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

Stimuli-Responsive DNA-Switchable Biointerfaces

Switchable interfaces, also known as smart interfaces, can alter their macroscopic properties in response to external stimuli. Compared to an artificial switchable interface, DNA-based switchable biointerfaces have high diversity, uniformity, reproducibility, and functionality and are easily designed and developed with atomic precision because the sequence of the DNA strand strictly governs the structural and active properties of its assembly. Moreover, various structures such as double strands based on the Watson-Crick base-pairing rule, G-quadruplexes, i-Motifs, triplexes, and parallel-stranded duplexes exist between or among DNA strands to enrich the structures of DNA biointerfaces. In this article, the design, stimulus responses, and applications of switchable DNA biointerfaces were discussed in terms of single-switch, dual-response, and sequential operation. The applications related to sensing, imaging, delivery, logic gates, and nanomechines were introduced in terms of the design and construction of DNA biointerfaces. Future directions and challenges were also outlined for this rapidly emerging field.

Graphene-based nanomaterials in biosystems

Graphene-based nanomaterials have emerged as a novel type of materials with exceptional physicochemical properties and numerous applications in various areas. In this review, we summarize recent advances in studying interactions between graphene and biosystems. We first provide a brief introduction on graphene and its derivatives, and then discuss on the toxicology and biocompatibility of graphene, including the extracellular interactions between graphene and biomacromolecules, cellular studies of graphene, and in vivo toxicological effects. Next, we focus on various graphene-based practical applications in antibacterial materials, wound addressing, drug delivery, and water purification. We finally present perspectives on challenges and future developments in these exciting fields.

Comparisons between Graphene Oxide and Graphdiyne Oxide in Physicochemistry Biology and Cytotoxicity

Graphdiyne (GDY) and graphene are regarded as two promising two-dimensional carbon-based materials, which have unique planar structure and novel electronic properties. Differences between the two carbon allotropes in their physicochemistry biology and cytotoxicity have never been explored. Here, we chemically functionalized the surface of the two carbon allotropes using similar oxidation processes and compared their physicochemistry, biology, and mutagenesis. Graphene oxide (GO) and GDY oxide (GDYO) showed similarities in their size, morphology, and physical spectral characteristics, excepting the differences in sp- and sp²-hybridizations and Fourier transform infrared spectroscopy. GDYO was well soluble in various media. In contrast, GO was only soluble in H₂O, but kinetically aggregated in 0.9% NaCl, phosphate buffered saline, and cell media within 24 h incubation when its concentrations increased. GO nanoparticles adhered and aggregated to the surface of a human hepatocyte membrane, resulting in cell membrane ruffle, methuosis, and apoptosis. Adhesion of GO to cells caused cell stress and induced reactive oxygen species. In contrast, GDYO did not adhere to the cell membrane to produce the related consequences. Both GDYO and GO showed in vivo mutagenesis potential but no erythrocyte-killing effect, and both were antioxidant and bioequivalent at binding to single-stranded DNA and doxorubicin, thus causing fluorescence quenching. The present study significantly enriches our existing knowledge of GO/alkene and GDYO/alkyne chemistry.

Logic circuit controlled multi-responsive branched DNA scaffolds

A logic circuit controlled multi-responsive sensing platform built on a three-way DNA junction (TWJ) is reported. It enabled the construction of novel fluorescent sensing platforms responsive to any target out of HIV gene, ATP and pH value, and furthermore were logically regulated by two other targets and then behaved as different logic circuits, which consist of two tandem AND gates or cascaded NAND and INH gates by varying the positions of the fluorescent tags.

An amperometric aptasensor for ultrasensitive detection of sulfadimethoxine based on exonuclease-assisted target recycling and new signal tracer for amplification

