Resonance scattering spectral detection of trace ATP based on label-free aptamer reaction and nanogold catalysis

Reduced graphene oxide as a resonance light-scattering probe for thrombin detection using dual-aptamer-based dsDNA

This paper describes a reduced graphene oxide (RGO)-based resonance light-scattering (RLS) method for thrombin detection by using double strand DNA (dsDNA) as a binding element. dsDNA is obtained by hybridizing DNA1 and DNA2, which respectively consist of one aptamer of thrombin and the complementary strand of the other aptamer of thrombin. When thrombin is added, the specific binding of two aptamers to thrombin results in a complex (DNA1-thrombin-DNA2) and triggers the release of the complementary strand of two aptamers from dsDNA. The released ssDNA can be self-assembled on the surface of RGO to form a stable DNA1-thrombin-DNA2-RGO complex, which increases RLS signals. This simple and rapid method has enabled the detection of thrombin in the picomolar level in buffer and human serum samples. This study is the first to use RGO as a platform in RLS sensor, which can extend the application of RGO.

Optical Aptasensors for Adenosine Triphosphate

Nucleic acids are among the most researched and applied biomolecules. Their diverse two- and three-dimensional structures in conjunction with their robust chemistry and ease of manipulation provide a rare opportunity for sensor applications. Moreover, their high biocompatibility has seen them being used in the construction of in vivo assays. Various nucleic acid-based devices have been extensively studied as either the principal element in discrete molecule-like sensors or as the main component in the fabrication of sensing devices. The use of aptamers in sensors - aptasensors, in particular, has led to improvements in sensitivity, selectivity, and multiplexing capacity for a wide verity of analytes like proteins, nucleic acids, as well as small biomolecules such as glucose and adenosine triphosphate (ATP). This article reviews the progress in the use of aptamers as the principal component in sensors for optical detection of ATP with an emphasis on sensing mechanism, performance, and applications with some discussion on challenges and perspectives.

An efficient signal-on aptamer-based biosensor for adenosine triphosphate detection using graphene oxide both as an electrochemical and electrochemiluminescence signal indicator

An efficient aptasensor was developed in which graphene oxide (GO) was employed as an indicator for both electrochemical impedance spectroscopy and electrochemiluminescence (ECL) signal generation. The aptasensor was fabricated by self-assembling the ECL probe of a thiolated adenosine triphosphate binding aptamer (ABA) tagged with a Ru complex (Ru(bpy)3(2+) derivatives) onto the surface of gold nanoparticle (AuNP) modified glassy carbon electrode (GCE). ABA immobilized onto AuNP modified GCE could strongly adsorb GO due to the strong π-π interaction between ABA and graphene oxide; ECL quenching of the Ru complex then takes place because of energy transfer and electron transfer, and a large increase of the electron transfer resistance (Ret) of the electrode. While in the presence of target adenosine triphosphate (ATP), the ABA prefers to form ABA-ATP bioaffinity complexes, which have weak affinity to graphene oxide and keep the graphene oxide away from the electrode surface, thus allowing the ECL signal enhancement, and in conjunction with the decrease of the Ret. Because of the high ECL quenching efficiency, unique structure, and electronic properties of graphene oxide, the Ret and ECL intensity versus the logarithm of ATP concentration was linear in the wide range from 10 pM to 10 nM with an ultra-low detection limit of 6.7 pM to 4.8 pM, respectively. The proposed aptasensor exhibited excellent reproducibility, stability, and outstanding selectivity, and ATP could be effectively distinguished from its analogues. More significantly, this efficient ECL aptasensor strategy based on GO acting both as an electrochemical and ECL signal indicator is general and can be easily extended to other biological binding events.

