Optical aptasensors for the analysis of the vascular endothelial growth factor (VEGF)

The vascular endothelial growth factor, VEGF, is an important biomarker for different diseases and clinical disorders. We present a series of optical aptasensor-based sensing platforms for VEGF that include the following: (i) A FRET-based sensor that involves the VEGF-induced separation of aptamer-functionalized quantum dots blocked by a quencher nucleic acid (detection limit 1 nM). (ii) A FRET-based sensor based on the VEGF-induced assembly of the aptamer subunits functionalized with QDs and a dye acceptor (Cy5), respectively (detection limit 12 nM). (iii) A chemiluminescence aptasensor based on VEGF-induced assembly of a hemin/G-quadruplex catalyst (detection limit 18 nM). (iv) A chemiluminescence aptasensor based on the VEGF-stimulated assembly of two aptamer subunits into the hemin/G-quadruplex catalyst (detection limit 2.6 nM). (v) A chemiluminescence resonance energy transfer (CRET) aptasensor based on the VEGF-induced assembly of a semiconductor QDs-hemin/G-quadruplex supramolecular structure (detection limit 875 pM). Furthermore, an amplified optical aptasensor system based on the Exonuclease III (Exo III) recycling of the VEGF analyte was developed. In this system, one aptamer subunit is modified at its 5' and 3' ends with QDs and a black hole quencher, respectively. The VEGF-induced self-assembly of the aptamer subunits result in the digestion of the quencher units and the autonomous recycling of the analyte, while triggering-on the luminescence of the QDs (detection limit 5 pM). The system was implemented to analyze VEGF in human sera samples.     

Carbon nanocapsules as an effective sensing platform for fluorescence-enhanced nucleic acid detection

In this communication, we demonstrate the proof of concept that carbon nanocapsules (CNCs) can be used as an effective fluorescent sensing platform for nucleic acid detection with selectivity down to single-base mismatch. The detection is accomplished by two steps: (1) CNC adsorbs and quenches the fluorescence of the dye-labeled single-stranded DNA (ssDNA) probe; (2) in the presence of the target, a hybridization event occurs, which produces a double-stranded DNA (dsDNA) that detaches from the CNC surface, leading to recovery of the dye fluorescence.     

Coordination polymer nanobelts for nucleic acid detection

Herein, coordination polymer nanobelts (CPNBs) were prepared rapidly and on a large scale, by directly mixing aqueous AgNO(3) solution and an ethanol solution of 4, 4'-bipyridine at room temperature. The application of such CPNBs as a fluorescent sensing platform for nucleic acid detection was further explored. CPNB is a π-rich structure, the strong π-π stacking interactions between unpaired DNA bases and CPNB leads to adsorption of fluorescently labeled single-stranded DNA (ssDNA) accompanied by 66% fluorescence quenching. However, the presence of target ssDNA will hybridize with the probe. The resultant helix cannot be adsorbed by CPNB due to its rigid conformation and the absence of unpaired DNA bases. Thus, a significant fluorescence enhancement, 73% fluorescence recovery, was observed in DNA detection as long as the target exists. The present system has excellent sensitivity; a substantial fluorescence enhancement was observed when the concentration of the target was as low as 5 nM. It also exhibits outstanding discrimination ability down to a single-base mismatch.     

Double-strand DNA-templated formation of copper nanoparticles as fluorescent probe for label-free aptamer sensor

Double-strand DNA (dsDNA) can act as an efficient template for the formation of copper nanoparticles (Cu NPs) at low concentration of CuSO(4), and the formed Cu NPs have excellent fluorescence, whereas a single-strand DNA (ssDNA) template does not support Cu NPs' formation. This property of dsDNA-Cu NPs makes it suitable for DNA sensing. However, exploration of dsDNA-Cu NPs applied in biological analysis is still at an early stage. In this regard, we report herein for the first time a sensitive, cost-effective, and simple aptamer sensor (aptasensor) using dsDNA-Cu NPs as fluorescent probe. The design consists of a dsDNA with reporter DNA (here, aptamer) as template for the formation of Cu NPs, and the formed dsDNA-Cu NPs show high fluorescence. Using adenosine triphosphate (ATP) as a model analyte, the introduction of ATP triggers the structure switching of reporter DNA to form aptamer-ATP complex, causing the destruction of the double helix and thus no formation of the Cu NPs, resulting in low fluorescence. The preferable linear range (0.05-500 μM), sensitivity (LOD 28 nM), and simplicity for the detection of ATP indicate that dsDNA-Cu NPs may have great prospects in the field of biological analysis. We also use this novel fluorescent probe to determine ATP in 1% human serum and human adenocarcinoma HeLa cells. The dsDNA-Cu NPs probes provide recovery of 104-108% in 1% human serum and a prominent fluorescent signal is obtained in cellular ATP assay, revealing the practicality of using dsDNA-Cu NPs for the determination of ATP in real samples. Besides, this design is simply based on nucleic acid hybridization, so it can be generally applied to other aptamers for label-free detection of a broad range of analytes. Successful detection of cocaine with detection limit of 0.1 μM demonstrates its potential to be a general method.     

