DNA aptamer folding on gold nanoparticles: from colloid chemistry to biosensors

We have investigated the effect of the folding of DNA aptamers on the colloidal stability of gold nanoparticles (AuNPs) to which an aptamer is tethered. On the basis of the studies of two different aptamers (adenosine aptamer and K+ aptamer), we discovered a unique colloidal stabilization effect associated with aptamer folding: AuNPs to which folded aptamer structures are attached are more stable toward salt-induced aggregation than those tethered to unfolded aptamers. This colloidal stabilization effect is more significant when a DNA spacer was incorporated between AuNP and the aptamer or when lower aptamer surface graft densities were used. The conformation that aptamers adopt on the surface appears to be a key factor that determines the relative stability of different AuNPs. Dynamic light scattering experiments revealed that the sizes of AuNPs modified with folded aptamers were larger than those of AuNPs modified with unfolded (but largely collapsed) aptamers in salt solution. From both the electrostatic and steric stabilization points of view, the folded aptamers that are more extended from the surface have a higher stabilization effect on AuNP than the unfolded aptamers. On the basis of this unique phenomenon, colorimetric biosensors have been developed for the detection of adenosine, K+, adenosine deaminase, and its inhibitors. Moreover, distinct AuNP aggregation and redispersion stages can be readily operated by controlling aptamer folding and unfolding states with the addition of adenosine and adenosine deaminase.     

A sensitive, label-free, aptamer-based biosensor using a gold nanoparticle-initiated chemiluminescence system

We report a label-free, aptamer-based chemiluminescent biosensor. The biosensor relies upon the catalytic activity of unmodified gold nanoparticles (AuNPs) on the luminol-H(2)O(2) chemiluminescence (CL) reaction, and the interaction of unmodified AuNPs with the aptamer. The unmodified AuNPs can effectively differentiate unstructured and folded aptamer. The binding of the aptamer with the target can induce the AuNP aggregation in the presence of 0.5 M NaCl, and after aggregation the catalytic activity of the AuNPs on the luminol-H(2)O(2) CL reaction is greatly enhanced. During the assay, no covalent functionalization of the AuNPs or aptamer is required. The detection limit of thrombin was estimated to be as low as 26 fM, and the sensitivity was more than 4 orders of magnitude better than that of known AuNP-based colorimetric methods for the detection of thrombin. This aptamer-based biosensor offers the advantages of being simple, cheap, rapid, and sensitive.     

Preparation of brightly fluorescent silica nanoparticles modified with lucigenin and chitosan,and their application to an aptamer-based sandwich assay for thrombin

We report on the preparation of fluorescent silica nanoparticles (SiNPs) modified with chitosan and lucigenin by using a reverse microemulsion method. The introduction of chitosan to the lucigenin doped SiNPs is shown to improve the fluorescence quantum yield. The modified SiNPs were used as fluorescent markers in an aptamer-based method for selective determination of thrombin. In this protocol, thrombin was sandwiched between streptavidin-coated magnetic beads and the fluorescent SiNPs modified with a thrombin-binding aptamer. The method was successfully applied to the determination of thrombin in human serum and showed a detection limit as low as 0.02 nM. In our perception, the protocol presented here is promising in that such SiNPs may be applied to the sensitive fluorescent detection of other analytes by changing the corresponding aptamer.

The introduction of chitosan to the lucigenin doped SiNPs is shown to improve the fluorescence quantum yield. The modified SiNPs were used as fluorescent markers in an aptamer-based method for selective determination of thrombin. The effect of chitosan concentration on fluorescence intensity of lucigenin/SiO₂ nanoparticles (the volume of chitosan solution is 100 μL)

     

A DNA hybridization detection based on fluorescence resonance energy transfer between dye-doped core-shell silica nanoparticles and gold nanoparticles

