loop) as a template is atypically synthesized. Intriguingly, the dark DNA Ag NCs can be lit to display strong red-emission nanoclusters. Building upon these exciting findings, an unprecedented and upgraded turn-on biosensing system [entropy-driven catalysis circuit (EDCC)-Ag NCs/graphene oxide (GO)] has been created, which employs an EDCC to precisely manipulate the conformational transition of DNA Ag NCs on the GO surface from adsorption to desorption. Benefiting from the effective quenching of GO and signal amplification capability of the EDCC, the newly developed EDCC-Ag NCs/GO biosensing system displays a high signal-to-background (S/B) ratio (26-fold) and sensitivity (limit of detection as low as 0.4 pM). Meanwhile, it has good specificity, excellent stability, and reliability in both buffer and biological samples. To the best of our knowledge, it is the first example that adopts an EDCC to precisely modulate the configuration transformation of DNA Ag NCs on the GO surface to obtain a biosensor with low background, strong fluorescence, high contrast, and sensitivity. This exciting finding may provide a new route to fabricate a novel turn-on biosensor based on hairpin-templated DNA Ag NCs in the optical imaging and bioanalytical fields.

pH-dependent complex formation with TAR RNA and DNA: application towards logic gates

Nucleic acid-based logic gates have shown great potential in biotechnology, medicine as well as diagnostics. Herein, we have constructed pH-responsive logic devices by utilizing HIV-1 TAR hairpins in combination with a thiazole peptide that exhibits turn-on fluorescence upon interacting with TAR RNA or DNA. Based on this, INHIBIT-AND and YES-INHIBIT-AND logic gates were constructed in parallel. The pH alteration leads to conformational changes of the hairpin structure, enabling the construction of a multi-reset reusable logic system which could be developed for in vitro sensing of the HIV-1 viral RNA.

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.

Graphene Oxide-Assisted Aptamer-Based Fluorescent Detection of Tetracycline Antibiotics

Tetracyclines are a group of common antibiotics, but owing to their toxicity, most of them are only used in animal husbandry and veterinary medicine. A DNA aptamer for tetracyclines has recently been reported. Upon aptamer binding, the fluorescence of tetracyclines was enhanced. This unique fluorescence enhancement was used to selectively detect the tetracyclines. The purpose of this study was to use graphene oxide (GO) to suppress the background fluorescence for enhanced detection. First, the adsorption of doxycycline on GO was studied. At pH 8.0, 82.7% of doxycycline was adsorbed by GO, and adding 2 µM aptamer desorbed 55.4% of doxycycline. With GO, the signal increase was comparable from pH 6 to 8, whereas without GO, the increase was significantly lower at pH 8. Under optimized condition, a detection limit of 1.6 nM doxycycline was achieved at pH 8.0 in the presence of GO, whereas without GO, the detection limit was 18.9 nM. This is an interesting example of the use of nanomaterials to enhance the performance of aptamer-based biosensors.

Controllable DNA nanodevices regulated by logic gates for multi-stimulus recognition

DNA biosensors have attracted considerable attention due to their great potential in environmental monitoring and medical diagnosis. Despite the great achievements, the single function and uncontrollability of the sensors restrict their further application. Therefore, it is necessary to construct controllable nanodevices with both sensing and responding capabilities to external stimuli. Herein, we develop a strategy to engineer structure-switching biosensors which can respond to external stimuli while preserving the sensing capability. The engineered nanodevice consists of an actuation module and a sensing module. Initially, the sensing module is disabled by a blocker strand which acts as an allosteric switch. Once the stimuli-responsive actuation module displaces the blocker DNA, the sensing module is activated. Based on the strategy, the engineered nanodevice could recognize both the target and external stimuli. As a demonstration of this strategy, a controllable Hg²⁺ sensor was designed, in which a 'YES', 'AND', and 'OR' logic gate is employed as the actuation module respectively to facilitate recognition of oligonucleotide inputs. The modular nature of the proposed strategy makes it easily generalizable to other structure-switching sensors. As a demonstration of this, we successfully apply it to the ATP sensor. The proposed strategy has potential in the fields of programmable biosensing, disease diagnosis, DNA computing, and intelligent nanodevices.

Wavelength-Dependent, Orthogonal Photoregulation of DNA Liberation for Logic Operations

In this study, we synthesized two phosphoramidites based on 2,7-bis-{4-nitro-8-[3-(2-propyl)-styryl]}-9,9-bis-[1-(3,6-dioxaheptyl)]-fluorene (BNSF) and 4,4'-bis-{8-[4-nitro-3-(2-propyl)-styryl]}-3,3'-di-methoxybiphenyl (BNSMB) structures as visible light-cleavable linkers for oligonucleotide conjugation. In addition to the commercial ultraviolet (UV) photocleavable (PC) linker, the BNSMB linker was further applied as a building component to construct photoregulated DNA devices as duplex structures, which are functionalized with fluorophores and quenchers. Selective cleavage of PC and BNSMB is achieved in response to ultraviolet (UV) and visible light irradiations as two inputs, respectively. This leads to controllable dissociation of pieces of DNA fragments, which is followed by changes of fluorescence emission as signal outputs of the system. By tuning the number and position of the photocleavable molecules, fluorophores, and quenchers, various DNA devices were developed, which mimic the functions of Boolean logic gates and achieve logic operations in AND, OR, NOR, and NAND gates in response to two different wavelengths of light inputs. By sequence design, the photolysis products can be precisely programmed in DNA devices and triggered to release in a selective and/or sequential manner. Thus, this photoregulated DNA device shows potential as a wavelength-dependent drug delivery system for selective control over the release of multiple individual therapeutic oligonucleotide-based drugs. We believe that our work not only enriches the library of photocleavable phosphoramidites available for bioconjugation but also paves the way for developing spatiotemporal-controlled, orthogonal-regulated DNA-based logic devices for a range of applications in materials science, polymers, chemistry, and biology.

Space-Confinment-Enhanced Fluorescence Detection of DNA on Hydrogel Particles Array

Fluorescent biosensors have been widely applied in DNA detection because of their reliability and reproducibility. However, low kinetics in DNA hybridization often brings out long test terms, thus restricting their practical use. Here, we demonstrate unexpected fast DNA fluorescence detection on the confined surface of hydrogel particles. When the pore size and surface charge of hydrogel particles are tailored, DNA molecules can be confined in the outer water layer of hydrogel particles. We fabricated a fluorescence-on DNA sensor based on the hydrogel particle array by utilizing the fluorescence quenching property of graphene oxide and its different adsorption behaviors toward single-strand DNA or double-strand DNA. Benefiting from the confinement effect of hydrogel particle surface and the enrichment effect of water evaporation, the DNA-recognition time was descreased significantly from 3000 s to less than 10 s under the target concentration of 400 nM. Moreover, rapid detection can be achieved at concentrations between 50 and 400 nM. The study provides another insight to fabricate fast biosensors and shows great potential in DNA diagnostics, gene analysis, and liquid biopsy.

