A Bioluminescent Protein-Graphene Oxide Donor-Quencher Pair in DNA Hybridization Assays

Despite fluorescent quenching with graphene oxide (GO) having shown great success in various applications - bioluminescent quenching has not yet been demonstrated using GO as a quencher. To explore the ability of GO to quench bioluminescence, we used Gaussia luciferase (Gluc) as a donor and GO as a quencher and demonstrated its application in sensing of two target analytes, HIV-1 DNA and IFN-γ. We demonstrated that the incubation of Gluc conjugated HIV-1 and IFN-γ oligonucleotide probes with GO provided for monitoring of probe-target interactions based on bioluminescence measurement in a solution phase sensing system. The limits of detection obtained for IFN-γ and HIV-1 DNA detection were 17 nM and 7.59 nM, respectively. Both sensing systems showed selectivity toward the target analyte. The detection of IFN-γ in saliva matrix was demonstrated. The use of GO as a quencher provides for high sensitivity while maintaining the selectivity of designed probes to their respective targets. The use of GO as a quencher provides for an easy assay design and low cost, environmentally friendly reporter.

Hybridization chain reaction and its applications in biosensing

To pursue the sensitive and efficient detection of informative biomolecules for bioanalysis and disease diagnosis, a series of signal amplification techniques have been put forward. Among them, hybridization chain reaction (HCR) is an isothermal and enzyme-free process where the cascade reaction of hybridization events is initiated by a target analyte, yielding a long nicked dsDNA molecule analogous to alternating copolymers. Compared with conventional polymerase chain reaction (PCR) that can proceed only with the aid of polymerases and complicated thermal cycling, HCR has attracted increasing attention because it can occur under mild conditions without using enzymes. As a powerful signal amplification tool, HCR has been employed to construct various simple, sensitive and economic biosensors for detecting nucleic acids, small molecules, cells, and proteins. Moreover, HCR has also been applied to assemble complex nanostructures, some of which even act as the carriers to execute the targeted delivery of anticancer drugs. Recently, HCR has engendered tremendous progress in RNA imaging applications, which can not only achieve endogenous RNA imaging in living cells or even living animals but also implement imaging-guided photodynamic therapy, paving a promising path to promote the development of theranostics. In this review, we begin with the fundamentals of HCR and then focus on summarizing the recent advances in HCR-based biosensors for biosensing and RNA imaging strategies. Further, the challenges and future perspective of HCR-based signal amplification in biosensing and theranostic application are discussed.

Colorimetric Detection of Class A Soybean Saponins by G-Quadruplex-Based Hybridization Chain Reaction

Soybean saponin is one of the important secondary metabolites in seeds, which has various beneficial physiological functions to human health. GmSg-1 gene is the key enzyme gene for synthesizing class A saponins. It is of great significance to realize the visual and rapid detection of class A saponins at the genetic level. The hybridization chain reaction (HCR) was employed to the visual detection of GmSg-1 gene, which was implemented by changing the length of the target fragment to 92 bp and using the hairpin probes we designed to detect the GmSg-1 ^a and GmSg-1 ^b genes. The best condition of HCR reaction is hemin (1.2 μM), Triton X-100 (0.002%), ABTS (3.8 μM), and H₂O₂ (1.5 mM). It was found that HCR has high specificity for GmSg-1 gene and could be applied to the visual detection of different soybean cultivars containing Aa type, Ab type, and Aa/Ab type saponins, which could provide technical reference and theoretical basis for molecular breeding of soybean and development of functional soybean products.

Label-free and enzyme-free detection of microRNA based on a hybridization chain reaction with hemin/G-quadruplex enzymatic catalysis-induced MoS2 quantum dots via the inner filter effect

A new simple, sensitive and specific strategy for microRNA analysis has been described based on a hybridization chain reaction with hemin/G-quadruplex enzymatic catalysis-induced MoS2 quantum dots via the inner filter effect. The target microRNA triggers the hybridization chain reaction between two DNA probes to generate long dsDNA with many hemin/G-quadruplex DNAzymes in the presence of hemin. With the assistance of H2O2, the produced hemin/G-quadruplex DNAzyme could oxidize o-phenylenediamine (OPD) to 2,3-diaminophenazine (DAP) directly, resulting in the fluorescence quenching of MoS2 quantum dots via the inner filter effect. As an example, the fluorescence response of MoS2 quantum dots is linearly related with the logarithm of the microRNA let-7a concentration with a detection limit of 42 fM. The proposed label-free assay has promising potential to be applied in practical diagnosis.

