Solid-state label-free integrated aptasensor based on graphene-mesoporous silica-gold nanoparticle hybrids and silver microspheres

"Fitting" makes "sensing" simple: label-free detection strategies based on nucleic acid aptamers

Nucleic acid aptamers are small sequences of DNA made via in vitro selection techniques to bind targets with high affinity and specificity. The term aptamer derives from the Latin, aptus, meaning "to fit", emphasizing the lock-and-key relationship between aptamers and their binding targets. In 2004, aptamers began to attract researchers' attention as new binding elements for biosensors (i.e. aptasensors). Their advantages over other sensors include a diverse range of possible target molecules, high target affinity, simple synthesis, and ability to form Watson-Crick base pairs. These attributes create an enormous array of possible sensing applications and target molecules, spanning nearly all detection methods and readout techniques. In particular, aptamers provide an opportunity for designing "label-free" sensors, meaning sensors that do not require covalently labeling a signal probe to either the analyte or the recognition element (here, the aptamer). "Label-free" systems previously could only analyze large molecules using a few readout techniques, such as when employing the other recognition elements like antibodies. "Label-free" methods are one of the most effective and promising strategies for faster, simpler, and more convenient detection, since they avoid the expensive and tedious labeling process and challenging labeling reactions, while retaining the highest degree of activity and affinity for the recognition element. "Label-free" sensors are one of the most promising future biosensors. In this Account, we describe our efforts exploring and constructing such label-free sensing strategies based on aptamers. Our methods have included using various readout techniques, employing novel nanomaterials, importing lab-on-a-chip platforms, and improving logical recognition. The resulting sensors demonstrate that aptamers are ideal tools for "label-free" sensors. We divide this Account into three main parts describing three strategies for designing "label-free" sensors: (1) Label-free, separation-free strategies. These include colorimetric sensors based on G-quadruplex-hemin complex, and fluorescent sensors based on fluorescent small molecules, novel conjugated polymers, and metal ion clusters. (2) Label-free, separation-required strategies. In this part, electrochemical sensors are introduced, including sensors with different subtechniques using an electrode array. (3) Logic sensors. Some logic recognition systems are introduced. We emphasize that label-free aptasensors are not merely simple. We hope our introduction illustrates the powerful, flexible, and smart functions of aptamers in carrying out various detection tasks or playing various recognition games. Our work is only a start. We believe this field will bring additional knowledge on general designs, anti-interference, multianalysis, minimization, and auto-operation of aptamer biosensors.

Graphene-Orange II composite nanosheets with electroactive functions as label-free aptasensing platform for "signal-on" detection of protein

The combination of novel nanomaterials and biomolecule recognition units is promising in developing sensitive biosensors. This paper presents a facile approach for the preparation of water-soluble electroactive dye-Orange II functionalized graphene nanosheets (O-GNs). The successful attachment of Orange II on the surface of graphene nanosheets not only prevents the agglomeration of the as-formed graphene nanocomposite in aqueous media, but also endows graphene nanosheets with excellent electroactive property. Integrating the unique properties of the as-prepared O-GNs (high conductivity, high specific surface area and electroactive function) with high affinity and specificity of aptamer, a new label-free electrochemical biosensing concept is demonstrated for the "signal-on" detection of targets such as thrombin and lysozyme. The present O-GNs-based aptasensor exhibits good current response to the above proteins. The linear ranges for thrombin and lysozyme are 1.0 × 10(-12)-4.0 × 10(-10)M and 5.0 × 10(-12)-7.0 × 10(-10)M, with the detection limit of 3.5 × 10(-13)M and 1.0 × 10(-12)M, respectively. In contrast to the common laborious and expensive labeling approaches, the present O-GNs based aptasensing process is highly simple, cost-efficient and does not need labeling and modification of aptamers or introduce additional electrochemical probes.

Graphene signal amplification for sensitive and real-time fluorescence anisotropy detection of small molecules

Fluorescence anisotropy (FA) is a reliable, sensitive, and robust assay approach for determination of many biological targets. However, it is generally not applicable for the assay of small molecules because their molecular masses are relatively too small to produce observable FA value changes. To address this issue, we report herein the development of a FA signal amplification strategy by employing graphene oxide (GO) as the signal amplifier. Because of the extraordinarily larger volume of GO, the fluorophore exhibits very high polarization when bound to GO. Conversely, low polarization is observed when the fluorophore is dissociated from the GO. As proof-of-principle, the approach was applied to FA detection of adenosine triphosphate (ATP) with a fluorescent aptamer. The aptamer exhibits very high polarization when bound to GO, while the FA is greatly reduced when the aptamer complexes with ATP, which exhibits a maximum signal change of 0.316 and a low detection limit of 100 nM ATP in buffer solution. Successful application of this strategy has been demonstrated that it can be constructed either in a "signal-off" or in a "signal-on" detection scheme. Moreover, because FA is less affected by environmental interferences, FA measurements could be conveniently used to directly detect as low as 1.0 μM adenosine triphosphate (ATP) in human serum. The universality of the approach could be achieved to detect an array of biological analytes when complemented with the use of functional DNA structures.