Portable and sensitive detection of non-glucose target by enzyme-encapsulated metal-organic-framework using personal glucose meter

Personal glucose meter (PGM) is one of the most commercially available POC (point-of-care) devices for monitoring the level of glucose reliably, yet its non-glucose quantification ability is limited since such strategy needs ingenious interface design and tedious enzyme conjugation. Herein, we constructed a portable and sensitive platform that can detect non-glucose target by combining enzyme-encapsulated zeolitic imidazole framework-90 (ZIF-90) with personal glucose meter. ZIF-90 is an ideal carrier and susceptor due to the extraordinary capability of packaging enzyme and stimuli-responsiveness. We selected adenosine-5'-triphosphate (ATP) as the target model of non-glucose analytes. Upon ATP-induced decomposition of MOF, the released enzyme (glucose oxidase or invertase) catalyzed substrate and gave rise to the change of the glucose concentration for PGM assay. This method determined ATP with a remarkably sensitivity of 233 nM and effective recovery in real serum samples. Our strategy provides a facile and practical approach for measuring the non-glucose target using PGM, and could potentially be applied in bimolecular detection in point-of-care diagnosis.

Construction of fluorescence logic gates responding to telomerase and miRNA based on DNA-templated silver nanoclusters and the hybridization chain reaction

In this study, we have developed novel fluorescence logic gates for simultaneous analysis of telomerase activity and miRNA. An imperfectly complementary duplex is assembled which can be destroyed by telomerase catalyzed extension or miRNA mediated strand displacement. The released single-stranded DNA further initiates the subsequent hybridization chain reaction. The output response of the OR gate originates from fuel strand-templated silver nanoclusters (AgNCs). On the other hand, a three-way junction is constructed for the AND gate, which can be destroyed in the presence of miRNA and telomerase. The finally released DNA is also applied to trigger the hybridization chain reaction for the generation of a fluorescence response. The constructed logic gates are sensitive and reliable in the analysis of telomerase and miRNA for potential practical applications.

Recent advances in the exonuclease III-assisted target signal amplification strategy for nucleic acid detection

The detection of nucleic acids has become significantly important in molecular diagnostics, gene therapy, mutation analysis, forensic investigations and biomedical development, and so on. In recent years, exonuclease III (Exo III) as an enzyme in the 3'-5' exonuclease family has evolved as a frequently used technique for signal amplification of low level DNA target detection. Different from the traditional target amplification strategies, the Exo III-assisted amplification strategy has been used for target DNA detection through directly amplifying the amounts of signal reagents. The Exo III-assisted amplification strategy has its unique advantages and characters, because the character of non-specific recognition of Exo III can overcome the limitation of a target-to-probe ratio of 1 : 1 in the traditional nucleic acid hybridization assay and acquire higher sensitivity. In this review, we selectively discuss the recent advances in the Exo III-assisted amplification strategy, including the amplification strategy integrated with nanomaterials, biosensors, hairpin probes and other nucleic acid detection methods. We also discuss the strengths and limitations of each strategy and methods to overcome the limitations.

Intracellular CircRNA imaging and signal amplification strategy based on the graphene oxide-DNA system

CircRNA is a type of covalently closed circular RNA molecule that serves as a potential biomarker for the disease early diagnosis and clinical researches. To achieve living cell imaging of specific circRNA, we developed a novel graphene oxide (GO)-based catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR) signal dual amplification system (GO-CHA-HCR, abbreviated GO-AR) for circ-Foxo3 imaging in living cells. The developed system consists of four types of designed hairpin DNA HP1, HP2, H1, and fluorophore-labeled H2, which are absorbed on the GO nanosheets surface leading to fluorescence quenching. In the presence of circ-Foxo3, the CHA cycle was initiated to form a hybrid chain with split fragments, which triggered the HCR cycle to generate dsDNA nanowires that were then released from GO. This process recovered the quenched fluorescence, realizing two-stage signal amplification. The GO-AR system effectively improved the signal-to-noise ratio compared to the traditional GO-CHA and GO-HCR detection system. The detection limit of circ-Foxo3 was as low as 15 pM with excellent sensitivity and selectivity. In addition, the enzyme-free sensing system was successfully applied in living cell circRNA imaging and serum circRNA detection, indicating its high potential in clinical diagnostics.

Zeptomole Imaging of Cytosolic MicroRNA Cancer Biomarkers with A Light-Controlled Nanoantenna

Detecting and quantifying intracellular microRNAs (miRNAs) are a critical step in resolving a cancer diagnostic and resolving the ensemble of gene products that orchestrate the living state of cells. However, the nanoprobe for detecting low abundance miRNAs in cell cytosol is restricted by either the "one-to-one" signal-trigger model or difficulty for cytosol delivery. To address these challenges, we designed a light-harvesting nanoantenna-based nanoprobe, which directs excitation energy to a single molecule to sensitively detect cytosolic miRNA. With light irradiation, the light-harvesting nanoantenna effectively disrupted lysosomal structures by generation of reactive oxygen species, substantially achieved cytosol delivery. The nanoantenna containing > 4000 donor dyes can efficiently transfer excitation energy to one or two acceptors with 99% efficiency, leading to unprecedented signal amplification and biosensing sensitivity. The designed nanoantenna can quantify cytosolic miR-210 at zeptomolar level. The fluorescence lifetime of the donor exhibited good relationship with miR-210 concentration in the range of 0.032 to 2.97 amol/ngRNA. The zeptomole sensitivity of nanoantenna provides accurate bioimaging of miR-210 both in multiple cell lines and in vivo assay, which creates a pathway for the creation of miRNA toolbox for quantitative epigenetics and personalized medicine.

Stimuli-responsive hydrogel microcapsules for the amplified detection of microRNAs

A method for the synthesis of DNA-based acrylamide hydrogel microcapsules loaded with quantum dots as a readout signal is introduced. The shell of DNA-acrylamide hydrogel microcapsules is encoded with microRNA-responsive functionalities, being capable of the detection of cancer-associated microRNA. The microRNA-141 (miR-141), a potential biomarker in prostate cancer, was employed as a model target in the microcapsular biosensor. The sensing principle of the microcapsular biosensor is based on the competitive sequence displacement of target miR-141 with the bridging DNA in the microcapsule's shell, leading to the unlocking of DNA-acrylamide hydrogel microcapsules and the release of the readout signal provided by fluorescent quantum dots. The readout signal is intensified as the concentration of miR-141 increases. While miR-141 was directly measured by DNA-acrylamide hydrogel microcapsules, the linear range for the detection of miR-141 is 2.5 to 50 μM and the limit of detection is 1.69 μM. To improve the sensitivity of the microcapsular biosensor for clinical needs, the isothermal strand displacement polymerization/nicking amplification machinery (SDP/NA) process was coupled to the DNA-acrylamide hydrogel microcapsule sensor for the microRNA detection. The linear range for the detection of miR-141 is improved to the range of 10² to 10⁵ pM and the limit of detection is 44.9 pM. Compared to direct microcapsular biosensing, the detection limit for miR-141 by microcapsules coupled with strand-displacement amplification is enhanced by four orders of magnitude.