A graphene oxide-based paper chip integrated with the hybridization chain reaction for peanut and soybean allergen gene detection

Allergen genes of the peanut and soybean were selected as model targets. Four hairpin DNA probes, H1, H2, H3, H4 were designed. Cy3-labeled H1 and H2 were used to detect peanut DNA, while FAM-labeled H3 and H4 were used to detect soybean DNA. Graphene oxide (GO) was used as the adsorption material for capturing the hairpin probes, and as a selective fluorescence quencher to reduce the background signal. To develop an allergen gene detection system with a GO-based paper chip format, we integrated the hybridization chain reaction (HCR) with fluorescence resonance energy transfer (FRET) in our design. The results showed that in the absence of peanut DNA (TP) and soybean DNA (TS), the detection probes attached to the GO surface, which quenched their fluorescence. In the presence of TP or TS, however, complementary probe binding to the targets initiated HCR, producing long double-stranded DNA products that could not be absorbed onto the GO surface. Hence, a strong red or green fluorescent signal was generated. The detection limit for both peanut and soybean DNA was 1 nM using this method, indicating the high sensitivity of our approach. This method also exhibited good specificity and a single chip could be used to simultaneously detect two different targets.

A review on graphene-based nanocomposites for electrochemical and fluorescent biosensors

Biosensors with high sensitivity, selectivity and a low limit of detection, reaching nano/picomolar concentrations of biomolecules, are important to the medical sciences and healthcare industry for evaluating physiological and metabolic parameters.

Design and synthesis of a vanadate-based ratiometric fluorescent probe for sequential recognition of Cu2+ ions and biothiols

YVO₄:Eu³⁺@CDs core–shell nanomaterial was synthesized through a simple self-assembly of carbon dots (CDs) with YVO₄:Eu³⁺, since the high affinity of oxygen-containing groups such as –COOH or –OH of CDs to the metal ions on the surface of YVO₄:Eu³⁺.

Chemical and Biological Sensing Using Hybridization Chain Reaction

Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.

Highly sensitive fluorogenic sensing of L-Cysteine in live cells using gelatin-stabilized gold nanoparticles decorated graphene nanosheets

A highly sensitive and selective fluorogenic sensing of L-Cysteine (L-Cys) was implemented based on gelatin stabilized gold nanoparticles decorated reduced graphene oxide (rGO/Au) nanohybrid. The rGO/Au nanohybrid was prepared by the one-pot hydrothermal method and well characterized by different physiochemical techniques. The nanohybrid exhibits a weak fluorescence of rGO due to the energy transfer from the rGO to Au NPs. The rGO/Au nanohybrid shows enhanced fluorescence activity due to the restoration of quenched fluorescence of rGO/Au nanohybrid in presence of L-Cys. The rGO/Au nanohybrid exhibits much lower detection limit of 0.51 nM for L-Cys with higher selectivity. The fluorescence sensing mechanism arose from the fluorescence recovery due to the stronger interaction between Au NPs and L-Cys, and consequently, the energy transfer was prevented between rGO and Au NPs. The practicability of rGO/Au sensor was implemented by invitro bioimaging measurements in Colo-205 (colorectal adenocarcinoma) and MKN-45 (gastric carcinoma) cancer live cells with excellent biocompatibility.

A target-initiated DNA network caged on magnetic particles for amplified chemiluminescence resonance energy transfer imaging of microRNA and targeted drug delivery

Chemiluminescence resonance energy transfer (CRET) DNA networks are constructed on magnetic particles initiated by target microRNA, which are further functionalized with aptamers for targeted drug delivery.

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.