"Click on the bidirectional switch": the aptasensor for simultaneous detection of lysozyme and ATP with high sensitivity and high selectivity

A bifunctional and simple aptasensor was designed to one-spot simultaneously detect two analytes, lysozyme and ATP. The aptasensor was obtained by the electronic interaction between methyl violet (MV) and dsDNA. The dsDNA was obtained by hybridization of ATP aptamer and lysozyme aptamer. And we used the resonance light scattering (RLS) technique to detect the concentration of lysozyme and ATP. During the procedure of detection, the aptasensor works like a bidirectional switch, the corresponding side of the dsDNA will open when the target (lysozyme or ATP) "click" the aptamer, which results in corresponding RLS signal change. By the combination of the RLS technique, it is found that the changed RLS intensity was proportional to the concentration of lysozyme and ATP. The mixtures of ATP and lysozyme also met two binary function relations. The results indicated that the aptasensor could achieve simultaneous detection of ATP and lysozyme, the detection limits of ATP and lysozyme could reach 10(-11) M and 10(-12) M, respectively. The aptasensor shows potential application for small molecule and protein detection by RLS, it could extend the application of RLS technique.

Label-free monitoring of plasmonic catalysis on the nanoscale

Plasmonics is the description of specific light matter interactions of metallic structures. In general the size of such structures is well in the nanometer regime and also determines such specific characteristics as color, field confinement etc. Plasmon-induced hot electrons play a vital role in so-called plasmonic catalysis, a field that has recently attracted attention as a new reaction platform. Current reports introduce such nanoscale catalysis as an effective approach to concentrate the energy of visible light and direct it to adsorbed molecules, thereby increasing the chemical reaction rate, and controlling the reaction selectivity. In this review, we present various plasmon-catalyzed reactions specifically monitored with Raman spectroscopy, namely surface-enhanced Raman scattering (SERS), remote SERS (Re-SERS) and tip-enhanced Raman scattering (TERS). These techniques utilize the signal enhancing effect of the metal nanoparticles. However, at the same time they can be used to control the actual reactivity. In the first part, the mechanism of plasmonic catalysis is introduced. Then it is shown how catalytic reactions can be spectroscopically investigated far beyond the diffraction limit using TERS. Finally, the sensitivity of the methods is discussed.

A cascade amplification strategy based on rolling circle amplification and hydroxylamine amplified gold nanoparticles enables chemiluminescence detection of adenosine triphosphate

A highly sensitive and selective chemiluminescent (CL) biosensor for adenosine triphosphate (ATP) was developed by taking advantage of the ATP-dependent enzymatic reaction (ATP-DER), the powerful signal amplification capability of rolling circle amplification (RCA), and hydroxylamine-amplified gold nanoparticles (Au NPs). The strategy relies on the ability of ATP, a cofactor of T4 DNA ligase, to trigger the ligation-RCA reaction. In the presence of ATP, the T4 DNA ligase catalyzes the ligation reaction between the two ends of the padlock probe, producing a closed circular DNA template that initiates the RCA reaction with phi29 DNA polymerase and dNTP. Therein, many complementary copies of the circular template can be generated. The ATP-DER is eventually converted into a detectable CL signal after a series of processes, including gold probe hybridization, hydroxylamine amplification, and oxidative gold metal dissolution coupled with a simple and sensitive luminol CL reaction. The CL signal is directly proportional to the ATP level. The results showed that the detection limit of the assay is 100 pM of ATP, which compares favorably with those of other ATP detection techniques. In addition, by taking advantage of ATP-DER, the proposed CL sensing system exhibits extraordinary specificity towards ATP and could distinguish the target molecule ATP from its analogues. The proposed method provides a new and versatile platform for the design of novel DNA ligation reaction-based CL sensing systems for other cofactors. This novel ATP-DER based CL sensing system may find wide applications in clinical diagnosis as well as in environmental and biomedical fields.

A proposed mechanism of the influence of gold nanoparticles on DNA hybridization

A combination of gold nanoparticles (AuNPs) and nucleic acids has been used in biosensing applications. However, there is a poor fundamental understanding of how gold nanoparticle surfaces influence the DNA hybridization process. Here, we measured the rate constants of the hybridization and dehybridization of DNA on gold nanoparticle surfaces to enable the determination of activation parameters using transition state theory. We show that the target bases need to be detached from the gold nanoparticle surfaces before zipping. This causes a shift of the rate-limiting step of hybridization to the mismatch-sensitive zipping step. Furthermore, our results propose that the binding of gold nanoparticles to the single-stranded DNA segments (commonly known as bubbles) in the duplex DNA stabilizes the bubbles and accelerates the dehybridization process. We employ the proposed mechanism of DNA hybridization/dehybridization to explain the ability of 5 nm diameter gold nanoparticles to help discriminate between single base-pair mismatched DNA molecules when performed in a NanoBioArray chip. The mechanistic insight into the DNA-gold nanoparticle hybridization/dehybridization process should lead to the development of new biosensors.

