Reversible formation of DNA G-quadruplex hairpin dimers from stilbenediether conjugates

Rapid and reversible G-quadruplex hairpin dimer formation is observed for bis(oligonucleotide) conjugates possessing stilbenediether (Sd) linkers connecting two short poly(G) sequences.     

Elongated thrombin binding aptamer: a G-quadruplex cation-sensitive conformational switch

Aptamer-based biosensors offer promising perspectives for high performance, specific detection of proteins. The thrombin binding aptamer (TBA) is a G-quadruplex-forming DNA sequence, which is frequently elongated at one end to increase its analytical performances in a biosensor configuration. Herein, we investigate how the elongation of TBA at its 5'?end affects its structure and stability. Circular dichroism spectroscopy shows that TBA folds in an antiparallel G-quadruplex conformation with all studied cations (Ba(2+), Ca(2+), K(+), Mg(2+), Na(+), NH(4)(+), Sr(2+) and the [Ru(NH(3))(6)](2+/3+) redox marker) whereas other structures are adopted by the elongated aptamers in the presence of some of these cations. The stability of each structure is evaluated on the basis of UV spectroscopy melting curves. Thermal difference spectra confirm the quadruplex character of all conformations. The elongated sequences can adopt a parallel or an antiparallel structure, depending on the nature of the cation; this can potentially confer an ion-sensitive switch behavior. This switch property is demonstrated with the frequently employed redox complex [Ru(NH(3))(6)](3+), which induces the parallel conformation at very low concentrations (10 equiv per strand). The addition of large amounts of K(+) reverts the conformation to the antiparallel form, and opens interesting perspectives for electrochemical biosensing or redox-active responsive devices.     

钾离子浓度依赖的铅离子稳定G-四链体构型转化

已有研究普遍认为铅离子(Pb²⁺)诱导富G适体链形成的G-四链体(Pb²⁺-G4)比钾离子(K⁺)诱导富G适体链形成的G-四链体(K⁺-G4)更为稳定,因而Pb²⁺可以置换K⁺-G4中的K⁺,而且K⁺的存在不影响Pb²⁺-G4的稳定性。有趣的是本研究发现K⁺ (20 μmol∙L⁻¹–1 mmol∙L⁻¹)不仅可以诱导10 µmol∙L⁻¹ Pb²⁺稳定的T2TT(Pb²⁺-T2TT,杂合G4结构)发生构型转换,甚至还可取代Pb²⁺-T2TT中的Pb²⁺,形成K⁺稳定的T2TT (K⁺-T2TT,平行G4结构),最终转化形成的K⁺-G4结构与单独K⁺诱导富G适体链形成K⁺-G4的构型基本一致。随后,进一步考察了另外7条富G适体链,发现这一转化过程具有一定的普适性。该研究结果为理解G4构型转化以及内嵌离子交换提供了新的视角,也为拓展G4在生化分析和生物领域的应用提供了新的理论基础。     

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.     

Cu x O@DNA sphere-based electrochemical bioassay for sensitive detection of Pb2+

Microchimica Acta - The authors show that copper nanoclusters capped with tannic acid (TA-CuNCs) are viable fluorescent probes for the determination of the activity of pyrophosphatase (PPase). The...     

Highly selective colorimetric and electrochemical Pb2+ detection based on TTF-pi-pyridine derivatives

[reaction: see text] The pyridineethenyl-substituted tetrathiafulvalene (TTF) compounds, 4-(4-pyridineethenyl)tetrathiafulvalene (1a) and 4,4'(5')-[bis-(4-pyridineethenyl)]tetrathiafulvalene (2a) together with the styryl-substituted TTF compounds, 4-styryltetrathiafulvalene (1b) and 4,4'(5')-bis-styryltetrathiafulvalene (2b), have been designed and synthesized. All these compounds exhibit strong absorption bands in the range of 370 to 550 nm, which are assigned to the intramolecular charge-transfer transition from the HOMO in TTF to the LUMO in the pyridyl or phenyl group. Compared to compounds 1b and 2b, the pyridineethenyl-substituted TTF compounds 1a and 2a show remarkable sensing and coordinating properties to Pb2+. With the addition of micromolar concentrations of Pb2+ to the solution, 1a or 2a displays dramatic changes in the UV-vis absorption spectrum, 1H NMR spectrum, and redox property.     

Electrochemical biosensor based on hairpin DNA probe using 2-nitroacridone as electrochemical indicator for detection of DNA species related to Chronic Myelogenous Leukemia

In this article, a new kind of hairpin DNA Electrochemical biosensor using nitroacridone as electrochemical indicator was first designed, and used to detect BCR/ABL fusion gene in Chronic Myelogenous Leukemia (CML). The results indicated that in pH 7.0 Tris–HCl buffer solution, the oxidation peak current was linear with the concentration of complementary strand in the range of 6.2 × 10⁻⁸–3.1 × 10⁻⁷ mol/l with a detection limit of 5.3 × 10⁻⁹ mol/l. This new hairpin DNA electrochemical biosensor demonstrates its excellent specificity for single-base mismatch and complementary (dsDNA) after hybridization, and this probe has been used for assay of PCR product of a real sample with satisfactory result.     

Molecular "light switch" for G-quadruplex DNA: cycling the switch on and off

We report a new G-quadruplex DNA "light switch", where the light switch can be cycled on and off through the successive introduction of G-quadruplex DNA and [Fe(CN)(6)](4-) ions.     