The risks caused by veterinary drug residues in animal foodstuffs are of great concern to the public. Accordingly, this work reported an amperometric aptasensor for highly sensitive detection of sulfadimethoxine (SDM). Functionalised fullerene (C₆₀)-doped graphene (C₆₀-rGO) nanohybrid was designed and prepared to load electroactive toluidine blue (Tb) through the π-π stacking, forming a C₆₀-rGO-Tb nanocomposite. Furthermore, the as-prepared nanocomposite was decorated with gold nanoparticles and used for the immobilization of signal probes to form a new signal tracer, which was coupled with exonuclease-catalyzed target recycling for amplification. To construct the aptasensor, a thiolated double-stranded DNA (dsDNA) of aptamer-capture probe complex was immobilised on a gold electrode surface through strong Au-S bond. In the presence of SDM, the aptamer preferred to form an aptamer-SDM complex, which led to the dissociation of dsDNA. Then aptamer could be selectively digested by RecJ_f exonuclease, resulting in liberated SDM molecules to participate in the next reaction cycling and achieve signal amplification. Then, capture probes released from the cyclic processes were hybridized with the signal tracer, which could further enhance electrochemical signal responses. On the basis of cascade signal amplification strategies, the proposed aptasensor exhibited a wide linear range from 10 fg/mL to 10 ng/mL for SDM with high sensitivity, good selectivity and satisfactory stability.

Application of DNA Machineries for the Barcode Patterned Detection of Genes or Proteins

The study introduces an analytical platform for the detection of genes or aptamer-ligand complexes by nucleic acid barcode patterns generated by DNA machineries. The DNA machineries consist of nucleic acid scaffolds that include specific recognition sites for the different genes or aptamer-ligand analytes. The binding of the analytes to the scaffolds initiate, in the presence of the nucleotide mixture, a cyclic polymerization/nicking machinery that yields displaced strands of variable lengths. The electrophoretic separation of the resulting strands provides barcode patterns for the specific detection of the different analytes. Mixtures of DNA machineries that yield, upon sensing of different genes (or aptamer ligands), one-, two-, or three-band barcode patterns are described. The combination of nucleic acid scaffolds acting, in the presence of polymerase/nicking enzyme and nucleotide mixture, as DNA machineries, that generate multiband barcode patterns provide an analytical platform for the detection of an individual gene out of many possible genes. The diversity of genes (or other analytes) that can be analyzed by the DNA machineries and the barcode patterned imaging is given by the Pascal's triangle. As a proof-of-concept, the detection of one of six genes, that is, TP53, Werner syndrome, Tay-Sachs normal gene, BRCA1, Tay-Sachs mutant gene, and cystic fibrosis disorder gene by six two-band barcode patterns is demonstrated. The advantages and limitations of the detection of analytes by polymerase/nicking DNA machineries that yield barcode patterns as imaging readout signals are discussed.

Covalent and Non-covalent Conjugation of Few-Layered Graphene Oxide and Ruthenium(II) Complex Hybrids and Their Energy Transfer Modulation via Enzymatic Hydrolysis

Pyrene-containing ruthenium(II) tris-bipyridine complexes have been prepared. These complexes have been non-covalently attached onto the few-layered graphene oxide (GO) sheets through their high binding affinity for flat π-surfaces. Alternatively, the reduced graphene oxide (rGO) sheets have also been covalently functionalized with the ruthenium(II) tris-bipyridine complex. The prepared conjugates have been characterized by transmission electron microscopy (TEM), energy-dispersive X-ray analysis (EDX), X-ray diffraction (XRD), atomic force microscopy (AFM), Raman spectroscopy, thermogravimetric analysis (TGA), and UV-visible absorption spectroscopy. The energy transfer properties of the resulted conjugates between the graphene and transition metal complexes have been studied via esterase hydrolysis. The energy transfer efficiencies were found to vary with the separation between the donor and the acceptor units.

Programmable DNA switches and their applications

DNA switches are ideally suited for numerous nanotechnological applications, and increasing efforts are being directed toward their engineering. In this review, we discuss how to engineer these switches starting from the selection of a specific DNA-based recognition element, to its adaptation and optimisation into a switch, with applications ranging from sensing to drug delivery, smart materials, molecular transporters, logic gates and others. We provide many examples showcasing their high programmability and recent advances towards their real life applications. We conclude with a short perspective on this exciting emerging field.