Application of Functionalized Graphene Oxide Based Biosensors for Health Monitoring: Simple Graphene Derivatives to 3D Printed Platforms

Biosensors hold great potential for revolutionizing personalized medicine and environmental monitoring. Their construction is the key factor which depends on either manufacturing techniques or robust sensing materials to improve efficacy of the device. Functional graphene is an attractive choice for transducing material due to its various advantages in interfacing with biorecognition elements. Graphene and its derivatives such as graphene oxide (GO) are thus being used extensively for biosensors for monitoring of diseases. In addition, graphene can be patterned to a variety of structures and is incorporated into biosensor devices such as microfluidic devices and electrochemical and plasmonic sensors. Among biosensing materials, GO is gaining much attention due to its easy synthesis process and patternable features, high functionality, and high electron transfer properties with a large surface area leading to sensitive point-of-use applications. Considering demand and recent challenges, this perspective review is an attempt to describe state-of-the-art biosensors based on functional graphene. Special emphasis is given to elucidating the mechanism of sensing while discussing different applications. Further, we describe the future prospects of functional GO-based biosensors for health care and environmental monitoring with a focus on additive manufacturing such as 3D printing.

In Vivo Monitoring of Intracellular Metabolite in a Microalgal Cell Using an Aptamer/Graphene Oxide Nanosheet Complex

Real-time sensing and imaging of intracellular metabolites in living cells are crucial tools for the characterization of complex biological processes, including the dynamic fluctuation of metabolites. Therefore, additional efforts are required to develop in vivo detection strategies for the visualization and quantification of specific target metabolites, particularly in microalgae. In this study, we developed a strategy to monitor a specific microalgal metabolite in living cells using an aptamer/graphene oxide nanosheet (GOnS) complex. As a proof-of-concept, β-carotene, an antioxidant pigment that accumulates in most microalgal species, was chosen as a target metabolite. To achieve this, a β-carotene-specific aptamer was selected through graphene oxide-assisted systematic evolution of ligands by exponential enrichment (GO-SELEX) and characterized thereafter. The aptamer could sensitively sense the changes in the concentration of β-carotene (i.e., the target metabolite) and more specifically bind to β-carotene than to nontargets. The selected aptamer was labeled with a fluorophore (fluorescein; FAM) and allowed to form an aptamer/GOnS complex that protected the aptamer from nucleic cleavages. The aptamer/GOnS complex was delivered into the cells via electroporation, thus enabling the sensitive monitoring of β-carotene in the cell by quantifying the aptamer fluorescence intensity. The results suggest that our biocompatible strategy could be employed to visualize and semiquantify intracellular microalgae metabolites in vivo, which holds a great potential in diverse fields such as metabolite analysis and mutant screening.

Versatile non-luminescent color palette based on guest exchange dynamics in paramagnetic cavitands

Multicolor luminescent portrayal of complexed arrays is indispensable for many aspects of science and technology. Nevertheless, challenges such as inaccessible readouts from opaque objects, a limited visible-light spectrum and restricted spectral resolution call for alternative approaches for multicolor representation. Here, we present a strategy for spatial COlor Display by Exploiting Host-guest Dynamics (CODE-HD), comprising a paramagnetic cavitand library and various guests. First, a set of lanthanide-cradled α-cyclodextrins (Ln-CDs) is designed to induce pseudo-contact shifts in the ¹⁹F-NMR spectrum of Ln-CD-bound guest. Then, capitalizing on reversible host-guest binding dynamics and using magnetization-transfer ¹⁹F-MRI, pseudo-colored maps of complexed arrays are acquired and applied in molecular-steganography scenarios, showing CODE-HD’s ability to generate versatile outputs for information encoding. By exploiting the widely shifted resonances induced by Ln-CDs, the guest versatility and supramolecular systems' reversibility, CODE-HD provides a switchable, polychromatic palette, as an advanced strategy for light-free, multicolor-mapping.

Host-guest supramolecular chemistry can be used as a tool to develop multicolor displays. Here, the authors present a system based on lanthanide-cradled cyclodextrins that allows to construct MRI-readable and erasable artificial non-luminescent color palettes.

Graphene, an Interesting Nanocarbon Allotrope for Biosensing Applications: Advances, Insights, and Prospects

Graphene, a relatively new two-dimensional (2D) nanomaterial, possesses unique structure (e.g. lighter, harder, and more flexible than steel) and tunable physicochemical (e.g. electronical, optical) properties with potentially wide eco-friendly and cost-effective usage in biosensing. Furthermore, graphene-related nanomaterials (e.g. graphene oxide, doped graphene, carbon nanotubes) have inculcated tremendous interest among scientists and industrials for the development of innovative biosensing platforms, such as arrays, sequencers and other nanooptical/biophotonic sensing systems (e.g. FET, FRET, CRET, GERS). Indeed, combinatorial functionalization approaches are constantly improving the overall properties of graphene, such as its sensitivity, stability, specificity, selectivity, and response for potential bioanalytical applications. These include real-time multiplex detection, tracking, qualitative, and quantitative characterization of molecules (i.e. analytes [H₂O₂, urea, nitrite, ATP or NADH]; ions [Hg²⁺, Pb²⁺, or Cu²⁺]; biomolecules (DNA, iRNA, peptides, proteins, vitamins or glucose; disease biomarkers such as genetic alterations in BRCA1, p53) and cells (cancer cells, stem cells, bacteria, or viruses). However, there is still a paucity of comparative reports that critically evaluate the relative toxicity of carbon nanoallotropes in humans. This manuscript comprehensively reviews the biosensing applications of graphene and its derivatives (i.e. GO and rGO). Prospects and challenges are also introduced.