A label-free DNAzyme-cleaving fluorescence method for the determination of trace Pb(2+) based on catalysis of AuPd nanoalloy on the reduction of rhodamine 6G

The substrate chain of double-stranded DNA (dsDNA) could be specifically cleaved by Pb(2+) to release single-stranded DNA (ssDNA) that adsorbs onto the AuPd nanoalloy (AuPdNP) to form a stable AuPdNP-ssDNA complex, but the dsDNA can not protect AuPdNPs in large AuPdNP aggregates (AuPdNPA) under the action of NaCl. AuPdNP-ssDNA and large AuPdNPA could be separated by centrifugation. On increasing the concentration of Pb(2+) , the amount of released ssDNA increased; AuPdNP-ssDNA increased in the centrifugation solution exhibiting a catalytic effect on the slow reaction of rhodamine 6G (Rh6G) and NaH2 PO2 , which led to fluorescence quenching at 552 nm. The decrease in fluorescence intensity (ΔF) was linear to the concentration of Pb(2+) within the range 0.33-8.00 nmol/L, with a detection limit of 0.21 nmol/L. The proposed method was applied to detect Pb(2+) in water samples, with satisfactory results.

A new and highly sensitive resonance Rayleigh scattering assay for lysozyme using aptamer-nanogold as a probe

Gold nanoparticles (GN), 10 nm in size, were modified by using lysozyme aptamer (Apt) to obtain a stable Apt–GN probe in pH 8.05 Tris/HCl buffer solutions containing 0.04 mol/L NaCl. Upon addition of lysozyme (LYS), it reacted with the Apt of the probe to form a very stable Apt–LYS complex and to release GNs, which aggregated to form large clusters with a resonance Rayleigh scattering (RRS) peak at 368 nm. The enhanced peak intensity, ΔI, was linear to the LYS concentration in the range 0.2–5.2 nmol/L, with a detection limit of 0.05 nmol/L. The influence of foreign substance was tested, and the results showed that this RRS method has high selectivity. This Apt–GN RRS method was applied to the analysis of LYS in a real sample, with satisfactory results.

Optical aptasensors for quantitative detection of small biomolecules: a review

Aptasensors are aptamer-based biosensors with excellent recognition capability towards a wide range of targets. Specially, there have been ever-growing interests in the development of aptasensors for the detection of small molecules. This phenomenon is contributed to two reasons. On one hand, small biomolecules play an important role in living organisms with many kinds of biological function, such as antiarrhythmic effect and vasodilator activity of adenosine. On the other hand, the concentration of small molecules can be an indicator for disease diagnosis, for example, the concentration of ATP is closely associated with cell injury and cell viability. As a potential analysis tool in the construction of aptasensors, optical analysis has attracted much more interest of researchers due to its high sensitivity, quick response and simple operation. Besides, it promises the promotion of aptasensors in performance toward a new level. Review the development of optical aptasensors for small biomolecules will give readers an overall understanding of its progress and provide some theoretical guidelines for its future development. Hence, we give a mini-review on the advance of optical aptasensors for small biomolecules. This review focuses on recent achievements in the design of various optical aptasensors for small biomolecules, containing fluorescence aptasensors, colorimetric aptasensors, chemiluminescence aptasensors and other optical aptasensors.

Detection of adenosine triphosphate through polymerization-induced aggregation of actin-conjugated gold/silver nanorods

