Tao Bing

Carbon Dots Based Dual-Emission Silica Nanoparticles as a Ratiometric Nanosensor for Cu2+

A simple and effective strategy for designing ratiometric fluorescent nanosensor has been described in this work. A carbon dots (CDs) based dual-emission nanosensor for Cu(2+) detection was prepared by coating CDs on the surface of Rhodamine B-doped silica nanoparticles. The fluorescent CDs were synthesized using N-(β-aminoethyl)-γ-aminopropyl methyldimethoxysilane (AEAPMS) as the main raw material, so that the residual ethylenediamine groups and methoxysilane groups on the surface of CDs can serve as the Cu(2+) recognition sites and the silylation reaction groups. The obtained nanosensor showed characteristic fluorescence emissions of Rhodamine B (red) and CDs (blue) under a single excitation wavelength. Upon binding to Cu(2+), only the fluorescence of CDs was quenched, resulting in the ratiometric fluorescence response of the dual-emission silica nanoparticles. This ratiometric nanosensor exhibited good selectivity to Cu(2+) over other substances, such as metal ions, amino acids, proteins, and vitamin C. The ratio of F467/F585 linearly decreased with the increasing of Cu(2+) concentration in the range of 0 to 3 × 10(-6) M, a detection limit as low as 35.2 nM was achieved. Additionally, this nanosensor was successfully applied for the ratiometric fluorescence imaging of Cu(2+) in cells and determination of Cu(2+) in real tap water.

General Peroxidase Activity of G-Quadruplex−Hemin Complexes and Its Application in Ligand Screening

DNA sequences with repetitive G-rich structural motifs, which form special structures called G-quadruplexes, widely exist in the human genome. Here we report the general peroxidase activity of G-quadruplex-hemin complexes and discuss the connection between peroxidase activity and G-quadruplex structures. The high peroxidase activity of hemin complexed with intramolecular parallel G-quadruplex-forming sequences in gene promoters (such as c-Myc, VEGF, c-Kit21, HIF-1alpha, and RET) may imply a potential mechanism of hemin-mediated cellular injury. This peroxidase activity has also been demonstrated to be applicable for screening G-quadruplex ligands (potential anticancer reagents) using colorimetric and visual detection strategies.

Highly Selective Phthalocyanine-Thymine Conjugate Sensor for Hg2+ Based on Target Induced Aggregation

Here we describe a highly selective and reversible Hg(2+) sensor, tetra-(thymin-1-yl-acetamido)-phthalocyanine Zn(II) (4T-ZnPc), which combined the optical properties of phthalocyanine (Pc) and the specific interaction of Hg(2+) with thymine (T). The novel phthalocyanine-nucleobase conjugate, 4T-ZnPc, shows a typical ultraviolet-visible absorption spectrum with a split Q-band of monomeric Pc in dimethylformamide (DMF)-water (7:3, v/v) solution, as well as strong fluorescence emission. Upon addition of Hg(2+), the formation of T-Hg-T complex induces aggregation of 4T-ZnPc and results in significant decreases of fluorescence intensity and absorption of the Q-band. Furthermore, the sensor molecules, 4T-ZnPc, show excellent selectivity for Hg(2+), and other ions, such as Pb(2+), Co(2+), Ni(2+), Zn(2+), Cd(2+), Mn(2+), Mg(2+), Ca(2+), Na(+), and K(+), have almost no effect on the optical properties of 4T-ZnPc. This kind of sensor based on Pc may be expanded to the detection of other targets by substituting thymines with other ligands or groups that possess molecular recognition ability.

Conservative secondary structure motif of streptavidin-binding aptamers generated by different laboratories

Aptamers that are selected in vitro from random pools of DNA or RNA molecules by SELEX (Systematic evolution of ligands by exponential enrichment) technique have been extensively explored for analytical and biomedical applications. Although many aptamers with high affinity and specificity against specific ligands have been reported, there is still a lack of well characterized DNA aptamers. Here we report the selection of a group of aptamer candidates (85 mer) against streptavidin. Through comparing the predicted secondary structures of all the candidates, a conservative bulge-hairpin structure section (about 29 mer) was found, and then it was determined to be the binding motif to streptavidin. This binding motif was further discovered to also exist in streptavidin-binding aptamers (SBAs) selected by three other laboratories using different methods. The primary sequences of this secondary structure motif are very different, only several nucleotides in the loop and bulge area are critical for binding and other nucleotides are variable. The streptavidin binding of all the SBAs could be competed by biotin implying that they bind to the same site on streptavidin. These results suggest that the evolution of SBA is predominated by specific groups on streptavidin. The highly variable sequence composition of streptavidin-binding aptamer would make the design of aptameric sensor or device based on streptavidin more flexible and easy.

Specific mercury(II) adsorption by thymine-based sorbent.

A new kind of polymer sorbent based on the specific interaction of Hg(II) with nucleic acid base, thymine, is described for the selective adsorption of Hg(II) from aqueous solution. Two types of sorbents immobilized with thymine were prepared by one-step swelling and polymerization and graft polymerization, respectively. The maximum static adsorption capacity of the new polymer sorbents for Hg(II) is proportional to the density of thymine on their surface, up to 200mg/g. Moreover, the new kind polymer sorbent shows excellent selectivity for Hg(II) over other interfering ions, such as Cu(II), Cd(II), Zn(II), Co(II), Ca(II) and Mg(II), exhibits very fast kinetics for Hg(II) adsorption from aqueous solution, and can be easily regenerated by 1.0M HCl. It also has been successfully used for the selective adsorption of spiked Hg(II) from real tap water samples. This new thymine polymer sorbent holds a great promise in laboratory and industrial applications such as separation, on-line enrichment, solid-phase extraction, and removal of Hg(II) from pharmaceutical, food and environmental samples.