Dual-color graphene quantum dots and carbon nanoparticles biosensing platform combined with Exonuclease III-assisted signal amplification for simultaneous detection of multiple DNA targets

Sensitive and simultaneous detection of multiple biomarkers such as target DNA or proteins using biocompatible materials with good analysis performance remains an important challenge. Herein, we successfully developed a signal "off-on" highly sensitive multiplex detection platform based on the combination of dual-color graphene quantum dots (blue GQDs and green GQDs) modified DNA probes with carbon nanoparticles (CNPs), which is a cheap, effective nonfluorescent quencher to simultaneously quench the fluorescence of both GQDs-DNA probes. The Exo III-assisted sequence-independent target recycling and signal amplification strategy was integrated into this sensing platform, which endows it with high sensitivity towards the multiplex detection of targets DNA. The detection limits of 6.6 pM for HIV and 9.5 pM for HBV were achieved respectively, which is about 60-fold lower than that of traditional unamplified homogeneous fluorescent assay methods. Our proposed multiplex detecting platform is advantageous in both respective and simultaneous detection of multiple targets and can also discriminate perfectly matched targets from mismatched targets in both PBS buffer and 1% human serum samples, demonstrating its potential to be a reliable strategy for highly sensitive simultaneous detection of multiple target genes in practical diagnosis applications.

Aptamer-Functionalized Hybrid Nanostructures for Sensing, Drug Delivery, Catalysis and Mechanical Applications

Sequence-specific nucleic acids exhibiting selective recognition properties towards low-molecular-weight substrates and macromolecules (aptamers) find growing interest as functional biopolymers for analysis, medical applications such as imaging, drug delivery and even therapeutic agents, nanotechnology, material science and more. The present perspective article introduces a glossary of examples for diverse applications of aptamers mainly originated from our laboratory. These include the introduction of aptamer-functionalized nanomaterials such as graphene oxide, Ag nanoclusters and semiconductor quantum dots as functional hybrid nanomaterials for optical sensing of target analytes. The use of aptamer-functionalized DNA tetrahedra nanostructures for multiplex analysis and aptamer-loaded metal-organic framework nanoparticles acting as sense-and-treat are introduced. Aptamer-functionalized nano and microcarriers are presented as stimuli-responsive hybrid drug carriers for controlled and targeted drug release, including aptamer-functionalized SiO2 nanoparticles, carbon dots, metal-organic frameworks and microcapsules. A further application of aptamers involves the conjugation of aptamers to catalytic units as a means to mimic enzyme functions "nucleoapzymes". In addition, the formation and dissociation of aptamer-ligand complexes are applied to develop mechanical molecular devices and to switch nanostructures such as origami scaffolds. Finally, the article discusses future challenges in applying aptamers in material science, nanotechnology and catalysis.

Multiplexed and amplified chemiluminescence resonance energy transfer (CRET) detection of genes and microRNAs using dye-loaded hemin/G-quadruplex-modified UiO-66 metal-organic framework nanoparticles

Dye-loaded UiO-66 metal-organic framework nanoparticles (NMOFs) modified with catalytic hemin/G-quadruplex DNAzyme labels act as functional hybrid modules for the chemiluminescence resonance energy transfer (CRET) analysis of miRNAs (miRNA-155 or miRNA-21) or genes (p53 or BRCA1). The dye-loaded NMOFs (dye = fluorescein (Fl) or rhodamine 6G (Rh 6G)) are modified with hairpin probes that are engineered to include in their loop domains recognition sequences for the miRNAs or genes, and in their stem regions caged G-quadruplex domains. In the presence of the analytes miRNAs or genes, the hairpin structures are opened, leading, in the presence of hemin, to the self-assembly of hemin/G-quadruplex DNAzyme labels linked to the dye-loaded NMOFs. In the presence of luminol and H2O2, the hemin/G-quadruplex DNAzyme labels catalyze the generation of chemiluminescence that provides radiative energy to stimulate the process of CRET to the dye loaded in the NMOFs, resulting in the luminescence of the loaded dye without external excitation. The resulting CRET signals relate to the concentrations of the miRNAs or the genes and allow the sensitive analysis of miRNAs and genes. In addition, the DNA hairpin-functionalized dye-loaded NMOF sensing modules were further applied to develop amplified miRNA or gene CRET-based sensing platforms. The dye-loaded NMOFs were modified with hairpin probes that include in their loop domain the recognition sequences for miRNA-155 or miRNA-21 or the recognition sequences for the p53 or BRCA1 genes. Subjecting the hairpin-modified NMOFs to the respective miRNAs or genes, in the presence of two hairpins H i and H j that include in their stem regions caged G-quadruplex subunit domains, results in the analyte-triggered opening of the probe hairpin linked to the NMOFs, and the opened hairpin tethers induce the cross-opening of the hairpins H i and H j by the hybridization chain reaction, HCR, resulting in the assembly of G-quadruplex wires tethered to the NMOFs. The binding of hemin to the HCR-generated chains yields hemin/G-quadruplex DNAzyme wires that enhance, in the presence of luminol/H2O2, the CRET processes in the hybrid nanostructures. These amplification platforms lead to the amplified sensing of miRNAs and genes. By mixing the Fl- and Rh 6G-loaded hairpin-functionalized UiO NMOFs, the multiplexed CRET detection of miRNA-155, miRNA-21 and the p53 and BRCA1 genes is demonstrated.

Triggered Dimerization and Trimerization of DNA Tetrahedra for Multiplexed miRNA Detection and Imaging of Cancer Cells

The reversible and switchable triggered reconfiguration of tetrahedra nanostructures from monomer tetrahedra structures into dimer or trimer structures is introduced. The triggered bridging of monomer tetrahedra by K⁺ -ion-stabilized G-quadruplexes or T-A•T triplexes leads to dimer or trimer tetrahedra structures that are separated by crown ether or basic pH conditions, respectively. The signal-triggered dimerization/trimerization of DNA tetrahedra structures is used to develop multiplexed miRNA-sensing platforms, and the tetrahedra mixture is used for intracellular sensing and imaging of miRNAs.

Construction of a simple and intelligent DNA-based computing system for multiplexing logic operations

Over the past few decades, DNA-based computing technology has become a rapidly developing technology and shown remarkable capabilities in handling complex computational problems. However, most of the logical operations that DNA computer can achieve are still very basic or using large-scale operations to realize complex functions, especially in mathematics. Graphene oxide (GO) is an ideal nanomaterial for biological computing, which has been used in our previous work to perform basic logic operations. Here, we utilize GO to implement far more complex and large-scale logical computing. For the first time, in this work, we utilize the unique interaction between GO and a variety of classified single-stranded DNAs as the reaction platform, by segmenting and encoding the DNA sequences, and programming the interactions between inputs and between the inputs and reaction platform, two relative large-scale logic operations, 6-bit square-root and 9-bit cube-root logical circuits are realized. This study provides a simple but efficient method for advanced and large-scale logical mathematic operations in biotechnology, opening a new horizon for building biocomputer-based innovative functional devices.