A Highly Sensitive Strategy for Fluorescence Imaging of MicroRNA in Living Cells and in Vivo Based on Graphene Oxide-Enhanced Signal Molecules Quenching of Molecular Beacon

In situ imaging of microRNA (miRNA) in living cells and in vivo is beneficial for promoting the studies on miRNA-related physiological and pathological processes. However, the current strategies usually have a low signal-to-background ratio, which greatly affects the sensitivity and imaging performance. To solve this problem, we developed a highly sensitive strategy for fluorescence imaging of miRNA in living cells and in vivo based on graphene oxide (GO)-enhanced signal molecule quenching of a molecular beacon (MB). 2Cy5-MB was designed by coupling two Cy5 molecules onto the opposite ends of MB. The fluorescence intensities of two Cy5 molecules were reduced because of the self-quenching effect. After adsorbing on the GO surface, the fluorescence quenching of the molecules was enhanced by fluorescence resonance energy transfer. This double-quenching effect significantly reduced the fluorescence background. In the presence of one miRNA molecule, the fluorescence signals of two Cy5 molecules were simultaneously recovered. Therefore, a significantly enhanced signal-to-background ratio was obtained, which greatly improved the detection sensitivity. In the presence of miRNA, the fluorescence intensity of 2Cy5-MB-GO recovered about 156 times and the detection limit was 30 pM. Compared with 1Cy5-MB-GO, the elevated fluorescence intensity was enhanced 8 times and the detection limit was reduced by an order of magnitude. Furthermore, fluorescence imaging experiments demonstrated that 2Cy5-MB-GO could visually detect microRNA-21 in various cancer cells and tumor tissues. This simple and effective strategy provides a new sensing platform for highly sensitive detection and simultaneous imaging analysis of multiple low-level biomarkers in living cells and in vivo.

Optical nano-biosensing interface via nucleic acid amplification strategy: construction and application

Modern optical detection technology plays a critical role in current clinical detection due to its high sensitivity and accuracy. However, higher requirements such as extremely high detection sensitivity have been put forward due to the clinical needs for the early finding and diagnosing of malignant tumors which are significant for tumor therapy. The technology of isothermal amplification with nucleic acids opens up avenues for meeting this requirement. Recent reports have shown that a nucleic acid amplification-assisted modern optical sensing interface has achieved satisfactory sensitivity and accuracy, high speed and specificity. Compared with isothermal amplification technology designed to work completely in a solution system, solid biosensing interfaces demonstrated better performances in stability and sensitivity due to their ease of separation from the reaction mixture and the better signal transduction on these optical nano-biosensing interfaces. Also the flexibility and designability during the construction of these nano-biosensing interfaces provided a promising research topic for the ultrasensitive detection of cancer diseases. In this review, we describe the construction of the burgeoning number of optical nano-biosensing interfaces assisted by a nucleic acid amplification strategy, and provide insightful views on: (1) approaches to the smart fabrication of an optical nano-biosensing interface, (2) biosensing mechanisms via the nucleic acid amplification method, (3) the newest strategies and future perspectives.

An intelligent 1:2 demultiplexer as an intracellular theranostic device based on DNA/Ag cluster-gated nanovehicles

The logic device demultiplexer can convey a single input signal into one of multiple output channels. The choice of the output channel is controlled by a selector. Several molecules and biomolecules have been used to mimic the function of a demultiplexer. However, the practical application of logic devices still remains a big challenge. Herein, we design and construct an intelligent 1:2 demultiplexer as a theranostic device based on azobenzene (azo)-modified and DNA/Ag cluster-gated nanovehicles. The configuration of azo and the conformation of the DNA ensemble can be regulated by light irradiation and pH, respectively. The demultiplexer which uses light as the input and acid as the selector can emit red fluorescence or a release drug under different conditions. Depending on different cells, the intelligent logic device can select the mode of cellular imaging in healthy cells or tumor therapy in tumor cells. The study incorporates the logic gate with the theranostic device, paving the way for tangible applications of logic gates in the future.

DNA assay based on Nanoceria as Fluorescence Quenchers (NanoCeracQ DNA assay)

Functional nanomaterials with fluorescent or quenching abilities are important for the development of molecular probes for detection and studies of nucleic acids. Here, we describe a new class of molecular nanoprobes, the NanoCeracQ that uses nanoceria particles as a nanoquencher of fluorescent oligonucleotides for rapid and sensitive detection of DNA sequences and hybridization events. We show that nanoceria forms stable and reversible bionanoconjugates with oligonucleotides and can specifically recognize and detect DNA sequences in a single step. In absence of the target DNA, the nanoprobe produced minimal background fluorescence due to the high quenching efficiency of nanoceria. Competitive binding of the target induced a concentration dependent increase in the fluorescence signal due to hybridization and release of the fluorescent tag from the nanoparticle surface. The nanoprobe enabled sensitive detection of the complementary strand with a detection limit of 0.12 nM, using a single step procedure. The results show that biofunctionalized nanoceria can be used as a universal nanoquencher and nanosensing platform for fluorescent DNA detection and studies of nucleic acid interactions. This approach can find broad applications in molecular diagnostics, sensor development, gene expression profiling, imaging and forensic analysis.