A novel and efficient method to evaluate the DNA hybridization based on a fluorescence resonance energy transfer (FRET) system, with fluorescein isothiocyanate (FITC)-doped fluorescent silica nanoparticles (SiNPs) as donor and gold nanoparticles (AuNPs) as acceptor, has been reported. The strategy for specific DNA sequence detecting is based on DNA hybridization event, which is detected via excitation of SiNPs-oligonucleotide conjugates and energy transfer to AuNPs-oligonucleotide conjugates. The proximity required for FRET arises when the SiNPs-oligonucleotide conjugates hybridize with partly complementary AuNPs-oligonucleotide conjugates, resulting in the fluorescence quenching of donors, SiNPs-oligonucleotide conjugates, and the formation of a weakly fluorescent complex, SiNPs-dsDNA-AuNPs. Upon the addition of the target DNA sequence to SiNPs-dsDNA-AuNPs complex, the fluorescence restores (turn-on). Based on the restored fluorescence, a homogeneous assay for the target DNA is proposed. Our results have shown that the linear range for target DNA detection is 0-35.0 nM with a detection limit (3σ) of 3.0 picomole. Compared with FITC-dsDNA-AuNPs probe system, the sensitivity of the proposed probe system for target DNA detection is increased by a factor of 3.4-fold.     

Tween 20-stabilized gold nanoparticles combined with adenosine triphosphate-BODIPY conjugates for the fluorescence detection of adenosine with more than 1000-fold selectivity

This study describes the development of a simple, enzyme-free, label-free, sensitive, and selective system for detecting adenosine based on the use of Tween 20-stabilized gold nanoparticles (Tween 20-AuNPs) as an efficient fluorescence quencher for boron dipyrromethene-conjugated adenosine 5′-triphosphate (BODIPY-ATP) and as a recognition element for adenosine. BODIPY-ATP can interact with Tween 20-AuNPs through the coordination between the adenine group of BODIPY-ATP and Au atoms on the NP surface, thereby causing the fluorescence quenching of BODIPY-ATP through the nanometal surface energy transfer (NSET) effect. When adenosine attaches to the NP surface, the attached adenosine exhibits additional electrostatic attraction to BODIPY-ATP. As a result, the presence of adenosine enhances the efficiency of AuNPs in fluorescence quenching of BODIPY-ATP. The AuNP-induced fluorescence quenching of BODIPY-ATP progressively increased with an increase in the concentration of adenosine; the detection limit at a signal-to-noise ratio of 3 for adenosine was determined to be 60 nM. The selectivity of the proposed system was more than 1000-fold for adenosine over any adenosine analogs and other nucleotides. The proposed system combined with a phenylboronic acid-containing column was successfully applied to the determination of adenosine in urine.     

Visual detection of arginine based on the unique guanidino group-induced aggregation of gold nanoparticles

A simple, cost-effective and rapid method for visual detection of arginine based on the citrate-capped gold nanoparticles (AuNPs) aggregation has been developed in this paper. Arginine is the only amino acid with guanidino group, and has the highest isoelectric point (pI) at about 10.8. At pH 9.62, negatively charged citrate-capped AuNPs are well dispersed because of strong electrostatic repulsion. However, positively charged arginine (pH < pI) easily induces negatively charged citrate-capped AuNPs aggregation through electrostatic and hydrogen-bonding interactions, resulting in a red to blue color change of the solution. Using a UV–vis spectrophotometer, the method enables the detection of arginine in the range of 0.08–13.2 μM with a detection limit (3σ/slope) of 16 nM. Particularly, as low as 0.4 μM arginine can be easily detected by the naked eye without using any complicated or expensive instruments. Furthermore, this method can provide satisfactory results for the determination of arginine in arginine injection and compound amino acid injection samples.     

Aptamer enzymatic cleavage protection assay for the gold nanoparticle-based colorimetric sensing of small molecules

