Label-Free and Simple G-quadruplex-based Turn-Off Fluorescence Assay for the Detection of Kanamycin

We have developed a label-free and turn-off fluorescence assay for the determination of kanamycin. The detection system consists of an aptamer for specifically recognizing kanamycin and two auxiliary probes functionalized with two GGG repeats at the 3′ or 5′ ends for signal reporting. Two probes both hybridize with the aptamer and then their G-rich sequences combine to form a G-quadruplex. When thioflavin T, a fluorophore, is bound to the G-quadruplex, the fluorescence intensity of the solution dramatically increases. Upon the addition of the kanamycin, the aptamer–kanamycin binding inhibits the hybridization of two probes and aptamer, and restrains the GGG repeats from getting closer to form the G-quadruplex structure, resulting a significant decrease in the fluorescence intensity. The proposed aptamer-based fluorescent sensing platform showed a linear relationship with the concentration of kanamycin from 0.6 to 20.0?nM. The detection limit was determined to be 0.33?nM. The sensing platform provides resistance to interferences from other antibiotics and can be used to efficiently recognize kanamycin in real samples.     

A Label-free and Functional Fluorescent Oligonucleotide Probe Based on a G-Quadruplex Molecular Beacon for the Detection of Kanamycin

A label-free and turn-off fluorescent method for the quantitative detection of kanamycin based on a functional molecular beacon was developed. The molecular beacon consists of two hairpin structures with a split G-rich oligonucleotide in the middle. The kanamycin's aptamer formed the loops portion for recognizing kanamycin, and the G-quadruplex bound by Thioflavin T(ThT) was employed as the reporter. In the absence of target, the molecular beacon folded into double stem-loops and the splited G-rich oligonucleotid came close to form a G-quadruplex. When ThT bound to the G-quadruplex, the fluorescence intensity of the solution increased. Upon the addition of kanamycin, the function between kanamycin and aptamer unfolded the hairpin and disassembled the G-quadraplex structure, resulting in a significant decrease in the fluorescence intensity. A good linear relationship ranging from 0.7 nmol/L to 10 nmol/L was achieved and the limit of detection was 0.37 nmol/L. Besides, it could efficiently recognize kanamycin in real samples.     

基于芬顿反应和硫磺素T构建免标记荧光传感器用于葡萄糖的检测

基于芬顿反应和硫磺素T(ThT)构建新奇的免标记荧光传感器用于葡萄糖的检测。当无葡萄糖存在时,ThT诱导富G-DNA探针形成G-四链体/ThT复合物,ThT的荧光强度显著增强;当葡萄糖存在时,葡萄糖氧化酶催化葡萄糖产生H2 O2,在Fe^2+催化的芬顿反应作用下,H2 O2转化为羟基自由基(·OH),·OH引发DNA的氧化损伤导致富G-DNA探针裂解为短寡核苷酸片段而丧失形成G-四链体/ThT的能力,ThT的荧光强度显著降低,从而实现对葡萄糖的检测。在优化的检测条件下,G-四链体/ThT荧光强度变化和葡萄糖浓度在0.5~45μmol/L的范围内呈现较好的线性关系(R^2=0.99268),检出限为0.1μmol/L。利用本法对葡萄糖加标的血液样品进行分析,葡萄糖的回收率为90.7%~118.3%,相对标准偏差为1.7%~5.8%,方法可用于血糖检测。     