Ultrasensitive fluorescent aptasensor for MUC1 detection based on deoxyribonuclease I-aided target recycling signal amplification

A novel sensing strategy for sensitive detection of mucin 1 protein (MUC1) based on deoxyribonuclease I-aided target recycling signal amplification was proposed. In this paper, in the absence of MUC1, the MUC1 aptamer is absorbed on the surface of graphene oxide (GO) via π-stacking interactions. This results in quenching of the fluorescent label and no fluorescence signal is observed. Upon adding MUC1, the probe sequences could be specifically recognized by MUC1, leading to an increase in the fluorescence intensity. The detection limit is as low as 10 pg mL⁻¹, and a linear range from 50 pg mL⁻¹ to 100 ng mL⁻¹. The assay is specific and sensitive, and successfully applied to the determination of MUC1 in spiked human serum, urine and saliva. Importantly, the proposed aptasensing strategy has great potential in detecting various protein and even cancer cells.

A novel sensing strategy for sensitive detection of mucin 1 protein (MUC1) based on deoxyribonuclease I-aided target recycling signal amplification was proposed.

Lipid- and gut microbiota-modulating effects of graphene oxide nanoparticles in high-fat diet-induced hyperlipidemic mice

Graphene oxide (GO) suspensions can act as a good dispersant and drug delivery system for effective dispersion and drug sustained release. In this study, we investigated the impact of GO on blood/liver lipids and gut microbiota structure in high-fat diet (HFD)-induced hyperlipidemic mice. Oral administration of GO for 28 days remarkably decreased the lipid levels in blood and liver. GO did not decrease the total number of gut bacteria but increased the relative abundance of short-chain fatty acid (SCFA)-producing bacteria such as Clostridium clusters IV and Allobaculum spp. GO also enhanced the copying of bacterial butyryl coenzyme A transferase (BcoA), a key butyrate-producing gene. Although further pharmacological studies are still needed, these results provided an interesting hint that GO may exert beneficial effects on the host's metabolism via selective modulation of SCFA-producing gut microbes.

The impact of GO on blood/liver lipids and gut microbiota structure in high-fat diet (HFD)-induced hyperlipidemic mice was investigated. Oral administration of GO for 28 days remarkably decreased lipid levels in blood and liver and GO did not decrease the total number of gut bacteria but increased the relative abundance of short-chain fatty acid (SCFA)-producing bacteria.

Fluorescence and photoacoustic dual-mode imaging of tumor-related mRNA with a covalent linkage-based DNA nanoprobe

A fluorescence and photoacoustic dual-mode DNA nanoprobe based on covalent linkage was developed for detecting tumor-associated mRNA.

One-pot synthesis of amine-functionalized graphene oxide by microwave-assisted reactions: an outstanding alternative for supporting materials in supercapacitors

A simple and straightforward method using microwave-assisted reactions is presented for the functionalization of graphene oxide with aromatic and non-aromatic amines, notedly dibenzylamine (DBA), p-phenylenediamine (PPD), diisopropylamine (DPA) and piperidine (PA). The as-synthesized amine-functionalized graphene oxide materials (amine-GO) were characterized using spectroscopic techniques including XRD, FTIR, ¹³C NMR, XPS, TEM for imaging and thermogravimetric analysis (TGA). The characterization confirmed the functionalization for all amines, reaching relatively high surface nitrogen atomic concentrations of up to 8.8%. The investigations of electrochemical behavior for the amine-GOs show the significant improvement in GO's electrochemical properties through amine functionalization, exhibiting long life cycle stability and reaching specific capacitance values of up to 290 F g⁻¹ and 260 F g⁻¹ for GO-PA and GO-DPA samples, respectively, confirming their potential application as alternative supporting materials in supercapacitors.