Silver-Nanoparticle-Embedded Porous Silicon Disks Enabled SERS Signal Amplification for Selective Glutathione Detection

As the major redox couple and nonprotein thiol source in human tissues, the level of glutathione (GSH) has been a concern for its relation with many diseases. However, the similar physical and chemical properties of interference molecules such as cysteine (Cys) and homocysteine (Hcy) make discriminative detection of GSH in complex biological fluids challenging. Here we report a novel surface-enhanced Raman scattering (SERS) platform, based on silver-nanoparticle-embedded porous silicon disks (PSDs/Ag) substrates for highly sensitive and selective detection of GSH in biofluids. Silver nanoparticles (AgNPs) were reductively synthesized and aggregated directly into pores of PSDs, achieving a SERS enhancement factor (EF) up to 2.59 × 10⁷. Ellman's reagent 5,5'-ditho-bis (2-nitrobenzoic acid) (DTNB) was selected as the Raman reactive reporting agent, and the GSH quantification was determined using enzymatic recycling method, and allowed the detection limit of GSH to be down to 74.9 nM using a portable Raman spectrometer. Moreover, the significantly overwhelmed enhancement ratio of GSH over other substances enables the discrimination of GSH detection in complex biofluids.

Selective reduction-based, highly sensitive and homogeneous detection of iodide and melamine using chemical vapour generation-atomic fluorescence spectrometry

A selective reduction-based method was proposed for the sensitive detection of iodide and melamine using chemical vapour generation (CVG) coupled with atomic fluorescence spectrometry (AFS).

Redox Probing for Chemical Information of Oxidative Stress

Oxidative stress is implicated in many diseases yet no simple, rapid, and robust measurement is available at the point-of-care to assist clinicians in detecting oxidative stress. Here, we report results from a discovery-based research approach in which a redox mediator is used to probe serum samples for chemical information relevant to oxidative stress. Specifically, we use an iridium salt (K2IrCl6) to probe serum for reducing activities that can transfer electrons to iridium and thus generate detectable optical and electrochemical signals. We show that this Ir-reducing assay can detect various biological reductants and is especially sensitive to glutathione (GSH) compared to alternative assays. We performed an initial clinical evaluation using serum from 10 people diagnosed with schizophrenia, a mental health disorder that is increasingly linked to oxidative stress. The measured Ir-reducing capacity was able to discriminate people with schizophrenia from healthy controls (p < 0.005), and correlations were observed between Ir-reducing capacity and independent measures of symptom severity.

A label-free ratiometric electrochemical DNA sensor for monitoring intracellular redox homeostasis

A label-free ratiometric electrochemical determination of GSH by DNA metallization-mediated HCR amplification is reported.

DNase-targeted natural product screening based on a sensitive and selective DNase I detecting system

As a widely used deoxyribonuclease, DNase I is involved in many physiological processes including tumor cell proliferation, metastasis and apoptosis.

Hybridization chain reaction: a versatile molecular tool for biosensing, bioimaging, and biomedicine

This review provides a comprehensive overview of the fundamental principles, analysis techniques, and application fields of hybridization chain reaction and its development status.

A novel label-free fluorescent molecular beacon for the detection of 3′–5′ exonuclease enzymatic activity using DNA-templated copper nanoclusters

A label-free biosensor was developed for highly sensitive and selective determination of Exo III based on poly(T) molecular beacon-templated CuNPs.

Enzyme-free, signal-amplified nucleic acid circuits for biosensing and bioimaging analysis

Enzyme-free, signal-amplified nucleic acid circuits utilize programmed assembly reactions between nucleic acid substrates to transduce a chemical input into an amplified detection signal.

A DNA kinetics competition strategy of hybridization chain reaction for molecular information processing circuit construction

A DNA kinetics competition strategy of HCR for recognizing input combinations and input sequences has been proposed.

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.