Exploration of structure-switching in the design of aptamer biosensors

The process of "structure-switching" enables biomolecular switches to function as effective biosensing tools. Biomolecular switches can be activated or inactivated by binding to a specific target that triggers a precise conformational change in the biomolecules involved. Although many examples of aptamer-based biomolecular switches can be found in nature, substantial effort has been made in the last decade to engineer structure-switching aptamer sensors by coupling aptamers to a signal transduction method to generate a readout signal upon target binding to the aptamer domain. This chapter focuses on the progress of research on engineered structure-switching aptamer sensors. We begin by discussing the origin of the structure-switching aptamer design, highlight the key developments of structure-switching DNA aptamers for fluorescence-, electrochemistry-, and colorimetry-based detection, and introduce our recent efforts in exploring RNA aptamers to create structure-switching molecular sensors.

Graphene-based electrodes

Graphene, the thinnest two dimensional carbon material, has become the subject of intensive investigation in various research fields because of its remarkable electronic, mechanical, optical and thermal properties. Graphene-based electrodes, fabricated from mechanically cleaved graphene, chemical vapor deposition (CVD) grown graphene, or massively produced graphene derivatives from bulk graphite, have been applied in a broad range of applications, such as in light emitting diodes, touch screens, field-effect transistors, solar cells, supercapacitors, batteries, and sensors. In this Review, after a short introduction to the properties and synthetic methods of graphene and its derivatives, we will discuss the importance of graphene-based electrodes, their fabrication techniques, and application areas.

Graphene: an emerging electronic material

Graphene, a single layer of carbon atoms in a honeycomb lattice, offers a number of fundamentally superior qualities that make it a promising material for a wide range of applications, particularly in electronic devices. Its unique form factor and exceptional physical properties have the potential to enable an entirely new generation of technologies beyond the limits of conventional materials. The extraordinarily high carrier mobility and saturation velocity can enable a fast switching speed for radio-frequency analog circuits. Unadulterated graphene is a semi-metal, incapable of a true off-state, which typically precludes its applications in digital logic electronics without bandgap engineering. The versatility of graphene-based devices goes beyond conventional transistor circuits and includes flexible and transparent electronics, optoelectronics, sensors, electromechanical systems, and energy technologies. Many challenges remain before this relatively new material becomes commercially viable, but laboratory prototypes have already shown the numerous advantages and novel functionality that graphene provides.

Electrochemical Techniques as Powerful Readout Methods for Aptamer-based Biosensors

Aptamers are single-stranded nucleic acids that can be selected in vitro with special folding structures to bind to many different small-molecule, protein, and cellular targets. Over the past two decades, aptamers have become novel promising recognition elements for the fabrication of biosensors. These ‘aptasensors’ have several advantages over antibodies in that they are relatively easy to synthesise or modify in vitro, and can be appended with linkers and reporters for adaptation to various sensing strategies. In this chapter, we introduce the various electrochemical techniques that can be used as powerful readout methods for aptasensors, providing a brief introduction to aptamers and related electrochemical techniques, and then a detailed description of various branches within the field, including labelled strategies, unlabelled strategies, and enzyme-amplified strategies. For each type of approach, several basic and improved design principles will be addressed. It is hoped that, through this discussion, readers will get a sense of how several variables (aptamers, targets and redox reporters) are successfully combined with electrochemical techniques in order to produce a series of sensing platforms with high selectivity and sensitivity.

A simple one-step assay platform based on fluorescence quenching of macroporous silicon