A simple and straightforward method using microwave-assisted reactions is presented for the functionalization of graphene oxide with aromatic and non-aromatic amines.

Evanescent wave aptasensor for continuous and online aminoglycoside antibiotics detection based on target binding facilitated fluorescence quenching

The biosensors capable for on-site continuous and online monitoring of pollutants in environment are highly desired due to their practical importance and convenience. The group specific detection of pollutants is especially attractive due to the diversity of environmental pollutants. Here we devise an evanescent wave aptasensor based on target binding facilitated fluorescence quenching (FQ-EWA) for the online continuous and group-specific detection of aminoglycoside antibiotics (AMGAs). In FQ-EWA, a fluorophore labeled DNA aptamer selected against kanamycin was used for both the target recognition in solution and signal transduction on optical fiber of EWA. The aptamers form multiple-strand complex (M-Apt) in the absence of AMGAs. The binding between AMGA and the aptamer disrupts M-Apt and leads to the formation of AMGA -aptamer complex (AMGA-Apt). The photo-induced electron transfer between the fluorophore and AMGA partially quenches the fluorescence of AMGA-Apt. The structure-selective absorption of AMGA-Apt over M-Apt on the graphene oxide further quenches the fluorescence of AMGA-Apt. Meanwhile, the unbound aptamers in solution assemble with the unlabeled aptamers immobilized on the fiber to form M-Apt. The amount of M-Apt on the fiber is inversely proportional to the concentration of AMGAs, enabling the signal-off detection of AMGAs from 200nM to 200μM with a detection limit of 26nM. The whole detection process is carried out in an online mode without any offline operation, providing a great benefit for system automation and miniaturization. FQ-EWA also shows great surface regeneration capability and enables the continuous detection more than 60 times.

Fluorescence and Sensing Applications of Graphene Oxide and Graphene Quantum Dots: A Review

Graphene oxide and graphene quantum dots are attractive fluorophores that are inexpensive, nontoxic, photostable, water-soluble, biocompatible, and environmentally friendly. They find extensive applications in fluorescent biosensors and chemosensors, in which they serve as either fluorophores or quenchers. As fluorophores, they display tunable photoluminescence emission and the "giant red-edge effect". As quenchers, they exhibit a remarkable quenching efficiency through either electron transfer or Förster resonance energy transfer (FRET) process. In this review, the origin of fluorescence and the mechanism of excitation wavelength-dependent fluorescence of graphene oxide and graphene quantum dots are discussed. Sensor design strategies based on graphene oxide and graphene quantum dots are presented. The applications of these sensors in health care, the environment, agriculture, and food safety are highlighted.

Electrogenerated chemiluminescence logic gate operations based on molecule-responsive organic microwires

Complex logic gate operations using organic microwires as signal transducers based on electrogenerated chemiluminescence (ECL) intensity as the optical readout signal have been developed by taking advantage of the unique ECL reaction between organic semiconductor 9,10-bis(phenylethynyl)anthracene (BPEA) microwires and small molecules. The BPEA microwires, prepared on cleaned-ITO substrate using a simple physical vapor transport (PVT) method, were subsequently used for construction of the ECL sensors. The developed sensor exhibits high ECL efficiency and excellent stability in the presence of co-reactant tripropylamine. Based on the remarkable detection performance of BPEA MWs/TPrA system, the sensors manifested high sensitive ECL response in a wide linear range with low detection limit for the detection of dopamine, proline or methylene blue, which behaves on the basis of molecule-responsive ECL properties based on different ECL reaction mechanisms. Inspired by this, these sensing systems can be utilized to design OR, XOR and INHIBIT logic gates, which would be used for the determination of dopamine, proline and ethylene blue via logic outputs. Importantly, the individual logic gates can be easily brought together through three-input operations to function as integrated logic gates.