Target‐Triggered Assembly of Nanogap Antennas to Enhance the Fluorescence of Single Molecules and Their Application in MicroRNA Detection

Nanogap antennas are plasmonic nanostructures with a strong electromagnetic field generated at the gap region of two neighboring particles owing to the coupling of the collective surface plasmon resonance. They have great potential for improving the optical properties of fluorophores. Herein, nanogap antennas are constructed using an aqueous solution‐based method to overcome the defects of weak fluorescence and photobleaching associated with traditional organic dyes, and a highly sensitive nanogap antenna‐based sensing strategy is presented for the detection of low‐abundance nucleic acid biomarkers via a target‐triggered strand displacement amplification (SDA) reaction between two DNA hairpins that are tagged to the tips of gold nanorods (Au NRs). In the presence of targets, end‐to‐end Au NR dimers gradually form, and the fluorophores quenched by the Au NRs exhibit a dramatic fluorescence enhancement due to the plasmon‐enhanced fluorescence effect of nanogap antennas. Meanwhile, the SDA reaction results in secondary amplification of fluorescence signals. Combined with single‐molecule counting, this method applied in miRNA‐21 detection can achieve a low detection limit of 97.2 × 10^?18 m . Moreover, accurate discrimination between different cells through miRNA‐21 imaging demonstrates the potential of this method in monitoring the expression level of low‐abundance nucleic acid biomarkers.     

Fluorescence energy transfer between fluorescein label and DNA intercalators to detect nucleic acids hybridization in homogeneous media

A general approach to detecting nucleic acid sequences in homogeneous media by means of steady-state fluorescence measurements is proposed. The methodology combines the use of a fluorescence-labeled single-strand DNA model probe, the complementary single-strand DNA target, and a DNA intercalator. The probe was fluorescein labeled to a spacer arm at the N4 position of the cytosine amino groups in polyribocytidylic acid (5'), poly(C), which acts as a model DNA probe. The complementary strand was polyriboinosinic acid (5'), poly(I), as a model of the target, and the energy transfer acceptor was an intercalator, either ethidium bromide or ethidium homodimer. In previous papers we have shown that the fluorescence intensity of the fluorescein label decreases when labeled poly(C) hybridizes with poly(I), and this fluorescence quenching can be used to detect DNA hybridization or renaturation in homogeneous media. In this paper we demonstrate that fluorescence resonance energy transfer (FRET) between fluorescein labeled to poly(C) and an intercalator agent takes place when single-stranded poly(C) hybridizes with poly(I), and we show how the fluorescence energy transfer further decreases the steady-state fluorescence intensity of the label, thus increasing the detection limit of the method. The main aim of this work was to develop a truly homogeneous detection system for specific nucleic acid hybridization in solution using steady-state fluorescence and FRET, but with the advantage of only having to label the probe with the energy donor since the energy acceptor is intercalated spontaneously. Moreover, the site label is not critical and can be labeled randomly in the DNA strand. Thus, the method is simpler than those published previously based on FRET. The experiments were carried out in both direct and competitive formats.     