Logic Gates Based on DNA Aptamers

DNA bio-computing is an emerging trend in modern science that is based on interactions among biomolecules. Special types of DNAs are aptamers that are capable of selectively forming complexes with target compounds. This review is devoted to a discussion of logic gates based on aptamers for the purposes of medicine and analytical chemistry. The review considers different approaches to the creation of logic gates and identifies the general algorithms of their creation, as well as describes the methods of obtaining an output signal which can be divided into optical and electrochemical. Aptameric logic gates based on DNA origami and DNA nanorobots are also shown. The information presented in this article can be useful when creating new logic gates using existing aptamers and aptamers that will be selected in the future.

pH-Dependent adsorption of aromatic compounds on graphene oxide: An experimental, molecular dynamics simulation and density functional theory investigation

This work provides a comprehensive understanding for the pH-dependent adsorption of aromatic compounds (ACs) on graphene oxide (GO). Isothermal and kinetics experiments indicated both adsorption capacity and adsorption rate were suppressed at higher pH, and the mechanisms were revealed by molecular dynamics simulations and density functional theory calculations. More specifically, π-π, hydrogen bond, vdWs, and water-mediated steric hindrance interactions were examined to reveal how pH affected the adsorption capacity, and microscopic dynamic adsorption process was captured to reveal how pH affected the adsorption rate. Results showed the reduced adsorption capacity at higher pH was mediated by increased electrostatic repulsion, weakened π-π interaction, and increased water-mediated steric hindrance. The pH-dependent behaviour of GO was responsible for the effect of pH on adsorption rate. Self-aggregation of GO at lower pH helped to capture ACs and created more favourable adsorption sites. Upon the adsorption of ACs on GO, GO/water/AC/water/GO sandwich-like structure formed, which was also mediated by solution pH. Overall, pH affects the adsorption of ACs on GO by regulating driving forces, adsorption process, and the configuration property of GOAC complex.

DNA Tetrahedra Modules as Versatile Optical Sensing Platforms for Multiplexed Analysis of miRNAs, Endonucleases, and Aptamer-Ligand Complexes

The sensing modules for analyzing miRNAs or the endonucleases consist of tetrahedra functionalized with three different fluorophore-quencher pairs in spatially quenched configurations and hairpin units acting as recognition elements for the analytes. Three different miRNAs (miRNA-21, miRNA-221, and miRNA-155) or three different endonucleases (Nt.BbvCI, EcoRI, and HindIII) uncage the respective hairpins, leading to the switched-on fluorescence of the respective fluorophores and to the multiplex detection of the respective analytes. In addition, a tetrahedron module for the multiplexed analysis of aptamer ligand complexes (ligands = ATP, thrombin, VEGF) is introduced. The module includes edges modified with three spatially separated fluorophore-quencher pairs that were stretched by the respective aptamer strands to yield a switched-on fluorescent state. Formation of the respective aptamer ligands reconfigures the edges into fluorophore-quenched caged-hairpin structures that enable the multiplexed analysis of the aptamer-ligand complexes. The facile permeation of the tetrahedra structures into cells is used for the imaging of MCF-7 and HepG2 cancer cells and their discrimination from normal epithelial MCF-10A breast cells.

Competitive aptasensor for the ultrasensitive multiplexed detection of cancer biomarkers by fluorescent nanoparticle counting

Cancer biomarker quantification in human serum is of great importance for accurate patient diagnosis and informed clinical management. To date, ultrasensitive multiplexed detection of proteins without amplification is still a major challenge. Herein, we proposed a competitive aptasensor strategy for ultrasensitive multiplexed cancer biomarker detection by fluorescent nanoparticle (FNP) counting. The sequences are designed such that the binding abilities of linker DNA (L-DNA) with DNA-functionalized FNPs (DNA-FNPs) and aptamer are comparable. As long as one target binds with one molecule of aptamer, a signalling FNP forms a sandwich-structured nanocomposite, which was subsequently observed and enumerated with a fluorescence microscope. This 1 : 1 target-to-signal FNP production assured an improved sensitivity, benefiting from the reasonably good brightness and photostability of FNPs. For both singleplexed and multiplexed detection, this proposed strategy achieved an approximately 1000-fold improved limit of detection than the conventional method with the detection volume of 3.2 μL. Notably, the results for carcinoembryonic antigen (CEA) detection obtained directly from 9 human serum samples (colorectal/lung/healthy individuals) were consistent with that obtained by ELISA, showing potential application in clinical diagnosis.

CuBr2/EDTA-mediated ATRP for ultrasensitive fluorescence detection of lung cancer DNA

In this paper, we reported a system for the ultrasensitive fluorescence detection of cytokeratin fragment antigen 21-1 DNA (CYFRA21-1 DNA) for the early diagnosis of lung cancer. The approach used electron transfer atom transfer radical polymerization (ARGET-ATRP) with ethylenediaminetetraacetic acid (EDTA) as the metal ligand. Firstly, thiolated peptide nucleic acid (PNA) was linked to aminated magnetic beads solutions (MBs) by a cross-linking agent and then hybridized with CYFRA21-1 DNA (tDNA). Subsequently, Zr4+ was introduced into the MBs by conjugating with the phosphate group of tDNA, and the initiator of ARGET-ATRP was introduced into via phosphate-Zr4+-carboxylate chemistry. Next, Cu(II)Br/EDTA was reduced to Cu(I)/EDTA by ascorbic acid (AA) to trigger ARGET-ATRP and then a large amount of fluorescein-o-acrylate (FA) molecules were grafted from the surface of the MBs, which amplified significantly the fluorescent signal. Under optimal conditions, a strong linear relationship of tDNA over the range from 0.1 fM to 1 nM (R2 = 0.9988). The limit of detection was as low as 23.8 aM (~143 molecules). The fluorescence detection based on the ARGET-ATRP strategy yielded excellent sensitivity, selectivity, outstanding anti-interference properties, and cost-effectiveness. These results indicated that this strategy has considerable potential for biological detection and early clinical diagnosis.