Triplex DNA-based Bioanalytical Platform for Highly Sensitive Homogeneous Electrochemical Detection of Melamine

Melamine detection has attracted much attention since the discovery of the damage of melamine to human health. Herein, we have developed a sensitive homogeneous electroanalytical platform for melamine detection, which is relied on the formation of triplex molecular beacon integrated with exonuclease III (Exo III)-mediated signal amplification. The formation of triplex molecular beacon was triggered by the recognition and incorporation of melamine to the abasic (AP) site contained in the triplex stem. The stem of the triplex molecular beacon was designed to have a protruding double-strand DNA, which can be recognized and hydrolyzed by Exo III for releasing methylene blue (MB)-labeled mononucleotide. These released MB molecules exhibit high diffusivity toward indium tin oxide electrode with negative charge, thus producing a significantly increased electrochemical response. Taking advantages of the high binding affinity of the DNA triplex structure containing AP sites towards melamine and the unique features of Exo III, this sensing platform is capable for sensitive and selective melamine assay with a detection limit as low as 8.7 nM. Furthermore, this strategy shows good applicability for melamine assay in real samples. Therefore, this strategy broadens the application of triplex DNA and presents a new method for sensitive detection of melamine.

Exonuclease-Catalyzed Methylene Blue Releasing and Enriching onto a Dodecanethiol Monolayer for an Immobilization-Free and Highly Sensitive Electrochemical Nucleic Acid Biosensor

Herein, a unique and versatile immobilization-free electrochemical nucleic acid biosensor architecture is proposed for the first time based on the catalyzed release of a methylene blue (MB)-tagged mononucleotide by exonuclease III (Exo III) and the successive enrichment onto a dodecanethiol monolayer, which can be attributed to the hydrophobic force between the alkyl chain of the dodecanethiol monolayer and the hydrophobic part of the MB-tagged mononucleotide. The fabricated biosensor demonstrates considerable advantages including assay simplicity, rapidness, and high sensitivity owing to its immobilization-free and homogenous operation for the biorecognition and amplification process. A low detection limit of approximately 1 pM toward the target DNA could be achieved with an excellent selectivity. The proposed immobilization-free electrochemical biosensing strategy was also extended for the assay of Exo I and III activity. Furthermore, it might be easily extended for the detection of a wide spectrum of targets and thus provide a promising avenue for the development of immobilization-free and sensitive electrochemical biosensors.

A label-free visual platform for self-correcting logic gate construction and sensitive biosensing based on enzyme-mimetic coordination polymer nanoparticles

In molecular logic gates, the occurrence of erroneous procedures is a frequently encountered and critical problem in data transmission, and thus it is highly desirable to develop novel logic systems with self-correction abilities. Herein, based on the horseradish peroxidase (HRP)-like activity of the novel metal coordination polymer nanoparticles formed between Cu²⁺ and guanosine monophosphate (GMP), denoted as Cu-GMP CPNs, a label-free visual platform was constructed and successfully utilized for both self-correcting logic gate construction and sensitive biosensing. The HRP-mimicking ability of Cu-GMP CPNs was verified and utilized for the sensitive detection of both H₂O₂ and glucose. More importantly, a set of logic gates (AND, OR, NOR, INHIBIT, and XNOR) were fabricated, in which two intermediate outputs, i.e., color change and precipitate formation, were combined in an "AND" mode to produce the final output, and thus the as-proposed logic system exhibited the self-correction ability to automatically correct the erroneous intermediate outputs induced by interfering substances such as HRP. Moreover, in addition to the unique feature of self-correction, the as-proposed logic system also exhibited the advantages of simple operation, rapid response and easy detection of the visual outputs by the naked eye, thus expanding its practical applications to a variety of fields. Therefore, the label-free visual platform we have proposed here offers a promising strategy for logic gate fabrication and may pave the way for the development of novel molecular computing with self-correction abilities.

DNA Domino-Based Nanoscale Logic Circuit: A Versatile Strategy for Ultrasensitive Multiplexed Analysis of Nucleic Acids