We have developed a simple and selective nanosensor for the optical detection of adenosine triphosphate (ATP) using globular actin-conjugated gold/silver nanorods (G-actin-Au/Ag NRs). By simply mixing G-actin and Au/Ag NRs (length ~56 nm and diameter ~12 nm), G-actin-Au/Ag NRs were prepared which were stable in physiological solutions (25 mM Tris-HCl, 150 mM NaCl, 5.0 mM KCl, 3.0 mM MgCl2 and 1.0 mM CaCl2; pH 7.4). Introduction of ATP into the G-actin-Au/Ag NR solutions in the presence of excess G-actin induced the formation of filamentous actin-conjugated Au/Ag NR aggregates through ATP-induced polymerization of G-actin. When compared to G-actin-modified spherical Au nanoparticles having a size of 13 nm or 56 nm, G-actin-Au/Ag NRs provided better sensitivity for ATP, mainly because the longitudinal surface plasmon absorbance of the Au/Ag NR has a more sensitive response to aggregation. This G-actin-Au/Ag NR probe provided high sensitivity (limit of detection 25 nM) for ATP with remarkable selectivity (>10-fold) over other adenine nucleotides (adenosine, adenosine monophosphate and adenosine diphosphate) and nucleoside triphosphates (guanosine triphosphate, cytidine triphosphate and uridine triphosphate). It also allowed the determination of ATP concentrations in plasma samples without conducting tedious sample pretreatments; the only necessary step was simple dilution. Our experimental results are in good agreement with those obtained from a commercial luciferin-luciferase bioluminescence assay. Our simple, sensitive and selective approach appears to have a practical potential for the clinical diagnosis of diseases (e.g. cystic fibrosis) associated with changes in ATP concentrations.

Resonance light scattering determination of trace bisphenol A with signal amplification by aptamer-nanogold catalysis

HAuCl4 was reduced by sodium citrate to prepare 10 nm gold nanoparticles (AuNPs) that were modified by the bisphenol A aptamer (Apt) to obtain an aptamer-nanogold probe (Apt-AuNP) for bisphenol A (BPA). The probes were aggregated nonspecifically to form large clusters, which showed a strong resonance light scattering (RLS) peak at 520 nm, under preparation conditions (pH 7.6 Na2HPO4-NaH2PO4 buffer and ultrasonication). Upon addition of BPA, the probe reacted specifically to form dispersed BPA-Apt-AuNP conjugates that exhibited strong catalysis of the two particle reactions of glucose-Cu(II) and hydrazine hydrochloride-Cu(II) with a strong RLS peak at 360 nm and 510 nm respectively. When the BPA concentration increased, the RLS intensity at 360 nm and 510 nm increased respectively. Accordingly, two new and highly-sensitive RLS methods were established for the detection of BPA, using the Apt-AuNP catalytic amplification.

A simple and sensitive resonance Rayleigh scattering method for determination of As(III) using aptamer-modified nanogold as a probe

A simple and selective aptamer (ssDNA)-modified nanogold probe (AussDNA) was prepared for the determination of trace As(III) in HEPES buffer solution (pH 8.2) containing 0.05 mol/L NaCl. The method coupled the aptamer reaction of AussDNA-As(III) and the resonance Rayleigh scattering (RRS) of nanogold aggregations at 278 nm. When the As(III) concentration increased, the RRS intensity at 278 nm increased to form more nanogold aggregation and a stable As(III)-ssDNA complex. Under selected conditions, the increased RRS intensity (ΔI) was linear to the concentration of As(III) in the range 3.8-230.4 ng/mL, with a detection limit of 1.9 ng/mL. This RRS method was applied to detect As(III) in water samples, with simplicity, sensitivity and selectivity.

Signal-amplification detection of small molecules by use of Mg2+-dependent DNAzyme

Because small molecules can be beneficial or toxic in biology and the environment, specific and sensitive detection of small molecules is one of the most important objectives of the scientific community. In this study, new signal amplification assays for detection of small molecules based on Mg(2+)-dependent DNAzyme were developed. A cleavable DNA substrate containing a ribonucleotide, the ends of which were labeled with black hole quencher (BHQ) and 6-carboxyfluorescein (FAM), was used for fluorescence detection. When the small molecule of interest is added to the assay solution, the Mg(2+)-dependent DNAzyme is activated, facilitating hybridization between the Mg(2+)-dependent DNAzyme and the DNA substrate. Binding of the substrate to the DNAzyme structure results in hydrolytic cleavage of the substrate in the presence of Mg(2+) ions. The fluorescence signal was amplified by continuous cleavage of the enzyme substrate. Ochratoxin A (OTA) and adenosine triphosphate (ATP) were used as model analytes in these experiments. This method can detect OTA specifically with a detection limit as low as 140 pmol L(-1) and detect ATP specifically with a detection limit as low as 13 nmol L(-1). Moreover, this method is potentially extendable to detection of other small molecules which are able to dissociate the aptamer from the DNAzyme, leading to activation of the DNAzyme.