Aptamer-based ATP assay using a luminescent light switching complex

With the increasing applications of nucleic acid aptamers as a new class of molecular recognition probes in bioanalysis and biosensor development, the development of general and simple signaling strategies to transduce aptamer-target binding events to detectable signals is demanding. We have developed a new signaling method based on aptamers and a DNA molecular light switching complex, [Ru(phen)2(dppz)]2+, for sensitive protein detection. In this work, we have demonstrated the applicability of this signaling mechanism to small-molecule detection using ATP as a model target. Our results have shown that upon ATP binding to the folded aptamer where [Ru(phen)2(dppz)]2+ intercalated, the conformational change or distortion of the aptamer is large enough to cause a significant luminescence change of [Ru(phen)2(dppz)]2+. By monitoring the ATP-dependent luminescence intensity change, we have achieved ATP detection with high selectivity and high sensitivity down to 1 nM in homogeneous solution. The method is very simple without the needs for covalently labeling aptamers or using costly enzymes and multistep analysis as other reported fluorescence/luminescence assays for ATP. The successful detection of ATP indicates that using the signaling aptamers with [Ru(phen)2(dppz)]2+ is expected to be a general method for aptamer-based target detection.     

A universal nucleic acid sequence biosensor with nanomolar detection limits

A quantitative universal biosensor was developed on the basis of olignucleotide sandwich hybridization for the rapid (30 min total assay time) and highly sensitive (1 nM) detection of specific nucleic acid sequences. The biosensor consists of a universal membrane and a universal dye-entrapping liposomal nanovesicle. Two oligonucleotides, a reporter and a capture probe that can hybridize specifically with the target nucleic acid sequence, can be coupled to the universal biosensor components within a 10-min incubation period, thus converting it into a specific assay. The liposomal nanovesicles bear a generic oligonucleotide sequence on their outer surface. The reporter probes consist of two parts: the 3' end is complementary to the generic liposomal oligonucleotide, and the 5' end is complementary to the target sequence. Streptavidin is immobilized in the detection zone of the universal membranes. The capture probes are biotinylated at the 5' end and are complementary to another segment in the target sequence. Thus, by incubating the liposomal nanovesicles with the reporter probes, the target sequence, and the capture probes in a hybridization buffer for 20 min, a sandwich complex is formed. The mixture is applied to the membrane, migrates along the strip, and is captured in the detection zone via streptavidin-biotin binding. The biosensor assay was optimized with respect to hybridization conditions, concentrations of all components, and length of the generic probe. It was tested using synthetic DNA sequences and authentic RNA sequences isolated and amplified using nucleic acid sequence-based amplification (NASBA) from Escherichia coli, Bacillus anthracis, and Cryptosporidium parvum. Dose-response curves were carried out using a portable reflectometer for the instantaneous quantification of liposomal nanovesicles in the detection zone. Limits of detection of 1 fmol per assay (1 nM) and dynamic ranges between 1 fmol and at least 750 fmol (1-750 nM) were obtained. The universal biosensors were compared to specific RNA biosensors developed earlier and were found to match or exceed their performance characteristics. In addition, no changes to hybridization conditions were required when switching to the detection of a new target sequence or when using actual nucleic acid sequence-based amplified RNA sequences. Therefore, the universal biosensor described is an excellent tool for use in laboratories or at test sites for rapidly investigating and quantifying any nucleic acid sequence of interest.     

Rotating rod renewable microcolumns for automated, solid-phase DNA hybridization studies

The development of a new temperature-controlled renewable microcolumn flow cell for solid-phase nucleic acid hybridization in an automated sequential injection system is described. The flow cell included a stepper motor-driven rotating rod with the working end cut to a 45 degrees angle. In one position, the end of the rod prevented passage of microbeads while allowing fluid flow; rotation of the rod by 180 degrees releases the beads. This system was used to rapidly test many hybridization and elution protocols to examine the temperature and solution conditions required for sequence-specific nucleic acid hybridization. Target nucleic acids labeled with a near-infrared fluorescent dye were detected immediately postcolumn during all column perfusion and elution steps using a flow-through fluorescence detector. Temperature control of the column and the presence of Triton X-100 surfactant were critical for specific hybridization. Perfusion of the column with complementary oligonucleotide (200 microL, 10 nM) resulted in hybridization with 8% of the DNA binding sites on the microbeads with a solution residence time of less than 1 s and a total sample perfusion time of 40 s. The use of the renewable column system for detection of an unlabeled PCR product in a sandwich assay was also demonstrated.     