基于硫代黄素T诱导G-四联体构成的生物传感器检测铅离子

硫代黄素T(ThT)荧光分子在自由状态下荧光强度很弱, 通过在Tris-HCl缓冲液中加入Pb²⁺的适配体即富含G的DNA序列, 可与ThT荧光分子形成G-四联体结构, 使荧光信号迅速增强; 向溶液中加入Pb²⁺, Pb²⁺与其适配体有很好的结合特异性, 可生成更牢固的G-四联体结构, 使ThT分子被释放出来, 导致溶液的荧光强度降低, 基于此可检测溶液中的Pb²⁺离子. 实验中优化了缓冲溶液组成、 ThT荧光分子浓度、 Pb²⁺适配体浓度及反应时间等条件. 结果表明, 在10 mmol/L Tris-HCl(pH=8.3, 含2 mmol/L MgCl₂)缓冲溶液中, ThT荧光分子和Pb²⁺适配体的浓度分别为10 μmol/L和200 nmol/L, 反应10 min时, 随着溶液中Pb ²⁺浓度的增加, 荧光强度减弱. Pb²⁺浓度在20~1000 nmol/L范围内时, 荧光强度与Pb²⁺的浓度呈现良好的线性关系(R²=0.9941), 检出限为1 nmol/L. 实际水样测试结果表明, 该方法的回收率在98.8%~101.3%之间. 该传感器灵敏、 快速、 无需化学修饰荧光分子且成本低.     

Structure-switching signaling aptamers

Aptamers are single-stranded nucleic acids with defined tertiary structures for selective binding to target molecules. Aptamers are also able to bind a complementary DNA sequence to form a duplex structure. In this report, we describe a strategy for designing aptamer-based fluorescent reporters that function by switching structures from DNA/DNA duplex to DNA/target complex. The duplex is formed between a fluorophore-labeled DNA aptamer and a small oligonucleotide modified with a quenching moiety (denoted QDNA). When the target is absent, the aptamer binds to QDNA, bringing the fluorophore and the quencher into close proximity for maximum fluorescence quenching. When the target is introduced, the aptamer prefers to form the aptamer-target complex. The switch of the binding partners for the aptamer occurs in conjunction with the generation of a strong fluorescence signal owing to the dissociation of QDNA. Herein, we report on the preparation of several structure-switching reporters from two existing DNA aptamers. Our design strategy is easy to generalize for any aptamer without prior knowledge of its secondary or tertiary structure, and should be suited for the development of aptamer-based reporters for real-time sensing applications.     

Aptamer Biosensor for Selective and Rapid Determination of Insulin

Insulin plays an important role in glucose metabolism and its detection in biological fluids is of interest. In this study, a triple-helix molecular switch was employed for the simple, sensitive, and rapid determination of insulin. The triple-helix molecular switch was composed of a target specific aptamer sequence flanked by two arm segments and a dual-labeled oligonucleotide acting as a signal transduction probe. This approach takes advantage of unique properties of aptamers and triple-helix molecular switches such as high affinity, selectivity, and stability. In the absence of insulin, the fluorescence of triple-helix molecular switch is on. Upon addition of insulin, the aptamer binds to its target, leading to the release of the signal transduction probe, folding of the signal transduction probe to a stem loop structure, and the quenching of the fluorescence. This sensor showed a high selectivity toward insulin and a limit of detection as low as 9.97 nM. The sensor was employed for the determination of insulin in biological samples. This platform may be generalizable for a variety of molecules.     

A Label-Free Fluorometric Glutathione Assay Based on a Conformational Switch of G-quadruplex

In this paper, a label-free fluorescent method for glutathione (GSH) detection based on a thioflavin T/G-quadruplex conformational switch is developed. The sensing assay is fabricated depending on the virtue of mercury ions to form a thymine–thymine mismatch, which collapses the distance between two ssDNA and directs the guanine-rich part to form an intra-strand asymmetric split G-quadruplex. The newly formed G-quadruplex efficiently reacts with thioflavin T and enhances the fluorescent intensity. In the presence of GSH, Hg²⁺ is absorbed, destroying the G-quadruplex formation with a significant decrease in fluorescence emission. The proposed fluorescent assay exhibits a linear range between 0.03–5 μM of GSH with a detection limit of 9.8 nM. Furthermore, the efficacy of this method is examined using human serum samples to detect GSH. Besides GSH, other amino acids are also investigated in standard samples, which display satisfactory sensitivity and selectivity. Above all, we develop a method with features including potentiality, facility, sensitivity, and selectivity for analyzing GSH for clinical diagnostics.     