A label-free, homogeneous aptamer-based sensor strategy was designed for the facile colorimetric detection of small target molecules. The format relied on the target-induced protection of DNA aptamer from the enzymatic digestion and its transduction into a detectable signal through the length-dependent adsorption of single-stranded DNA onto unmodified gold nanoparticles (AuNPs). The proof-of-principle of the approach was established by employing the anti-tyrosinamide aptamer as a model functional nucleic acid. In the absence of target, the aptamer was cleaved by the phosphodiesterase I enzymatic probe, leading to the release of mononucleotides and short DNA fragments. These governed effective electrostatic stabilization of AuNPs so that the nanoparticles remained dispersed and red-colored upon salt addition. Upon tyrosinamide binding, the enzymatic cleavage was impeded, resulting in the protection of the aptamer structure. As this long DNA molecule was unable to electrostatically stabilize AuNPs, the resulting colloidal solution turned blue after salt addition due to the formation of nanoparticle aggregates. The quantitative determination of the target can be achieved by monitoring the ratio of absorbance at 650 and 520 nm of the gold colloidal solution. A limit of detection of ∼5 μM and a linear range up to 100 μM were obtained. The sensing platform was further applied, through the same experimental protocol, to the adenosine detection by using its DNA aptamer as recognition tool. This strategy could extend the potentialities, in terms of both simplicity and general applicability, of the aptamer-based sensing approaches.     

A sensitive, label free electrochemical aptasensor for ATP detection

A sensitive, label free electrochemical aptasensor for small molecular detection has been developed in this work based on gold nanoparticles (AuNPs) amplification. This aptasensor was fabricated as a tertiary hybrid DNA-AuNPs system, which involved the anchored DNA (ADNA) immobilized on gold electrode, reporter DNA (RDNA) tethered with AuNPs and target-responsive DNA (TRDNA) linking ADNA and RDNA. Electrochemical signal is derived from chronocoulometric interrogation of [Ru(NH₃)₆]³⁺ (RuHex) that quantitatively binds to surface-confined DNA via electrostatic interaction. Using adenosine triphosphate (ATP) as a model analyte and ATP-binding aptamer as a model molecular reorganization element, the introduction of ATP triggers the structure switching of the TRDNA to form aptamer-ATP complex, which results in the dissociation of the RDNA capped AuNPs (RDNA-AuNPs) and release of abundant RuHex molecules trapped by RDNA-AuNPs. The incorporation of AuNPs in this strategy significantly enhances the sensitivity because of the amplification of electrochemical signal by the RDNA-AuNPs/RuHex system. Under optimized conditions, a wide linear dynamic range of 4 orders of magnitude (1 nM-10 μM) was reached with the minimum detectable concentration at sub-nanomolar level (0.2 nM). Those results demonstrate that our nanoparticles-based amplification strategy is feasible for ATP assay and presents a potential universal method for other small molecular aptasensors.     

Label-free colorimetric sensing of ascorbic acid based on Fenton reaction with unmodified gold nanoparticle probes and multiple molecular logic gates

A label-free strategy based on Fenton reaction with unmodified gold nanoparticles (AuNPs) as probe is demonstrated for ascorbic acid (AA) sensing. AuNPs is stable in the presence of single stranded DNA (ssDNA) which prevents salt-induced aggregation of AuNPs in solution. The hydroxyl free radicals generated by Fenton reaction lead to ssDNA cleavage into different sequence fragments which induce aggregation of AuNPs to produce a red-to-blue color change. As an efficient biological antioxidant, AA could effectively scavenge free radicals to avoid the cleavage of ssDNA, so that it prevents color change of the AuNPs solution. Thus, the color change of AuNPs in the presence and absence of AA provides a new approach for the detection of AA. The absorbance ratio at two wavelengths, A₆₇₀/A₅₂₀, decreases linearly with AA content within 1–15 μM, giving rise to a detection limit of 0.3 μM and a RSD of 2.8% (10 μM). The color display of AuNPs solution makes it feasible for the estimation of AA content by naked eye visualization. Moreover, based on Fenton reaction and unmodified gold nanoparticles, a multiple logic gate system includes two logic operations, i.e., INHIBIT and NOR, has been designed with small molecules (AA, l-cysteine, glutathione) as inputs and the colorimetric changes of AuNPs solution as outputs.     