We synthesized 3D macroporous silicon through a simple electrochemical dissolution process and systematically estimated its protein adsorption and effect on fluorescence emission. Compared with conventional 2D polystyrene plate, the macroporous silicon showed a superior protein adsorption capacity and significant fluorescence quenching effect. We developed a 3D macroporous silicon-based adenosine assay system through the following fabrication process: streptavidin molecules that have been immobilized on the surface of macroporous silicon are attached with biotin-linked and adenosine-specific DNA aptamer, followed by hybridization between the attached aptamer and fluorescent chemical (carboxytetramethylrhodamine/CTMR) that is conjugated with a short complementary DNA sequence. In the absence of adenosine, the aptamer-CTMR complexes remain closely attached to the surface of porous silicon, hence fluorescence being significantly quenched. Upon binding to adenosine, the DNA aptamer is subject to structure switching that leads to dissociation of CTMR from DNA aptamer, and consequently the CTMR fluorescence is restored, indicating a simple one-step assay of adenosine. Compared to the conventional 2D PS and ZnO nanorods-based assays, adenosine at much lower (sub-micromolar) concentration was successfully detected through the 3D macroporous silicon-based assay. The three-dimensionally and densely immobilized aptamer probes and effective fluorescence quenching on the surface of macroporous silicon enables adenosine to be detected at lower levels. Although the adenosine detection is reported here as a proof-of-concept, the developed macroporous silicon-based simple one-step assay platform can be applied in general to fluorescence quenching -based detection of many other biomolecules.

Direct detection of adenosine in undiluted serum using a luminescent aptamer sensor attached to a terbium complex

Aptamers, single-stranded nucleic acids that can selectively bind to various target molecules, have been widely used for constructing biosensors. A major challenge in this field, however, is direct sensing of analytes in complex biological media such as undiluted serum. While progress has been made in developing an inhomogeneous assay by using a preseparation step to wash away the interferences within serum, a facile strategy for direct detection of targets in homogeneous unprocessed serum is highly desired. We herein report a turn-on luminescent aptamer biosensor for the direct detection of adenosine in undiluted and unprocessed serum, by taking advantage of a terbium chelate complex with long luminescence lifetime to achieve time-resolved detection. The sensor exhibits a detection limit of 60 μM adenosine while marinating excellent selectivity that is comparable to those in buffer. The approach demonstrated here can be applied for direct detection and quantification of a broad range of analytes in biological media by using other aptamers.

Label-free aptasensor for thrombin determination based on the nanostructured phenazine mediator

New aptasensors based on DNA aptamer and polycarboxylated thiacalix[4]arenes in cone, 1,3-alternate and partial cone configurations bearing Neutral Red (NR) at substituents at the lower rim have been developed and applied for thrombin detection. The assembly of the biorecognition layer was optimized by AFM and EIS study to reach the maximal coverage and regular composition of the surface layer. The interaction of the NR groups with thrombin suppressed the electron hopping between oxidized and reduced mediator groups. This regularly decreased the NR peak current and increased the resistance of the charge transfer. The aptasensor makes it possible to detect from 1 nM to 1 μM of thrombin with the detection limit of 0.05-0.5 nM. No effect of the 1000 excess of bovine serum albumin on the signal was observed. The influence of thiacalix[4]arene configuration on the sensitivity of aptasensor signal toward thrombin is discussed.

Fractal gold modified electrode for ultrasensitive thrombin detection

We report a label-free and ultrasensitive aptasensor based on a fractal gold modified (FracAu) electrode for thrombin detection with a femtomolar detection limit. The FracAu electrode was prepared by electrodeposition of hydrogen tetrachloroaurate (HAuCl(4)) onto a bare indium tin oxide (ITO) electrode surface. After this process the electrode was characterized by SEM. A thiol-modified aptamer against thrombin was immobilized on the FracAu electrode through a self-assembling process. Upon thrombin binding, the interfacial electron transfer of the FracAu electrode was perturbed by the formation of an aptamer-thrombin complex. The concentration of thrombin in the sample solution was determined by measuring the change in the oxidation peak current of hydroxymethyl ferrocene (C(11)H(12)FeO) with differential pulse voltammetry (DPV). The current response (reduced peak current) had a linear relationship with the logarithm of thrombin concentrations in the range of 10(-15) to 10(-10) M with a detection limit of 5.7 fM. Furthermore, the as-prepared FracAu electrode exhibited high selectivity. The application of FracAu electrodes may be extended to prepare other types of biosensors, such as immunosensors, enzyme biosensors and DNA biosensors. These results show that FracAu electrodes have great promise for clinical diagnosis of disease-related biomarkers.

Interface engineering catalytic graphene for smart colorimetric biosensing

Herein a hybrid catalyst consisting of "naked" Au-NPs in situ grown on graphene sheets is engineered, which exhibits a synergetic effect in mimicking peroxidase at its interface, although free Au-NPs or graphene alone has very little activity. What is more, one of the unique features of our synergetic catalyst is that its interface can be reversibly switched from "inactive" to "active" upon treatment with different ssDNA species in solution, thus providing a powerful and versatile basis for designing graphene/DNA-based label-free colorimetric biosensors. Compared with other signal transduction modes in traditional graphene/aptamer-based systems, our novel signaling strategy not only avoids any labeling or modification procedures but also reduces the background signal due to the "off-on" switching mode during the sensing. Furthermore, this facile and general approach can be applicable to the other extended graphene/aptamer-based systems for colorimetric detection of a wide range of analytes. We envision that the tunable graphene-based smart interface could find potential applications in the development of biocatalysis, bioassays, and smart material devices in the future.