Single-molecule investigation of human telomeric G-quadruplex interactions with Thioflavin T

The interactions between human telomere sequence and a typical highly selective G-quadruplex ligand ThT were studied at the single-molecule level through α-hemolysin protein nanopore.     

Principal factors that determine the extension of detection range in molecular beacon aptamer/conjugated polyelectrolyte bioassays

A strategy to extend the detection range of weakly-binding targets is reported that takes advantage of fluorescence resonance energy transfer (FRET)-based bioassays based on molecular beacon aptamers (MBAs) and cationic conjugated polyelectrolytes (CPEs). In comparison to other aptamer-target pairs, the aptamer-based adenosine triphosphate (ATP) detection assays are limited by the relatively weak binding between the two partners. In response, a series of MBAs were designed that have different stem stabilities while keeping the constant ATP-specific aptamer sequence in the loop part. The MBAs are labeled with a fluorophore and a quencher at both termini. In the absence of ATP, the hairpin MBAs can be opened by CPEs via a combination of electrostatic and hydrophobic interactions, showing a FRET-sensitized fluorophore signal. In the presence of ATP, the aptamer forms a G-quadruplex and the FRET signal decreases due to tighter contact between the fluorophore and quencher in the ATP/MBA/CPE triplex structure. The FRET-sensitized signal is inversely proportional to [ATP]. The extension of the detection range is determined by the competition between opening of the ATP/MBA G-quadruplex by CPEs and the composite influence by ATP/aptamer binding and the stem interactions. With increasing stem stability, the weak binding of ATP and its aptamer is successfully compensated to show the resistance to disruption by CPEs, resulting in a substantially broadened detection range (from millimolar up to nanomolar concentrations) and a remarkably improved limit of detection. From a general perspective, this strategy has the potential to be extended to other chemical- and biological-assays with low target binding affinity.     

Inner filter effect (IFE) as a simple and selective sensing platform for detection of tetracycline using milk-based nitrogen-doped carbon nanodots as fluorescence probe

A simple, selective, and sensitive turn-off fluorescent assay for detecting of tetracycline in pharmaceutical dosage form based on inner filter effect (IFE) sensing platform has been described. In this IFE sensing strategy, N-doped carbon dots (CDs) were prepared by one-pot solvothermal synthesis using milk as a precursor and were directly used as a fluorophore in IFE. The prepared CDs were characterized by common spectroscopic and microscopic techniques. The CDs exhibited excitation-wavelength dependent emission with 10% as the fluorescence quantum yield. The fluorescence of CDs was decreased in correlation to the addition of absorber (tetracycline), as the excitation spectrum of the fluorophore (CDs) matches the absorption spectrum of the absorber. The present IFE-based sensing platform showed a good linear relationship from 2.0 µM to 200 µM (R² = 0.9960) and provided a detection limit of 0.6 µM (signal-to-noise ratio of 3). Additionally, the cytotoxic effects of CDs were determined using normal healthy male Balb/C mice model treated with various doses of CDs and at the end of the study, no mortality or even no sign of toxicity was observed at oral doses of 100 and 200 mg/kg CDs in all treated animals. The proposed nanoprobe assay is a free from interferences, low-cost, biocompatible, and accurate for the detection of tetracycline in pharmaceutical formulation.     

Ultrasensitive detection of potassium ions based on target induced DNA conformational switch enhanced fluorescence polarization

We have developed a simple, highly sensitive and selective fluorescence polarization assay for the detection of potassium ions based on target induced DNA conformational switch from hairpin to G-quadruplex enhanced fluorescence polarization. The assay was applied in the detection of low nM concentrations of potassium ions and was highly selective over other cations.     

Aptamer-Based Fluorescence Nanoprobe for Sensitive and Selective Detection of Potassium

A new aptamer-based fluorescence nanoprobe for potassium ion (K⁺) has been developed. The nanoprobe employs gold nanoparticles (AuNPs) as the sensing platform and Rhodamine B as the fluorescence indicator. Aptamer acts as the switch of fluorescence signal of Rhodamine B. In the presence of K⁺, aptamer departs from AuNPs as a result of the formation of G-quartets with K⁺, leading to the decrease of fluorescence signals. Under the optimum conditions, the limit of detection (LOD) for K⁺ is as low as 3.8 nM. The proposed method was successfully applied in the determination of K⁺ in human saliva sample.     