Polyamine-functionalized carbon quantum dots as fluorescent probes for selective and sensitive detection of copper ions

A novel sensing system has been designed for Cu(2+) ion detection based on the quenched fluorescence (FL) signal of branched poly(ethylenimine) (BPEI)-functionalized carbon quantum dots (CQDs). Cu(2+) ions can be captured by the amino groups of the BPEI-CQDs to form an absorbent complex at the surface of CQDs, resulting in a strong quenching of the CQDs' FL via an inner filter effect. Herein, we have demonstrated that this facile methodology can offer a rapid, reliable, and selective detection of Cu(2+) with a detection limit as low as 6 nM and a dynamic range from 10 to 1100 nM. Furthermore, the detection results for Cu(2+) ions in a river water sample obtained by this sensing system agreed well with that by inductively couple plasma mass spectrometry, suggesting the potential application of this sensing system.     

Efficient fluorescence turn-on probe for zirconium via a target-triggered DNA molecular beacon strategy

It is well-known that Zr(4+) could selectively bind with two phosphate-functionalized molecules through a coordinate covalent interaction to form a sandwich-structured complex (-PO(3)(2-)-Zr(4+)-PO(3)(2-)-). In this paper, we for the first time converted such interaction into fluorescence sensing systems for Zr(4+) via a target-triggered DNA molecular beacon strategy. In the new designed sensing system, two phosphorylated and pyrene-labeled oligonucleotides were chosen as both recognition and reporter units, which will be linked by target Zr(4+) to form a hairpin structure and bring the two labeled pyrene molecules into close proximity, resulting in a "turn-on" excimer fluorescence signal. Moreover, γ-cyclodextrin was introduced to afford an amplified fluorescence signal and, therefore, provided an improved sensitivity for the target Zr(4+). This allows detection of Zr(4+) with high sensitivity (limit of detection, LOD = 200 nM) and excellent selectivity. The proposed sensing system has also been used for detection of Zr(4+) in river water samples with satisfactory result.     

2,4,6-Tris (2-pyridyl)-1,3,5-triazine nanobelts as an effective fluorescent sensing platform for DNA detection

In the present study, we report on the use of 2,4,6-tris (2-pyridyl)-1,3,5-triazine nanobelts (TPTNBs) as an effective fluorescent sensing platform for DNA detection for the first time. The general concept used in this approach is based on adsorption of fluorescently labeled single-stranded DNA (ssDNA) probe by TPTNB, due to the strong pi-pi stacking between unpaired DNA bases and TPTNB. As a result, the fluorophor is brought into close proximity of TPTNB, leading to fluorescence quenching. Upon presence of the target ssDNA, specific hybridization with the target takes place to form a double-stranded DNA (dsDNA). The resultant dsDNA cannot be adsorbed by TPTNB due to its rigid conformation and the absence of unpaired DNA bases. Thus, the fluorophor is seperated from TPTNB accompanied by fluorescence recovery. The present system shows a detection limit as low as 3 nM and has a high selectivity down to single-base mismatch.     

Fluorescence detection of DNA, adenosine-5'-triphosphate (ATP), and telomerase activity by zinc(II)-protoporphyrin IX/G-quadruplex labels

The zinc(II)-protoporphyrin IX (ZnPPIX) fluorophore binds to G-quadruplexes, and this results in the enhanced fluorescence of the fluorophore. This property enabled the development of DNA sensors, aptasensors, and a sensor following telomerase activity. The DNA sensor is based on the design of a hairpin structure that includes a "caged" inactive G-quadruplex sequence. Upon opening the hairpin by the analyte DNA, the resulting fluorescence of the ZnPPIX/G-quadruplex provides the readout signal for the sensing event (detection limit 5 nM). Addition of Exonuclease III to the system allows the recycling of the analyte and its amplified analysis (detection limit, 200 pM). The association of the ZnPPIX to G-quadruplex aptamer-substrate complexes allowed the detection of adenosine-5'-triphosphate (ATP, detection limit 10 μM). Finally, the association of ZnPPIX to the G-quadruplex repeat units of telomers allowed the detection of telomerase activity originating from 380 ± 20 cancer 293T cell extract.     