Polysaccharide-enhanced ARGET ATRP signal amplification for ultrasensitive fluorescent detection of lung cancer CYFRA 21-1 DNA

An ultrasensitive fluorescence biosensor for detecting cytokeratin fragment antigen 21-1 (CYFRA 21-1) DNA of non-small cell lung carcinoma (NSCLC) is designed using polysaccharide and activator regenerated by electron transfer atom transfer radical polymerization (ARGET ATRP) signal amplification strategy. Thiolated peptide nucleic acid (PNA) is fixed on magnetic nanoparticles (MNPs) by a cross-linking agent and hybridized with CYFRA 21-1 DNA. Hyaluronic acid (HA) is linked to PNA/tDNA heteroduplexes in the form of carboxy-Zr⁴⁺-phosphate. Subsequently, multiple 2-bromo-2-methylpropionic acid (BMP) molecules are linked with HA to initiate ARGET ATRP reaction. Finally, a large number of fluorescein o-acrylate (FA) monomers are polymerized on the macro-initiators, and the fluorescence signal is significantly amplified. Under optimal conditions, this biosensor shows a significant linear correlation between the fluorescence intensity and logarithm of CYFRA 21-1 DNA concentration (0.1 fM to 0.1 nM), and the limit of detection is as low as 78 aM. Furthermore, the sensor has a good ability to detect CYFRA 21-1 DNA in serum samples and to recognize mismatched bases. It suggests that the strategy has broad application in early diagnosis by virtue of its high sensitivity and selectivity. Graphical abstract A novel and highly sensitive fluorescence biosensor for quantitatively detecting CYFRA 21-1 DNA via dual signal amplification of hyaluronic acid and ARGET ATRP reaction was developed. This proposed method has a low detection limit, wide detection range, high selectivity, and strong anti-interference.

Graphene-Based Steganographic Aptasensor for Information Computing and Monitoring Toxins of Biofilm in Food

Fungi-forming biofilm would produce various toxins in food. The toxin contamination will cause great harm to food and human health. Herein, a novel graphene-based steganographic aptasensor was assembled for multifunctional applications, which depended on the specific recognition and information encoding ability of DNA aptamers [mycotoxins, including zearalenone (ZEN) and ochratoxin A (OTA) aptamers, as models] and the selective absorption and fluorescence quenching capacities of graphene oxide (GO). The graphene-based steganographic aptasensor can be regarded as an information encryption and steganographic system using GO as a cover, aptamers for specific target recognition as information carriers and dual targets (ZEN and OTA) as special keys. In our work, the fluorescence of capture probes (Cy3 aptamer and Alexa Fluor 488 aptamer) was quenched by GO to realize information encryption. In the presence of dual targets in the GO-APT solution, Cy3 aptamer (APT1), and Alexa Fluor 488 aptamer (APT2) were released from the surface of GO, decrypting the hidden information. In addition, our work offers a sensor for rapid and sensitive simultaneous fluorescence determination of ZEN and OTA. The detection limit of the aptasensor was 1.797 ng/ml for ZEN and 1.484 ng/ml for OTA. In addition, the graphene-based steganographic aptasensor can be used to construct a molecular logic gate system in which GO, aptamers, and mycotoxins are employed as the input and compounds and fluorescence signals were used as the output. This would be helpful to control the biofilm toxin in the future.

Covalent Organic Frameworks: Design, Synthesis, and Functions

Covalent organic frameworks (COFs) are a class of crystalline porous organic polymers with permanent porosity and highly ordered structures. Unlike other polymers, a significant feature of COFs is that they are structurally predesignable, synthetically controllable, and functionally manageable. In principle, the topological design diagram offers geometric guidance for the structural tiling of extended porous polygons, and the polycondensation reactions provide synthetic ways to construct the predesigned primary and high-order structures. Progress over the past decade in the chemistry of these two aspects undoubtedly established the base of the COF field. By virtue of the availability of organic units and the diversity of topologies and linkages, COFs have emerged as a new field of organic materials that offer a powerful molecular platform for complex structural design and tailor-made functional development. Here we target a comprehensive review of the COF field, provide a historic overview of the chemistry of the COF field, survey the advances in the topology design and synthetic reactions, illustrate the structural features and diversities, scrutinize the development and potential of various functions through elucidating structure-function correlations based on interactions with photons, electrons, holes, spins, ions, and molecules, discuss the key fundamental and challenging issues that need to be addressed, and predict the future directions from chemistry, physics, and materials perspectives.

Red phosphorus decorated graphene oxide nanosheets: label-free DNA detection

A straightforward synthetic strategy is developed in this study to synthesize highly fluorescent red phosphorus on nitrogen-doped reduced graphene oxide (f-RP@N-rGO) nanosheets in an aqueous medium; this is used as a novel detection platform for the label-free real-time sensing of nucleic acids with low background noise and a high signal-to-noise ratio.

Aptamer-Based Fluorescent Biosensing of Adenosine Triphosphate and Cytochrome c via Aggregation-Induced Emission Enhancement on Novel Label-Free DNA-Capped Silver Nanoclusters/Graphene Oxide Nanohybrids

Four fluorescent DNA-stabilized fluorescent silver nanoclusters (DNA-AgNCs) were designed and synthesized with differences in lengths of cytosine-rich DNA strand (as the stabilizing agent) and target-specific strand DNA aptamers for adenosine triphosphate (ATP) and cytochrome c (Cyt c). After their nanohybrid formation with graphene oxide (GO), it was unexpectedly found that, depending on the composition of the base and length of the strand DNA aptamer, the fluorescence intensity of three of the nanohybrids significantly enhanced. Our experimental observations and quantum mechanical calculations provided an insight into the mechanisms underlying the behavior of DNA-AgNCs/GO nanohybrids. The enhanced fluorescence was found to be attributed to the aggregation-induced emission enhancement (AIE) characteristic of the DNA-AgNCs adsorbed on the GO surface, as confirmed evidently by both fluorescence and transmission electron microscopies. The AIE is a result of hardness and oxidation properties of GO, which lead to enhanced argenophilic interaction and thus to increased Ag(I)-DNA complex shell aggregation. Consequently, two of the DNA-AgNCs/GO nanohybrids were successfully extended to construct highly selective, sensitive, label-free, and simple aptasensors for biosensing of ATP (LOD = 0.42 nM) and Cyt c (LOD = 2.3 nM) in lysed Escherichia coli DH5 α cells and mouse embryonic stem cells, respectively. These fundamental findings are expected to significantly influence the designing and engineering of new AgNCs/GO-based AIE biosensors.