Label-Free Fluorescence Molecular Beacon Probes Based on G-Triplex DNA and Thioflavin T for Protein Detection

Protein detection plays an important role in biological and biomedical sciences. The immunoassay based on fluorescence labeling has good specificity but a high labeling cost. Herein, on the basis of G-triplex molecular beacon (G3MB) and thioflavin T (ThT), we developed a simple and label-free biosensor for protein detection. The biotin and streptavidin were used as model enzymes. In the presence of target streptavidin (SA), the streptavidin hybridized with G3MB-b (biotin-linked-G-triplex molecular beacon) perfectly and formed larger steric hindrance, which hindered the hydrolysis of probes by exonuclease III (Exo III). In the absence of target streptavidin, the exonuclease III successively cleaved the stem of G3MB-b and released the G-rich sequences which self-assembled into a G-triplex and subsequently activated the fluorescence signal of thioflavin T. Compared with the traditional G-quadruplex molecular beacon (G4MB), the G3MB only needed a lower dosage of exonuclease III and a shorter reaction time to reach the optimal detection performance, because the concise sequence of G-triplex was good for the molecular beacon design. Moreover, fluorescence experiment results exhibited that the G3MB-b had good sensitivity and specificity for streptavidin detection. The developed label-free biosensor provides a valuable and general platform for protein detection.     

苝二酰亚胺衍生物/三联吡啶铂配合物超分子在G-四链体检测中的应用

合成了3种三联吡啶铂(Ⅱ)配合物(Pt1、Pt2、Pt3)和两种苝二酰亚胺衍生物(PDI1、PDI2),构建了三联吡啶铂配合物/苝二酰亚胺衍生物超分子体系。所得超分子体系可作为"turn-on"型荧光传感器用于检测c-myc G-四链体。三联吡啶铂配合物可通过电子转移作用猝灭苝二酰亚胺的荧光,利用最小二乘法求得三联吡啶铂配合物与PDIs的结合常数为5.57×104~5.28×106 L/mol。加入G-四链体后,三联吡啶铂配合物/苝二酰亚胺超分子发生解离,苝二酰亚胺衍生物的荧光得到恢复。在Pt2/PDI2体系中加入1.5μmol/L c-myc G-四链体可使其荧光增强63倍。在c-myc的浓度为25nmol/L~1.0μmol/L范围内,Pt2/PDI2超分子体系荧光增强(F/F0)与c-myc的浓度呈良好的线性关系(R2=0.995),检测限为1.37nmol/L,表明Pt2/PDI2超分子体系可用于检测c-myc序列DNA。     

Aptamer-based silver nanosensor for multiple protein detection

In the present work we design a novel aptamer-based silver nanosensor for one-spot simultaneously detection of multiple proteins. SS-DNA modified AgNPs were immobilized on the aldehyde coated glass slide to form an AgNP array. Then dye-labeled aptamer sequences were allowed to hybridize with their complementary strands assembled on the surface of AgNPs. The target proteins were introduced to associate with the corresponding aptamers to form the aptamer-target complexes. The removal of the aptamer-target complexes resulted in a remarkable decrease in fluorescent signals. This nanosensor is found to be highly sensitive for the detection of proteins. When thrombin was employed as a sample model, the limit of detection of the optimized nanosenor was 0.4 fmol with a linear response of 0.8 fmol to 0.5 pmol. We further demonstrated the multiple protein detection of IgE and thrombin using multicolor silver nanoprobes, which shows effective recognition of the relative protein individually or simultaneously. This silver nanosensor offers a unique heterogeneous approach for protein detection with several advantages, such as high sensitivity, rapidity, high throughput, and miniaturization.     

Sensitive detection of protein by an aptamer-based label-free fluorescing molecular switch

We report an aptamer-based method for the sensitive detection of proteins by a label-free fluorescing molecular switch (ethidium bromide), which shows promising potential in making protein assay simple and economical.     