Ultratrace measurements of nucleic acids by baseline-corrected adsorptive stripping square-wave voltammetry

The direct and reliable electrochemical detection of DNA is of paramount importance to the development of modern DNA hybridization chips, for the detection of nucleic acids following their electrophoretic separations, or for the sensing of DNA damage and interactions. Such solid electrode voltammetric measurements of nucleic acids have been traditionally hampered by the large solvent decomposition background current that obscures the oxidation signals of the purine nucleobases. This paper reports on the use of adsorptive stripping square-wave voltammetry, in connection with the "moving average baseline correction" approach, for monitoring ultratrace levels of DNA and RNA. Compared to other baseline-fitted or background-subtraction protocols, the moving average baseline scheme is particularly effective in isolating the small purine nucleobase peaks, which appear as small shoulders on the steep background discharge contribution. The remarkably flat baseline thus obtained (up to extreme potentials) leads to a dramatic lowering of the detection limits to the femtomole level and to a performance that compares favorably with that of computerized chronopotentiometric measurements of nucleic acids. Combined with the speed of square-wave voltammetric measurements, such developments should expand the role of voltammetry in DNA diagnostics and nucleic acid research.     

Nucleic Acid Nanostructures for Chemical and Biological Sensing

The nanoscale features of DNA have made it a useful molecule for bottom‐up construction of nanomaterials, for example, two‐ and three‐dimensional lattices, nanomachines, and nanodevices. One of the emerging applications of such DNA‐based nanostructures is in chemical and biological sensing, where they have proven to be cost‐effective, sensitive and have shown promise as point‐of‐care diagnostic tools. DNA is an ideal molecule for sensing not only because of its specificity but also because it is robust and can function under a broad range of biologically relevant temperatures and conditions. DNA nanostructure‐based sensors provide biocompatibility and highly specific detection based on the molecular recognition properties of DNA. They can be used for the detection of single nucleotide polymorphism and to sense pH both in solution and in cells. They have also been used to detect clinically relevant tumor biomarkers. In this review, recent advances in DNA‐based biosensors for pH, nucleic acids, tumor biomarkers and cancer cell detection are introduced. Some challenges that lie ahead for such biosensors to effectively compete with established technologies are also discussed.     

Nucleic acid-functionalized Pt nanoparticles: Catalytic labels for the amplified electrochemical detection of biomolecules

Nucleic acid-functionalized Pt nanoparticles (Pt-NPs) act as catalytic labels for the amplified electrochemical detection of DNA hybridization and aptamer/protein recognition. Hybridization of the nucleic acid-modified Pt-NPs with a sensing nucleic acid/analyte DNA complex associated with an electrode enables the amperometric, amplified, detection of the DNA by the Pt NP electrocatalyzed reduction of H2O2 (sensitivity limit, 1 x 10(-11) M). Similarly, the association of aptamer-functionalized Pt- NPs to a thrombin aptamer/thrombin complex associated with an electrode allowed the amplified, electrocatalytic detection of thrombin with a sensitivity limit corresponding to 1 x 10(-9) M.     

Single-stranded DNA binding protein-assisted fluorescence polarization aptamer assay for detection of small molecules

Here, we describe a new fluorescence polarization aptamer assay (FPAA) strategy which is based on the use of the single-stranded DNA binding (SSB) protein from Escherichia coli as a strong FP signal enhancer tool. This approach relied on the unique ability of the SSB protein to bind the nucleic acid aptamer in its free state but not in its target-bound folded one. Such a feature was exploited by using the antiadenosine (Ade)-DNA aptamer (Apt-A) as a model functional nucleic acid. Two fluorophores (fluorescein and Texas Red) were introduced into different sites of Apt-A to design a dozen fluorescent tracers. In the absence of the Ade target, the binding of the labeled aptamers to SSB governed a very high fluorescence anisotropy increase (in the 0.130-0.200 range) as the consequence of (i) the large global diffusion difference between the free and SSB-bound tracers and (ii) the restricted movement of the dye in the SSB-bound state. When the analyte was introduced into the reaction system, the formation of the folded tertiary structure of the Ade-Apt-A complex triggered the release of the labeled nucleic acids from the protein, leading to a strong decrease in the fluorescence anisotropy. The key factors involved in the fluorescence anisotropy change were considered through the development of a competitive displacement model, and the optimal tracer candidate was selected for the Ade assay under buffer and realistic (diluted human serum) conditions. The SSB-assisted principle was found to operate also with another aptamer system, i.e., the antiargininamide DNA aptamer, and a different biosensing configuration, i.e., the sandwich-like design, suggesting the broad usefulness of the present approach. This sensing platform allowed generation of a fluorescence anisotropy signal for aptamer probes which did not operate under the direct format and greatly improved the assay response relative to that of the most previously reported small target FPAA.