Fluorescent biosensors enabled by graphene and graphene oxide

During the past few years, graphene and graphene oxide (GO) have attracted numerous attentions for the potential applications in various fields from energy technology, biosensing to biomedical diagnosis and therapy due to their various functionalization, high volume surface ratio, unique physical and electrical properties. Among which, graphene and graphene oxide based fluorescent biosensors enabled by their fluorescence-quenching properties have attracted great interests. The fluorescence of fluorophore or dye labeled on probes (such as molecular beacon, aptamer, DNAzymes and so on) was quenched after adsorbed on to the surface of graphene. While in the present of the targets, due to the strong interactions between probes and targets, the probes were detached from the surface of graphene, generating dramatic fluorescence, which could be used as signals for detection of the targets. This strategy was simple and economy, together with great programmable abilities of probes; we could realize detection of different kinds of species. In this review, we first briefly introduced the history of graphene and graphene oxide, and then summarized the fluorescent biosensors enabled by graphene and GO, with a detailed account of the design mechanism and comparison with other nanomaterials (e.g. carbon nanotubes and gold nanoparticles). Following that, different sensing platforms for detection of DNAs, ions, biomolecules and pathogens or cells as well as the cytotoxicity issue of graphene and GO based in vivo biosensing were further discussed. We hope that this review would do some help to researchers who are interested in graphene related biosening research work.

A highly sensitive aptasensor for OTA detection based on hybridization chain reaction and fluorescent perylene probe

An optical aptasensor was developed for ultrasensitive detection of ochratoxin A (OTA) based on hybridization chain reaction (HCR) amplification strategy and fluorescent perylene probe (PAPDI)/DNA composites. Dendritic DNA concatamers were synthesized by HCR strategy and modified on magnetic nanoparticles through aptamer as medium. A large amount of PAPDI probe aggregated under the induction of DNA concatamers and caused fluorescence quenching. In the presence of OTA, the PAPDI/DNA composites were released from magnetic nanoparticles due to the strong affinity between aptamer and OTA. In ethanol, PAPDI monomers disaggregated and produced strong fluorescence. The present method displays excellent sensitivity and selectivity towards OTA.

Merocyanine 540 adsorbed on polyethylenimine-functionalized graphene oxide nanocomposites as a turn-on fluorescent sensor for bovine serum albumin

We suggest a simple, fast, sensitive and selective BSA sensor designed by assembling MC540 molecules on PEI–GO nanocomposites.

A highly sensitive strategy for base excision repair enzyme activity detection based on graphene oxide mediated fluorescence quenching and hybridization chain reaction

We report a highly sensitive strategy for UDG activity detection by combining HCR amplification and a GO-based fluorescence quenching platform.

Silver nanocluster-lightened hybridization chain reaction

A hybridization chain reaction (HCR) lightened by DNA-stabilized silver nanoclusters (AgNCs) as a label-free and turn on fluorescence platform for nucleic acid assays.

Enzyme-free fluorescent biosensor for the detection of DNA based on core-shell Fe3O4 polydopamine nanoparticles and hybridization chain reaction amplification

A novel, highly sensitive assay for quantitative determination of DNA is developed based on hybridization chain reaction (HCR) amplification and the separation via core-shell Fe3O4 polydopamine nanoparticles (Fe3O4@PDA NPs). In this assay, two hairpin probes are designed, one of which is labeled with a 6-carboxyfluorescein (FAM). Without target DNA, auxiliary hairpin probes are stable in solution. However, when target DNA is present, the HCR between the two hairpins is triggered. The HCR products have sticky ends of 24 nt, which are much longer than the length of sticky ends of auxiliary hairpins (6 nt) and make the adsorption much easier by Fe3O4@PDA NPs. With the addition of Fe3O4@PDA NPs, HCR products could be adsorbed because of the strong interaction between their sticky ends and Fe3O4@PDA NPs. As a result, supernatant of the solution with target DNA emits weak fluorescence after separation by magnet, which is much lower than that of the blank solution. The detection limit of the proposed method is as low as 0.05 nM. And the sensing method exhibits high selectivity for the determination between perfectly complementary sequence and target with single base-pair mismatch. Importantly, the application of the sensor for DNA detection in human serum shows that the proposed method works well for biological samples.

Sensitive mutant DNA biomarker detection based on magnetic nanoparticles and nicking endonuclease assisted fluorescence signal amplification

Amplified fluorescence target DNA detection was developed combining nicking endonuclease assisted target recycling and magnetic nanoparticles with low background signal.

l-Cysteine induced hemin/G-quadruplex concatemers electrocatalytic amplification with Pt–Pd supported on fullerene as a nanocarrier for sensing the spore wall protein of Nosema bombycis

This work described an amplified immunosensor for sensing spore wall protein (SWP) ofN. bombycisbased on a novel electrocatalytic function of C₆₀@Pt–Pd loaded with hemin/G-quadruplex.