Detection of glucose in synthetic tear fluid using dually functionalized gold nanoparticles

A simple fluorescent sensing of glucose in aqueous fluids (e.g. tear fluid) using dually functionalized gold nanoparticles is presented. As a first step gold nanoparticles (AuNPs) were synthesized using oxidised dextran which acted both as reducing and stabilizing agent. Aminophenyl boronic acid was conjugated onto AuNPs by Schiff's base formation and the formed Schiff's base was stabilized by sodium borohydride reduction. Rhodamine B isothiocyanate (RBITC) was then assembled onto the modified AuNPs. The fluorescence of RBITC was nearly quenched and found to be revived when glucose was added. It is reasoned that the glucose binding induces restructuring of the surface assembly resulting in an overall increase in the size and thereby enhancing the distance between the gold core and fluorophore. TEM image and size measurements using dynamic light scattering (DLS) in fact, reflected this possibility. The increase in fluorescence was proportional with the concentration of glucose enabling quantitative detection. A good linearity was observed between the fluorescence intensity and glucose concentration in a range of 0.025-0.125 μM with detection limit of 0.005 ± 0.002 μM. The potential of the method was demonstrated by measuring glucose in real tear fluids collected from volunteers. The method is extremely sensitive and can be employed to measure low concentration of glucose in aqueous fluids such as tear.     

Visual detection of melamine in milk samples based on label-free and labeled gold nanoparticles

Melamine that can cause serious damage to the organs of animal or human beings was found to bind to polythymine via hydrogen bonding. With this novel discovery, colorimetric detection of melamine based on label-free and labeled gold nanoparticles was developed, respectively. Both of the methods revealed good selectivity for melamine over other components that may exist in milk and good anti-influence ability. The raw milk samples were pretreated according to the National standard method combined with a solid phase extraction monolithic column. The accurate quantification of melamine as low as 41.7 nM and 46.5 nM was obtained, respectively. It also guarantees fast and reliable readout with naked eyes, making visual detection possible. Further comparison between label-free and labeled based methods was discussed in this paper.     

A novel colorimetric aptasensor for detection of chloramphenicol based on lanthanum ion–assisted gold nanoparticle aggregation and smartphone imaging

A label-free, rapid response colorimetric aptasensor for sensitive detection of chloramphenicol (CAP) was proposed, which was based on the strategy of ssDNA-modified gold nanoparticle (AuNP) aggregation assisted by lanthanum (La³⁺) ions. The AuNPs generated a color change that could be monitored in the red, green, and blue and analyzed by the smartphone imaging app. La³⁺, as a trigger agent, strongly combined with the phosphate groups of the surface of ssDNA-AuNPs probe, which helps create AuNP aggregation and the color change of AuNPs from red to blue. On the contrary, when mixing with CAP, the aptamer (Apt) bound to CAP to form a rigid structure of the Apt-CAP complex, and La³⁺ attached to the phosphate groups of the complex, which prevented the aptamer from binding to the surface of the AuNPs. As a result, the color of the AuNPs changed to violet-red. Finally, UV-vis absorption spectroscopy and the smartphone imaging app were employed to determine CAP with a lower detection limit of 7.65 nM and 5.88 nM, respectively. The proposed strategy featuring high selectivity and strong anti-interference ability for detection of CAP in practical samples was achieved. It is worth mentioning that the simple and portable colorimetric aptasensor will be used for facilitating on-site detection of food samples.

     

Highly Sensitive Voltammetric Thrombin Aptamer Sensor Based on the Synergistic Effect of Doping/Depositing Gold Nanoparticles in Polydopamine Film

A highly sensitive square‐wave voltammetric thrombin (TB) aptamer sensor was developed using functional polydopamine (PD) film by doping and depositing gold nanoparticles into the bulk and the surface of PD. The aptamer sensor was fabricated by immobilizing a thiolated TB‐binding aptamer (TBA) on the AuNPs‐doped/deposited PD film. AuNPs‐supported methylene blue labels were used for the detection of human α‐TB. Under the optimized conditions, the aptamer sensor’s dynamic range and the detection limit were determined to be 2.0 pM–50 nM and 0.97±0.06 pM, respectively. Finally, the proposed aptamer sensor was successfully examined in human serum samples and satisfactory results were obtained.     