A novel label-free electrochemical aptasensor based on graphene-polyaniline composite film for dopamine determination

A novel label-free electrochemical aptasensor based on graphene-polyaniline (GR-PANI) nanocomposites film for dopamine (DA) determination was reported. The resulting GR-PANI layer exhibited good current response for DA determination. The good electron transfer activity might be attributed to the effect of GR and PANI. The highly conductive and biocompatible nanostructure of GR-PANI nanocomposites was characterized by scanning electron microscopy (SEM), cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). To quantify the amount of DA, the peaks of square-wave voltammetry (SWV) were monitored using the redox couple of an [Fe(CN)(6)](4-/3-) probe. The electrochemical aptasensor showed a linear response to DA in the range 0.007-90 nmol/L and a limit of detection of 0.00198 nmol/L (S/N=3). The electrochemical aptasensor was successfully tested on human serum samples.

Enzyme-free amplified detection of DNA by an autonomous ligation DNAzyme machinery

The Zn(2+)-dependent ligation DNAzyme is implemented as a biocatalyst for the amplified detection of a target DNA by the autonomous replication of a nucleic acid reporter unit that is generated by the catalyzed ligation process. The reporter units enhance the formation of active DNAzyme units, thus leading to the isothermal autocatalytic formation of the reporter elements. The system was further developed and applied for the amplified detection of Tay-Sachs genetic disorder mutant, with a detection limit of 1.0 × 10(-11) M. Besides providing a versatile paradigm for the amplified detection of DNA, the system reveals a new, enzyme-free, isothermal, autocatalytic mechanism that introduces means for effective programmed synthesis.

In situ loading of well-dispersed gold nanoparticles on two-dimensional graphene oxide/SiO2 composite nanosheets and their catalytic properties

We demonstrated a simple, in situ reduction route to the synthesis of two-dimensional graphene oxide/SiO(2) (GSCN) hybrid nanostructures consisting of Au nanoparticles (Au NPs) supported on the both sides of GSCN. The as-prepared GSCN/Au NPs hybrid nanomaterials exhibited good catalytic activity for the reduction of 4-nitrophenol. This approach provided a useful platform based on GO hybrid nanomaterials for the fabrication of GSCN/Au NPs hybrid nanomaterials, which could be very useful in catalytic applications.

Electrochemical nanomaterial-based nucleic acid aptasensors

Recent progress in the development of electrochemical nanomaterial-aptamer-based biosensors is summarized. Aptamers are nucleic acid ligands that can be generated against amino acids, drugs, proteins, and other molecules. They are isolated from a large random library of synthetic nucleic acids by an iterative process of binding, separation, and amplification, called systematic evolution of ligands by exponential enrichment (SELEX). In this review, different methods of integrating aptamers with different nanomaterials and nanoparticles for electrochemical biosensing application are described.

Graphene and other nanomaterial-based electrochemical aptasensors

Electrochemical aptasensors, which are based on the specificity of aptamer-target recognition, with electrochemical transduction for analytical purposes have received particular attention due to their high sensitivity and selectivity, simple instrumentation, as well as low production cost. Aptamers are functional nucleic acids with specific and high affinity to their targets, similar to antibodies. However, they are completely selected in vitro in contrast to antibodies. Due to their stability, easy chemical modifications and proneness to nanostructured device construction, aptamer-based sensors have been incorporated in a variety of applications including electrochemical sensing devices. In recent years, the performance of aptasensors has been augmented by incorporating novel nanomaterials in the preparation of better electrochemical sensors. In this review, we summarize the recent trends in the use of nanomaterials for developing electrochemical aptasensors.

Nicking enzyme based homogeneous aptasensors for amplification detection of protein

A simple and highly sensitive homogeneous aptasensor is developed, which relies on nicking enzyme. The sensitivity of this newly proposed aptasensor is about three orders of magnitude higher than that of traditional homogeneous aptasensors. Furthermore, it is capable of detecting target protein in real samples.

Target-induced conjunction of split aptamer as new chiral selector for oligopeptide on graphene-mesoporous silica-gold nanoparticle hybrids modified sensing platform

A new electrochemical label-free biosensor based on target-induced conjunction of a split aptamer as new chiral selector for oligopeptide using graphene-mesoporous silica-gold NP hybrids (GSGHs) as magnified sensing platform is firstly reported, which showed high sensitivity and selectivity for the detection of D-vasopressin (D-VP).