Bifunctional combined aptamer for simultaneous separation and detection of thrombin.

Here we report on the construction and evaluation of a bifunctional combined aptamer (BCA) that consists of a DNA streptavidin-binding aptamer (SBA), a DNA thrombin-binding aptamer (TBA) and a fluorophore. The BCA adopts a new conformation that is very different from simply linking the conformations of the two individual aptamers together, so that it does not bind to streptavidin in the absence of thrombin. Binding of this novel DNA aptamer to streptavidin is triggered by the thrombin binding and depends on the concentration of thrombin. Meanwhile, fluorescence from the streptavidin captured BCA reflects the quantity of the target molecule in the sample. This aptamer combination strategy based on the SBA holds good potential for applications in simultaneous detection and separation of targets of aptamers or certain DNA and RNA targets.

DNA aptamer evolved by cell-SELEX for recognition of prostate cancer.

Morbidity and mortality of prostate cancer (PCa) have increased in recent years worldwide. Currently existing methods for diagnosis and treatment do not make the situation improve, especially for hormone refractory prostate cancer (HRPC). The lack of molecular probes for PCa hindered the early diagnosis of metastasis and accurate staging for PCa. In this work, we have developed a new aptamer probe Wy-5a against PCa cell line PC-3 by cell-SELEX technique. Wy-5a shows high specificity to the target cells with dissociation constants in the nanomolar range, and does not recognize other tested PCa cell lines and other tested tumor cell lines. The staining of clinical tissue sections with fluorescent dye labeled Wy-5a shows that sections from high risk group with metastasis exhibited stronger fluorescence and sections from Benign Prostatic Hyperplasia (BPH) did not exhibit notable fluorescence, which suggests that aptamer Wy-5a may bind to protein related to the progression of PCa. The high affinity and specificity of Wy-5a makes this aptamer hold potential for application in diagnosis and target therapy of PCa.

G-quadruplex DNA aptamers for zeatin recognizing

Zeatins, a major type of cytokinin, are ubiquitous in higher plants, and involve in regulating a wide range of developmental processes. The development of highly specific ligands to zeatins would be very useful in plant biological research. Here we describe a group of oligonucleotide ligands (aptamers) generated against trans-zeatin. The optimized aptamers possess strong affinity to trans-zeatin and trans-zeatin riboside (Kd=3-5 μM), and relatively weak affinity (Kd=27-30 μM) to cis-zeatin and dihydrozeatin. These aptamers adopt a hairpin-G-quadruplex structure for binding to zeatin. A fluorescence turn-on aptasensor based on graphene oxide (GO) was developed for the recognition of zeatins. The specificity assay of this aptasensor shows good response to zeatins, and no response to the adenine derivatives (analog of zeatins) abundantly existing in biological samples. These results show the great potential of these aptamers in chemical analysis and biological investigation of zeatins.

G-quadruplex DNA aptamers generated for systemin

Ligands specific to bioactive molecules play important roles in biomedical researches and applications, such as biological assay, diagnosis and therapy. Systemin is a peptide hormone firstly identified in plant. In this paper we report the selection of a group of DNA aptamers that can specifically bind to systemin. Through comparing the predicted secondary structures of all the aptamers, a hairpin structure with G-rich loop was determined to be the binding motif of these aptamers. The G-rich loop region of this binding motif was further characterized to fold into an antiparallel G-quadruplex by truncation-mutation assay and CD spectrum. The apparent equilibrium dissociation constant (K(d)) of one strong binding sequence (S-5-1) was measured to be 0.5 μM. The specificity assay shows that S-5-1 strongly bind to whole systemin, weakly bind to truncated or mutated systemin and does not bind to the scrambled peptide with the same amino acid composition as systemin. The high affinity and specificity make S-5-1 hold potentials to serve as a molecular ligand applied in detection, separation and functional investigation of systemin in plants.

Specific DNA G-quadruplexes bind to ethanolamines

A significant number of G‐quadruplex‐forming sequences have been revealed in human genome by bioinformatic searches, implying that G‐quadruplexes may be involved in important biological processes and may be new chemotherapeutic targets. Therefore, it is important to discover the potential interactions of G‐quadruplexes with other molecules or groups. Here we describe a class of G‐quadruplexes, which can bind to ethanolamine groups that widely exist in biomolecules and drug molecules. The specific interaction of these G‐quadruplexes with ethanolamine groups was identified by high performance affinity chromatography (HPAC) using immobilized ethanolamine and diethanolamine as stationary phase reagents. The circular dichroism (CD) spectra and native polyacrylamide gel electrophoresis (PAGE) show that these ethanolamine binding quadruplexes adopt an intramolecularly parallel structure. The relationship of ethanolamine binding and G‐quadruplexe structure provides new clues for the G‐quadruplex‐related studies as well as for the molecular designs of therapeutic reagents.