Direct electrochemical detection of kanamycin based on peroxidase-like activity of gold nanoparticles

An enzyme-free, ultrasensitive electrochemical detection of kanamycin residue was achieved based on mimetic peroxidase activity of gold nanoparticles (AuNPs) and target-induced replacement of the aptamer. AuNPs which were synthesized using tyrosine as a reducing and capping agent, exhibited mimetic peroxidase activity. In the presence of kanamycin-specific aptamer, however, the single-stranded DNA (ssDNA) adsorbed on the surface of AuNPs via the interaction between the bases of ssDNA and AuNPs, and therefore blocked the catalytic site of AuNPs, and inhibited their peroxidase activity. While in the presence of target kanamycin, it bound with the adsorbed aptamer on AuNPs with high affinity, exposed the surface of AuNPs and recovered the peroxidase activity. Then AuNPs catalyzed the reaction between H₂O₂ and reduced thionine to produce oxidized thionine. The latter exhibited a distinct reduction peak on gold electrode in differential pulse voltammetry (DPV), and could be utilized to quantify the concentration of kanamycin. Under the optimized conditions, the proposed electrochemical assay showed an extremely high sensitivity towards kanamycin, with a linear relationship between the peak current and the concentration of kanamycin in the range of 0.1–60 nM, and a detection limit of 0.06 nM. Moreover, the established approach was successfully applied in the detection of kanamycin in honey samples. Therefore, the proposed electrochemical assay has great potential in the fields of food quality control and environmental monitoring.     

Simultaneously fluorescence detecting thrombin and lysozyme based on magnetic nanoparticle condensation

In this protocol, a fluorescent aptasensor based on magnetic separation for simultaneous detection thrombin and lysozyme was proposed. Firstly, one of the anti-thrombin aptamer and the anti-lysozyme aptamer were individually immobilized onto magnetic nanoparticles, acting as the protein captor. The other anti-thrombin aptamer was labeled with rhodamine B and the anti-lysozyme aptamer was labeled with fluorescein, employing as the protein report. By applying the sandwich detection strategy, the fluorescence response at 515 nm and 578 nm were respectively corresponding to lysozyme and thrombin with high selectivity and sensitivities. The fluorescence intensity was individually linear with the concentration of thrombin and lysozyme in the range of 0.13-4 nM and 0.56-12.3 nM, and the detection limits were 0.06 nM of thrombin and 0.2 nM of lysozyme, respectively. The preliminary study on simultaneous detection of thrombin and lysozyme in real plasma samples was also performed. It shows that the proposed approach has the good character for simultaneous multiple protein detection.     

Colorimetric adenosine aptasensor based on DNA cycling amplification and salt-induced aggregation of gold nanoparticles

An aptamer based assay is described for the colorimetric detection of adenosine. The presence of adenosine triggers the deformation of hairpin DNA oligonucleotide (HP1) containing adenosine aptamer and then hybridizes another unlabeled hairpin DNA oligonucleotide (HP2). This leads to the formation of a double strand with a blunt 3′ terminal. After exonuclease III (Exo III)-assisted degradation, the guanine-rich strand (GRS) is released from HP2. Hence, the adenosine-HP1 complex is released to the solution where it can hybridize another HP2 and initiate many cycles of the digestion reaction with the assistance of Exo III. This leads to the generation of a large number of GRS strands after multiple cycles. The GRS stabilize the red AuNPs against aggregation in the presence of potassium ions. If, however, GRS forms a G-quadruplex, it loses its ability to protect gold nanoparticles (AuNPs) from salt-induced AuNP aggregation. Therefore, the color of the solution changes from red to blue which can be visually observed. This colorimetric assay has a 0.13 nM detection limit and a wide linear range that extends from 5 nM to 1 μM.

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Graphical abstract Schematic presentation of a colorimetric aptamer biosensor for adenosine detection based on DNA cycling amplification and salt-induced aggregation of gold nanoparticles.