In recent years, the analytical application of logical nanodevices has attracted much attention for making accurate decisions on molecular diagnosis. Herein, a DNA domino-based nanoscale logic circuit has been constructed by integrating three logic gates (AND-AND-YES) for simultaneous analysis of multiple nucleic acid biomarkers. In the first AND gate, a chimeric target DNA comprising of four biomarkers was hybridized to three biomarker-specific oligonucleotides (TRs) via their 5'-end regions and to a capture probe-magnetic microparticle. After harvesting the complex, 3' overhang regions of the TRs were labeled with three distinct monolayer double-stranded (ds) DNA-gold nanoparticles (DNA-AuNPs). Upon gleaning the complex and addition of initiator oligonucleotide, a series of toehold-mediated strand displacement reactions, which are reminiscent of a domino chain, spontaneously occurred between the confined dsDNAs on the nanoparticles' surface in the second AND gate. The output of the second gate entered into the last gate and triggered an exponential hairpin assembly to form four-way junction nanostructures. The resulting nanostructures bear split parts of DNAzyme at each end of the four arms which, in the presence of hemin, form catalytic hemin/G-quadruplex DNAzymes with peroxidase activity. The smart biosensor has exhibited a turn-on signal when all biomarkers are present in the sample. In fact, should any of the biomarkers be nonexistent, the signal remains turned-off. The biosensor can detect the biomarkers with a LOD value of 100 aM and a noticeable capability to discriminate single-nucleotide substitutions.

Few-Layer Graphdiyne Nanosheets Applied for Multiplexed Real-Time DNA Detection

Despite recent progress in 2D nanomaterials-based biosensing, it remains challenging to achieve sensitive and high selective detection. This study develops few-layer graphdiyne (GD) nanosheets (NSs) that are used as novel sensing platforms for a variety of fluorophores real-time detection of DNA with low background and high signal-to-noise ratio, which show a distinguished fluorescence quenching ability and different affinities toward single-stranded DNA and double-stranded DNA. Importantly, for the first time, a few-layer GD NSs-based multiplexed DNA sensor is developed.

Ultrasensitive and in situ DNA detection in various pH environments based on a microfiber with a graphene oxide linking layer

Ultrasensitive and in situ DNA detection at different pH values, ranging from 4.3 to 8.5, based on a microfiber with a graphene oxide linking layer was proposed and experimentally demonstrated.

MoS2 quantum dots featured fluorescent biosensor for multiple detection of cancer

A novel MoS₂ quantum dot-based fluorescent biosensor is exploited to trace and visualize mucin 1-overexpression cancer cells.

A plasmonic multi-logic gate platform based on sequence-specific binding of estrogen receptors and gold nanorods

A hybrid system made of gold nanorods (AuNRs) and double-stranded DNA (dsDNA) is used to build a versatile multi-logic gate platform, capable of performing six different logic operations. The sequence-specific binding of transcription factors to the DNA drives the optical response of the design.

Tunable Supramolecular Interactions of Aggregation-Induced Emission Probe and Graphene Oxide with Biomolecules: An Approach toward Ultrasensitive Label-Free and "Turn-On" DNA Sensing

Aggregation-induced emission (AIE) probes have shown great potential applications in fluorescent sensing of biomolecules, and the integration of AIE probe and graphene oxide (GO) attracts intense interest in developing new tools for label-free and "turn-on" fluorescent biomolecular analysis. Herein, an ultrasensitive label-free and "turn-on" DNA sensing is realized by tuning the supramolecular interactions of AIE probe and GO with DNA. The investigation of supramolecular interactions of AIE probes and GO with DNA demonstrate that AIE probe with short alkyl chains substitute shows highest binding affinity with DNA strand, and GO with low oxidation degree possesses strong binding interactions to ssDNA and the highest fluorescence quenching efficiency. As a result, the optimized AIE probes and GO-based fluorescent sensor can selectively detect the target DNA sequence and exhibits the detection limitation as low as 0.17 × 10^-9 m. It is believed that the research efforts will provide an efficient approach to improve the performance of DNA sensing assay and an indepth understanding of the supramolecular interactions of AIE probes and GO with DNA, and thus facilitate their extended applications in biosensors and biomedicine.