Photosensitized H2 Evolution and NADPH Formation by Photosensitizer/Carbon Nitride Hybrid Nanoparticles

The broadband C₃N₄ semiconductor absorbs in the UV region, λ = 330-380 nm, a feature limiting its application for light-to-energy conversion. The unique surface adsorption properties of C₃N₄ allow, however, the binding of a photosensitizer, operating in the visible-solar spectrum to the surface of C₃N₄. Coupling of the energy levels of the photosensitizer with the energy levels of C₃N₄ allows effective photoinduced electron-transfer quenching and subsequent charge separation in the hybrid structures. Two methods to adsorb a photosensitizer on the C₃N₄ nanoparticles are described. One is exemplified by the adsorption of Zn(II)-protoporphyrin IX on C₃N₄ using π-π interactions. The second method utilizes the specific binding interactions of single-stranded nucleic acids on C₃N₄ and involves the binding of a Ru(II)-tris-bipyridine-modified nucleic acid on the C₃N₄ nanoparticles. Effective electron-transfer quenching of the photoexcited photosensitizers by C₃N₄ proceeds in the two hybrid systems. The two hybrid photosystems induce the effective photosensitized reduction of N,N'-dimethyl-4,4'-bipyridinium, MV²⁺, to MV^+•, in the presence of Na₂EDTA as a sacrificial electron donor. The generation of MV^+• is ca. 5-fold higher as compared to the formation of MV^+• in the presence of the photosensitizer alone (in the absence of C₃N₄). The effective generation of MV^+• in the photosystems is attributed to the efficient quenching of the photosensitizers, followed by effective charge separation of the electrons in the conduction band of C₃N₄ and the holes in the oxidized photosensitizer. The subsequent transfer of the conduction-band electrons to MV²⁺ and the oxidation of Na₂EDTA by the oxidized photosensitizers lead to the effective formation of MV^+•. The photogenerated MV^+• by the two hybrid photosystems is used to catalyze H₂ evolution in the presence of Pt nanoparticle catalysts and to mediate the reduction of NADP⁺ to NADPH, in the presence of ferredoxin-NADP⁺ reductase, FNR. The ability to couple the photogenerated NADPH to drive NADP⁺-dependent biocatalytic transformations is demonstrated.

Dual-Enhanced Raman Scattering-Based Characterization of Stem Cell Differentiation Using Graphene-Plasmonic Hybrid Nanoarray

Surface-enhanced Raman scattering (SERS) has demonstrated great potential to analyze a variety of bio/chemical molecular interactions within cells in a highly sensitive and selective manner. Despite significant advancements, it remains a critical challenge to ensure high sensitivity and selectivity, while achieving uniform signal enhancement and high reproducibility for quantitative detection of targeted biomarkers within a complex stem cell microenvironment. Herein, we demonstrate an innovative sensing platform, using graphene-coated homogeneous plasmonic metal (Au) nanoarrays, which synergize both electromagnetic mechanism (EM)- and chemical mechanism (CM)-based enhancement. Through the homogeneous plasmonic nanostructures, generated by laser interference lithography (LIL), highly reproducible enhancement of Raman signals could be obtained via a strong and uniform EM. Additionally, the graphene-functionalized surface simultaneously amplifies the Raman signals by an optimized CM, which aligns the energy level of the graphene oxide with the target molecule by tuning its oxidation levels, consequently increasing the sensitivity and accuracy of our sensing system. Using the dual-enhanced Raman scattering from both EM from the homogeneous plasmonic Au nanoarray and CM from the graphene surface, our graphene-Au hybrid nanoarray was successfully utilized to detect as well as quantify a specific biomarker (TuJ1) gene expression levels to characterize neuronal differentiation of human neural stem cells (hNSCs). Collectively, we believe our unique graphene-plasmonic hybrid nanoarray can be extended to a wide range of applications in the development of simple, rapid, and accurate sensing platforms for screening various bio/chemical molecules.

A Multicolor Fluorescence Nanoprobe Platform Using Two-Dimensional Metal Organic Framework Nanosheets and Double Stirring Bar Assisted Target Replacement for Multiple Bioanalytical Applications

Multicolor fluorescence probes can show fluorescence of different colors when detecting different targets, and the excellent feature can create a highly differentiated multicolor sensing platform. However, most of the previously reported multicolor luminescent materials usually suffer from high toxicity and photobleaching, complex preparation procedures, and poor water solubility, which may not be conducive to bioanalytical applications. Two-dimensional metal organic frameworks (2D MOFs), which have large specific surface areas with long-range fluorescence quenching coupled with biomolecular recognition events, have encouraged innovation in biomolecular probing. Here, we propose a 2D-MOF-based multicolor fluorescent aptamer nanoprobe using a double stirring bar assisted target replacement system for enzyme-free signal amplification. It utilizes the interaction between 2D MOFs and DNA molecules to detect multiple antibiotics quickly, sensitively, and selectively. Since 2D MOFs have excellent quenching efficiency for luminescence of fluorescent-dye-labeled single-strand DNA (ssDNA), the background fluorescence can be largely reduced and the signal-to-noise ratio can be improved. When the adsorbed ssDNA formed double helix double-stranded DNA with its complementary ssDNA, its fluorescence can be almost fully recovered. The assay was tested by detecting chloramphenicol (CAP), oxytocin (OTC), and kanamycin (KANA) in biological samples. The developed aptasensor was sufficiently sensitive to detect the antibiotic residues as low as 1.5 pM CAP, 2.4 pM OTC, and 1 pM KANA (S/N = 3). It has been preliminarily used for multicolor imaging of three different antibiotics in fish tissue slices with satisfactory results.

Progress in miRNA Detection Using Graphene Material-Based Biosensors

MicroRNAs (miRNAs) are short, endogenous, noncoding RNAs that play critical roles in physiologic and pathologic processes and are vital biomarkers for several disease diagnostics and therapeutics. Therefore, rapid, low-cost, sensitive, and selective detection of miRNAs is of paramount importance and has aroused increasing attention in the field of medical research. Among the various reported miRNA sensors, devices based on graphene and its derivatives, which form functional supramolecular nanoassemblies of π-conjugated molecules, have been revealed to have great potential due to their extraordinary electrical, chemical, optical, mechanical, and structural properties. This Review critically and comprehensively summarizes the recent progress in miRNA detection based on graphene and its derivative materials, with an emphasis on i) the underlying working principles of these types of sensors, and the unique roles and advantages of graphene materials; ii) state-of-the-art protocols recently developed for high-performance miRNA sensing, including representative examples; and iii) perspectives and current challenges for graphene sensors. This Review intends to provide readers with a deep understanding of the design and future of miRNA detection devices.

Fabrication of Electrochemical-Based Bioelectronic Device and Biosensor Composed of Biomaterial-Nanomaterial Hybrid

The field of bioelectronics has paved the way for the development of biochips, biomedical devices, biosensors and biocomputation devices. Various biosensors and biomedical devices have been developed to commercialize laboratory products and transform them into industry products in the clinical, pharmaceutical, environmental fields. Recently, the electrochemical bioelectronic devices that mimicked the functionality of living organisms in nature were applied to the use of bioelectronics device and biosensors. In particular, the electrochemical-based bioelectronic devices and biosensors composed of biomolecule-nanoparticle hybrids have been proposed to generate new functionality as alternatives to silicon-based electronic computation devices, such as information storage, process, computations and detection. In this chapter, we described the recent progress of bioelectronic devices and biosensors based on biomaterial-nanomaterial hybrid.