Simple, fast and selective detection of adenosine triphosphate at physiological pH using unmodified gold nanoparticles as colorimetric probes and metal ions as cross-linkers

We report a simple, fast and selective colorimetric assay of adenosine triphosphate (ATP) using unmodified gold nanoparticles (AuNPs) as probes and metal ions as cross-linkers. ATP can be assembled onto the surface of AuNPs through interaction between the electron-rich nitrogen atoms and the electron-deficient surface of AuNPs. Accordingly, Cu2+ ions induce a change in the color and UV/Vis absorbance of AuNPs by coordinating to the triphosphate groups and a ring nitrogen of ATP. A detection limit of 50 nM was achieved, which is comparable to or lower than that achievable by the currently used electrochemical, spectroscopic or chromatographic methods. The theoretical simplicity and high selectivity reported herein demonstrated that AuNPs-based colorimetric assay could be applied in a wide variety of fields by rationally designing the surface chemistry of AuNPs. In addition, our results indicate that ATP-modified AuNPs are less stable in Cu2+, Cd2+ or Zn2+-containing solutions due to the formation of the corresponding dimeric metal-ATP complexes.

Ultrasensitive aptamer biosensor for arsenic(III) detection in aqueous solution based on surfactant-induced aggregation of gold nanoparticles

This paper reports the colorimetric and resonance scattering (RS)-based biosensor for the ultrasensitive detection of As(III) in aqueous solution via aggregating gold nanoparticles (AuNPs) by the special interactions between arsenic-binding aptamer, target and cationic surfactant. Aptamers and the cationic surfactant could assemble to form a supramolecule, which prevented AuNPs from aggregating due to the exhaustion of cationic surfactant. The introduction of As(III) specifically interacted with the arsenic-binding aptamer to form the aptamer-As(III) complex, so that the following cationic surfactant could aggregate AuNPs and cause the remarkable change in color and RS intensity. The results of circular dichroism (CD) and scanning probe microscope (SPM) testified to the formation of the supramolecule and aptamer-As(III) complex, and the observation of transmission electron microscope (TEM) further confirmed that the aggregation of AuNPs could be controlled by the interactions among the aptamer, As(III) and cationic surfactant. The variations of absorbance and RS intensity were exponentially related to the concentration of As(III) in the range from 1 to 1500 ppb, with the detection limit of 40 ppb for the naked eye, 0.6 ppb for colorimetric assay and 0.77 ppb for RS assay. Additionally, the speed of the present biosensor was rapid, and it also exhibited high selectivity over other metal ions with an excellent recovery for detection in real water samples, suggesting that the proposed biosensor will play an important role in environmental detection.

An aptamer based resonance light scattering assay of prostate specific antigen

Prostate specific antigen (PSA) is a valuable tumor marker for prostate cancer screening. In this work, a novel and sensitive resonance light scattering (RLS) spectral assay of PSA was proposed based on PSA aptamer modified gold nanoparticles (AuNPs). The sulfhydryl modified single-strand aptamer could interact with AuNPs, which made the AuNPs stable in high concentration of salt. In pH 7.0 BR buffer solution, the highly selective combination of PSA and AuNPs-labeling aptamer resulted in the aggregation of AuNPs which showed high RLS intensity. Under the optimal conditions, the magnitude of enhanced RLS intensity (ΔI(RLS)) was proportional to the concentration of PSA in the range from 0.13 to 110 ng/mL, with a detection limit (LOD, 3σ) of 0.032 ng/mL. This developed RLS assay as well as a commercially available enzyme-linked immunosorbent assay (ELISA) kit was successfully applied to the detection of PSA in 15 serum samples, and an excellent correlation of the levels of PSA measured was obtained. This is the first report of the aptamer based RLS assay for PSA and it is also a significant application of instrumental analysis technique.

Nuclease cleavage-assisted target recycling for signal amplification of free-label impedimetric aptasensors

A simple, novel, label-free impedimetric aptasensor with signal amplification is developed for ultrasensitive detection of small molecules on a carbon nanotubes-based sensing platform by combining target-induced release of the aptamers and nuclease cleavage-assisted target recycling.