Adenosine triphosphate detection by controlled-release of carboxy fluorescein from mesoporous silica nanoparticles blocked with aptamer-based gold nanoparticles

In this paper, an adenosine-5′-triphosphate (ATP) controlled-release strategy to construct a fluorescence sensing platform has been designed. In the sensing platform, because of ATP aptamer and singlestranded DNA (ssDNA)-linked mesoporous silica nanoparticles (Si-MPs) were hybridized, the pores of Si-MPs were blocked with Au nanoparticles (AuNPs) modified with ATP aptamer. Carboxy fluorescein was plugged in channels of Si-MPs. In the presence of target molecule ATP, the ATP aptamer combined with ATP and the AuNPs got away from the pore of the surface of Si-MPs modified by ssDNA. 5-Carboxyfluorescein molecule was released to allow the fluorescent detection. By monitoring the fluorescence at 518 nm, ATP could be quantitatively detected with a detection limit of 6 × 10^–8 M. The linear response range was 6 × 10^–8 to 1 × 10^–6 M. This assay was also able to discriminate ATP from its analogs. The controlled-release aptamer-based biosensor could have an effective application in human breast cancer MCF-7 cells.     

Thioflavin T hydroxylation at basic pH and its effect on amyloid fibril detection

The fluorescent dye thioflavin T (ThT) is commonly used for in situ amyloid fibril detection. In this work, we focused on the spectroscopic properties and chemical stability of ThT in aqueous solution as a function of pH, temperature, and dye concentration. A reversible hydroxylation process occurs in alkaline solutions, which was characterized using a combination of UV-vis absorption spectroscopy, proton NMR, and density functional theory (DFT). On the basis of these studies, we propose a chemical structure for the hydroxylated form. Finally, by means of fluorescence spectroscopy, ThT hydroxylation effects on in situ amyloid detection have been investigated, providing new insights on the efficiency of the ThT assay for quantitative fibril evaluation at basic pH.     

Simple and sensitive fluorescence sensor for detection of potassium ion in the presence of high concentration of sodium ion using berberine–G-quadruplex complex as sensing element

In this work, a novel potassium ion (K⁺) sensor is presented using berberine–G-quadruplex complex as a fluorescent probe. This sensor is based on the K⁺that can induce the G-rich DNA to form G-quadruplex conformation. The G-quadruplex can bind berberine to form berberine–G-quadruplex complex, resulting in remarkable enhancement of fluorescence emission of the berberine–G-quadruplex system. In the presence of 800 mM sodium ion (Na⁺), the fluorescence of the berberine–G-quadruplex complex increased linearly with increasing K⁺ concentration in the range of 0.005–1.0 mM. The turn-on fluorescent assay is simple, inexpensive, and highly sensitive. We observed that Na⁺ in 10,000-fold molar excess does not interfere. The molecular mechanisms which produce enhanced fluorescence of berberine were discussed.     

Label-free fluorescent detection of thrombin using G-quadruplex-based DNAzyme as sensing platform

We report herein a label-free and sensitive fluorescent method for detection of thrombin using a G-quadruplex-based DNAzyme as the sensing platform. The thrombin-binding aptamer (TBA) is able to bind hemin to form the G-quadruplex-based DNAzyme, and thrombin can significantly enhance the activity of the G-quadruplex-based DNAzyme. The G-quadruplex-based DNAzyme is found to effectively catalyze the H(2)O(2)-mediated oxidation of thiamine, giving rise to fluorescence emission. This allows us to utilize the H(2)O(2)-thiamine fluorescent system for the quantitative analysis of thrombin. The assay shows a linear toward thrombin concentration in the range of 0.01-0.12 nM. The present limit of detection for thrombin is 1 pM, and the sensitivity for analyzing thrombin is improved by about 10,000-fold as compared with the reported colorimetric counterpart. The work also demonstrates that thiamine is an excellent substrate for the fluorescence assay using the G-quadruplex-based DNAzyme as the sensing platform.