     

An ultrasensitive quantum dots fluorescent polarization immunoassay based on the antibody modified Au nanoparticles amplifying for the detection of adenosine triphosphate

In this work, an ultrasensitive fluorescent polarization immunoassay (FPIA) method based on the quantum dot/aptamer/antibody/gold nanoparticles ensemble has been developed for the detection of adenosine triphosphate (ATP). DNA hybridization is formed when ATP is present in the PBS solution containing the DNA-conjugated quantum dots (QDs) and antibody-AuNPs. The substantial sensitivity improvement of the antibody-AuNPs-enhanced method is mainly attributed to the slower rotation of fluorescent unit when QDs-labeled oligonucleotides hybridize with antibody modified the gold nanoparticle. As a result, the fluorescent polarization (FP) values of the system increase significantly. Under the optimal conditions, a linear response with ATP concentration is ranged from 8 × 10⁻¹² M to 2.40 × 10⁻⁴ M. The detection limit reached as low as 1.8 pM. The developed work provides a sensitive and selective immunoassay protocol for ATP detection, which could be applied in more bioanalytical systems.     

Aptasensor for visual and fluorometric determination of lysozyme based on the inner filter effect of gold nanoparticles on CdTe quantum dots

The authors describe an aptasensor for visual and fluorescent detection of lysozyme via an inner filter effect (IFE). The assay is based on the fact that red gold nanoparticles (AuNPs) act as powerful absorbers of the green fluorescence of CdTe because of spectral overlap. If the lysozyme-binding aptamer is adsorbed onto the surface of the AuNPs, the salt-induced aggregation of AuNPs (that leads to a color change from red to blue) does not occur and the IFE remains efficient. If lysozyme is present, it will bind the aptamer and thereby prevent its adsorption on the AuNPs. As a result, the salt-triggered aggregation of the AuNPs will occur. Consequently, color will change from red to blue, and green fluorescence will pop up because the IFE is suppressed. Under optimum conditions, fluorescence is linearly related to lysozyme concentration in the 1.0 nM to 20 nM concentration range, with a 0.55 nM limit of detection. The method is perceived to be of wider applicability in that it may be used to design other visual and fluorescent assays if appropriate aptamers are available.

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Graphical abstract The fluorescence intensity of QDs is quenched by gold nanoparticles (AuNPs) due to an inner filter effect. Aptamers can adsorb on AuNPs to prevent the salt-induced aggregation. AuNPs serve a dual function as fluorescence quencher and colorimetric reporter.

     

Inner filter effect of gold nanoparticles on the fluorescence of quantum dots and its application to biological aminothiols detection

We have demonstrated the design of a new type fluorescence assay based on the inner filter effect (IFE) of gold nanoparticles (AuNPs) on the fluorescence of quantum dots (QDs). With a high extinction coefficient, AuNPs are expected to be capable of functioning as powerful absorbers. QDs with tunable emission wavelength are ideal fluorophores because the emission spectra of the rationally synthesized QDs can perfectly overlap with the absorption band of the absorber. Aminothiols are chosen as the model analytes, and the IFE-based fluorescent method for detection of aminothiols was suggested. Under the optimum conditions, the response is linearly proportional to the concentration of cysteine in the range of 0.05-0.9 μg mL⁻¹. The present IFE-based fluorescent strategy could be also used to detect glutathione and homocysteine. The linear concentration ranges were 0.05-1.0 μg mL⁻¹ for glutathione and 0.01-1.0 μg mL⁻¹ for homocysteine.     

Functionalized carbon dots as sensors for gold nanoparticles in spiked samples: Formation of nanohybrids

This paper reports the synthesis, passivation and functionalization of luminescent carbon dots (CDs) possessing surface thiol ending groups. A simple procedure involving amidation of passivated carbon dots (p-CDs) with cysteamine boosts their photoluminescent properties and enables their use as easily controlled fluorescent nanosensors for determining citrate–gold nanoparticles (AuNPs). The mechanism behind the quenching phenomenon was established from fluorescence measurements at high temperatures and lifetime tests, and found to involve static quenching leading to the formation of CD–AuNP nanohybrids. A method for determining AuNPs in complex matrices was developed and validated by application to spiked drinking water and mussel tissues. The limits of detection and quantitation for AuNPs thus obtained were 0.20 and 0.66 nmol L^–1, respectively.