Two-Dimensional Graphene Family Material: Assembly, Biocompatibility and Sensors Applications

Graphene and its chemically exfoliated derivatives—GO and rGO—are the key members of graphene family materials (GFM). The atomically thick crystal structure and the large continuous π conjugate of graphene imparts it with unique electrical, mechanical, optical, thermal, and chemical properties. Although those properties of GO and rGO are compromised, they have better scalability and chemical tunability. All GFMs can be subject to noncovalent modification due to the large basal plane. Besides, they have satisfying biocompatibility. Thus, GFMs are promising materials for biological, chemical and mechanical sensors. The present review summarizes how to incorporate GFMs into different sensing system including fluorescence aptamer-based sensors, field-effect transistors (FET), and electrochemical sensors, as well as, how to covalently and/or non-covalently modify GFMs to achieve various detection purpose. Sensing mechanisms and fabrication strategies that will influence the sensitivity of different sensing system are also reviewed.

A graphene oxide-based hairpin probe coupling duplex-specific nuclease signal amplification for detection and imaging of mRNA in living cells

In situ imaging of mRNA in living cells can help to monitor the real time mRNA expression and also useful for diagnosis and prognosis of the diseases. In this study, a new strategy was designed for simple, sensitive, and selective platform to detect the mRNA levels by combining a hairpin probe-graphene oxide (HP1/GO) and duplex-specific nuclease signal amplification (DSNSA). Initially, the DNA probe was adsorbed on the surface of GO to protect it from enzymatic digestion. Then, the target mRNA (T1) was hybridized with a partial hairpin probe which formed a duplex. Finally, under the action of DSN nuclease, the ssDNA in the DNA/RNA hybrid was selectively cleaved and produced small fragments. Then, T1 triggered the next reaction cycle, constituting a new circular exponential amplification. Here, we conclude that this assay is highly sensitive for the detection of target mRNA with the lower detection limit of 1 fM under optimal conditions. Furthermore, this strategy was successfully used for imaging of mRNA in living cells.

A Logic-Gated Modular Nanovesicle Enables Programmable Drug Release for On-Demand Chemotherapy

It remains a major challenge to achieve precise on-demand drug release. Here, we developed a modular nanomedicine integrated with logic-gated system enabling programmable drug release for on-demand chemotherapy.

Methods: We employed two different logical AND gates consisting of four interrelated moieties to construct the nanovesicles, denoted as v-A-CED₂, containing oxidation-responsive nanovesicles (v), radical generators (A), and Edman linker conjugated prodrugs (CED₂). The first AND logic gate is connected in parallel by mild hyperthermia (I) and acidic pH (II), which executes NIR laser triggered prodrug-to-drug transformation through Edman degradation. Meanwhile, the mild hyperthermia effect triggers alkyl radical generation (III) which contributes to internal oxidation and degradation of nanovesicles (IV). The second AND logic gate is therefore formed by the combination of I-IV to achieve programmable drug release by a single stimulus input NIR laser. The biodistribution of the nanovesicles was monitored by positron emission tomography (PET), photoacoustic, and fluorescence imaging.

Results: The developed modular nanovesicles exhibited high tumor accumulation and effective anticancer effects both in vitro and in vivo.

Conclusions: This study provides a novel paradigm of logic-gated programmable drug release system by a modular nanovesicle, which may shed light on innovation of anticancer agents and strategies.

Recent Progress in Fluorescence Signal Design for DNA-Based Logic Circuits

DNA-based logic circuits, encoding algorithms in DNA and processing information, are pushing the frontiers of molecular computers forward, owing to DNA's advantages of stability, accessibility, manipulability, and especially inherent biological significance and potential medical application. In recent years, numerous logic functions, from arithmetic to nonarithmetic, have been realized based on DNA. However, DNA can barely provide a detectable signal by itself, so that the DNA-based circuits depend on extrinsic signal actuators. The signal strategy of carrying out a response is becoming one of the design focuses in DNA-based logic circuit construction. Although work on sequence and structure design for DNA-based circuits has been well reviewed, the strategy on signal production lacks comprehensive summary. In this review, we focused on the latest designs of fluorescent output for DNA-based logic circuits. Several basic strategies are summarized and a few designs for developing multi-output systems are provided. Finally, some current difficulties and possible opportunities were also discussed.

Dual-Analyte Chronopotentiometric Aptasensing Platform Based on a G-Quadruplex/Hemin DNAzyme and Logic Gate Operations

Conventional potentiometric ion sensors that rely on a specific ion carrier in a polymeric membrane can hardly achieve multianalyte detection. Inspired by the remarkable ability of built-in logic gate sensors for multianalyte detection, herein we report a potentiometric aptasensing platform based on a G-quadruplex/hemin DNAzyme and logic gate operations for determination of two analytes using a single membrane electrode. A bifunctional probe with two aptamer units and a signal reporter oligonucleotide with a DNAzyme sequence are assembled on the magnetic beads to form a DNA hybrid structure. The "OR" and "INHIBIT" logic functions can be performed by using the two aptamers and their targets as inputs, and using the chronopotentiometric response based on the G-quadruplex/hemin DNAzyme-H₂O₂-mediated oxidation of 3,3',5,5'-tetramethylbenzidine as output. Kanamycin and oxytetracycline, as commonly used antibiotics, have been employed as the models and successfully measured.

Graphene-based aptasensors: from molecule-interface interactions to sensor design and biomedical diagnostics

Graphene-based nanomaterials have been widely utilized to fabricate various biosensors for environmental monitoring, food safety, and biomedical diagnostics. The combination of aptamers with graphene for creating biofunctional nanocomposites improved the sensitivity and selectivity of fabricated biosensors due to the unique molecular recognition and biocompatibility of aptamers. In this review, we highlight recent advances in the design, fabrication, and biomedical sensing application of graphene-based aptasensors within the last five years (2013-current). The typical studies on the biomedical fluorescence, colorimetric, electrochemical, electrochemiluminescence, photoelectrochemical, electronic, and force-based sensing of DNA, proteins, enzymes, small molecules, ions, and others are demonstrated and discussed in detail. More attention is paid to a few key points such as the conjugation of aptamers with graphene materials, the fabrication strategies of sensor architectures, and the importance of aptamers on improving the sensing performances. It is expected that this work will provide preliminary and useful guidance for readers to understand the fabrication of graphene-based biosensors and the corresponding sensing mechanisms in one way, and in another way will be helpful to develop novel high performance aptasensors for biological analysis and detection.

A multiplexed FRET aptasensor for the simultaneous detection of mycotoxins with magnetically controlled graphene oxide/Fe3O4 as a single energy acceptor

A multiplexed FRET aptasensor was developed for the simultaneous detection of AFB1 and FB1 with magnetically controlled GO/Fe₃O₄ as a single energy acceptor.