Graphene oxide directed in-situ deposition of electroactive silver nanoparticles and its electrochemical sensing application for DNA analysis

The development of high-performance biosensing platform is heavily dependent on the recognition property of the sensing layer and the output intensity of the signal probe. Herein, we present a simple and highly sensitive biosensing interface for DNA detection on the basis of graphene oxide nanosheets (GONs) directed in-situ deposition of silver nanoparticles (AgNPs). The fabrication process and electrochemical properties of the biosensing interface were probed by electrochemical techniques and scanning electron microscopy. The results indicate that GONs can specifically adsorb at the single-stranded DNA probe surface, and induces the deposition of highly electroactive AgNPs. Upon hybridization with complementary oligonucleotides to generate the duplex DNA on the electrode surface, the GONs with the deposited AgNPs will be liberated from the sensing interface due to the inferior affinity of GONs and duplex DNA, resulting in the reduction of the electrochemical signal. Such a strategy combines the superior recognition of GONs toward single-stranded DNA and double-stranded DNA, and the strong electrochemical response of in-situ deposited AgNPs. Under optimal conditions, the biosensor can detect target DNA over a wide range from 10 fM to 10 nM with a detection limit of 7.6 fM. Also, the developed biosensor shows outstanding discriminating ability toward oligonucleotides with different mismatching degrees.

Multifunctional Graphene/DNA-Based Platform for the Construction of Enzyme-Free Ternary Logic Gates

In this work, we have successfully realized multivalued logic circuits including ternary INHIBIT and ternary OR logic gates in an enzyme-free condition by integration of graphene oxide and DNA for the first time. Compared to the binary logic gate with two states of "0" and "1", the multivalued logic gate contains three different states of "0", "1", and "2", which can increase the information content in a system and further improve the ability of information processing. Such types of multivalued logic operations provide a wider field of vision toward DNA-based algebra logical operations to make applications more accurate with complexity reduction and accelerate the development of advanced logic gates.

Integration of DNA and graphene oxide for the construction of various advanced logic circuits

Multiple advanced logic circuits including the full-adder, full-subtract and majority logic gate have been successfully realized on a DNA/GO platform for the first time. All the logic gates were implemented in an enzyme-free condition. The investigation provides a wider field of vision towards prototypical DNA-based algebra logical operations and promotes the development of advanced logic circuits.

Biosensors based on graphene oxide and its biomedical application

Graphene oxide (GO) is one of the most attributed materials for opening new possibilities in the development of next generation biosensors. Due to the coexistence of hydrophobic domain from pristine graphite structure and hydrophilic oxygen containing functional groups, GO exhibits good water dispersibility, biocompatibility, and high affinity for specific biomolecules as well as properties of graphene itself partly depending on preparation methods. These properties of GO provided a lot of opportunities for the development of novel biological sensing platforms, including biosensors based on fluorescence resonance energy transfer (FRET), laser desorption/ionization mass spectrometry (LDI-MS), surface-enhanced Raman spectroscopy (SERS), and electrochemical detection. In this review, we classify GO-based biological sensors developed so far by their signal generation strategy and provide the comprehensive overview of them. In addition, we offer insights into how the GO attributed in each sensor system and how they improved the sensing performance.

An enzyme-free and resettable platform for the construction of advanced molecular logic devices based on magnetic beads and DNA

A series of multiple logic circuits based on magnetic beads and DNA are constructed to perform resettable nonarithmetic functions, including a digital comparator, 4-to-2 encoder and 2-to-3 decoder, 2-to-1 encoder and 1-to-2 decoder. The signal reporter is composed of a G-quadruplex/NMM complex and a AuNP-surface immobilized molecular beacon. It is the first time that the designed DNA-based nonarithmetic nanodevices can share the same DNA platform with a reset function, which has great potential application in information processing at the molecular level. Another novel feature of the designed system is that the developed nanodevices are operated on a simple DNA/magnetic bead platform and share a constant threshold setpoint without the assistance of any negative logic conversion. The reset function is realized by heating the output system and the magnetic separation of the computing modules. Due to the biocompatibility and design flexibility of DNA, these investigations may provide a new route towards the development of resettable advanced logic circuits in biological and biomedical fields.

Innovative Bimolecular-Based Advanced Logic Operations: A Prime Discriminator and An Odd Parity Checker

Herein, a novel logic operation of prime discriminator is first performed for the function of identifying the prime numbers from natural numbers less than 10. The prime discriminator logic operation is developed by DNA hybridizations and the conjugation of graphene oxide and single-stranded DNA as a reacting platform. On the basis of the similar reaction principle, an odd parity checker is also developed. The odd parity checker logic operation can identify the even numbers and odd numbers from natural numbers less than 10. Such advanced logic operations with digital recognition ability can provide a new field of vision toward prototypical DNA-based logic operations and promote the development of advanced logic circuits.