Development of an ultrasensitive rGO/AuNPs/ssDNA-based electrochemical aptasensor for detection of Pb2+

Journal of Solid State Electrochemistry - The present work is performed on Pb2+ detection via electrochemical sensor. The novel aptasensor was developed by modification of glassy carbon...     

Light-driven conformational regulation of human telomeric G-quadruplex DNA in physiological conditions

Human telomeric G-quadruplexes have raised broad interest not just due to their involvement in the regulation of gene expressions and telomerase activities but also because of their application in nanoarchitectures. Herein, three azobenzene derivatives 1-3 were synthesized with different substituent groups and their photo-isomerization properties were investigated by UV/Vis spectroscopy. Then circular dichroism spectroscopy (CD), fluorescence experiments and native-gel electrophoresis were performed to evaluate their capabilities of conformational photo-regulation both in the absence and presence of metal ions. The results suggested that the compounds synthesized can successfully regulate the conformation of human telomeric G-quadruplex DNA in K(+) conditions to some extent. This work will initiate the possibility for the design and intriguing application of light-induced switching to photoregulate the conformation of G-quadruplex DNA under physiological conditions, providing a possible pathway to control G-quadruplex conformation in biological applications and also expanding the potential use of G-quadruplexes in nanomachines.     

2-Aminopurine hairpin probes for the detection of ultraviolet-induced DNA damage

Nucleic acid exposure to radiation and chemical insults leads to damage and disease. Thus, detection and understanding DNA damage is important for elucidating molecular mechanisms of disease. However, current methods of DNA damage detection are either time-consuming, destroy the sample, or are too specific to be used for generic detection of damage. In this paper, we develop a fluorescence sensor of 2-aminopurine (2AP), a fluorescent analogue of adenine, incorporated in the loop of a hairpin probe for the quantification of ultraviolet (UV) C-induced nucleic acid damage. Our results show that the selectivity of the 2AP hairpin probe to UV-induced nucleic acid damage is comparable to molecular beacon (MB) probes of DNA damage. The calibration curve for the 2AP hairpin probe shows good linearity (R² = 0.98) with a limit of detection of 17.2 nM. This probe is a simple, fast and economic fluorescence sensor for the quantification of UV-induced damage in DNA.     

MnO2 nanozyme induced the chromogenic reactions of ABTS and TMB to visual detection of Fe2+ and Pb2+ ions in water

In this study, we used a simple and rapid colourimetric reaction for visual sensing of Fe²⁺ and Pb²⁺ ions in water by employing nano-MnO₂ as a natural oxidase mimic to respectively catalyse ABTS and TMB in citrate-phosphate buffer solution (C-PBS) at 25°C and pH 3.8. It was found that nano-MnO₂ possessed highly oxidase-mimicking activity with the K_m values of 0.030 and 0.027 toward ABTS and TMB, respectively, indicating TMB had a stronger affinity on nano-MnO₂ than ABTS. Interestingly, the presence of 0.01 mmol·L^?1 Fe²⁺/Pb²⁺ ion was able to significantly down-regulate the activity of MnO₂ nanozyme in nano-MnO₂-mediated ABTS reaction processes (P < 0.01), which mainly due to the strong adsorption of metal ion toward nano-MnO₂ surface via the electrostatic attractions, thus leading to the passivation and inactivation of MnO₂ nanozyme catalytic activity. Thereinto, Fe²⁺ reacted with multivalent manganese by oxidation-reduction, while Pb²⁺ was specifically adsorbed onto the surface of MnO₂ nanozyme and formed complexes. Notably, only Fe²⁺ ion inhibited the activity of MnO₂ nanozyme-TMB with a detection limit as low as 1.0 μmol·L^?1. In MnO₂ nanozyme-ABTS sensing systems, Fe²⁺ and Pb²⁺ ions detection limit of 0.5 and 2.0 μmol·L^?1 were, respectively, achieved with a linear response range of 0–0.02 and 0–0.8 mmol·L^?1, implying the developed MnO₂ nanozyme-ABTS sensor was potentially applicable for the visual determination of Fe²⁺ and Pb²⁺ ions in water. In the real water samples, MnO₂ nanozyme-ABTS achieved high accuracy (relative errors: 3.4?10.5%) and recovery (96?110%) for respective detection of Fe²⁺ and Pb²⁺ ions. The simple and rapid MnO₂ nanozyme-ABTS sensing systems might provide a practical assay for visual detection of Fe²⁺ and Pb²⁺ ions in the environmental water samples.     

Direct NMR detection of alkali metal ions bound to G-quadruplex DNA

We describe a general multinuclear (1H, 23Na, 87Rb) NMR approach for direct detection of alkali metal ions bound to G-quadruplex DNA. This study is motivated by our recent discovery that alkali metal ions (Na+, K+, Rb+) tightly bound to G-quadruplex DNA are actually "NMR visible" in solution (Wong, A.; Ida, R.; Wu, G. Biochem. Biophys. Res. Commun. 2005, 337, 363). Here solution and solid-state NMR methods are developed for studying ion binding to the classic G-quadruplex structures formed by three DNA oligomers: d(TG4T), d(G4T3G4), and d(G4T4G4). The present study yields the following major findings. (1) Alkali metal ions tightly bound to G-quadruplex DNA can be directly observed by NMR in solution. (2) Competitive ion binding to the G-quadruplex channel site can be directly monitored by simultaneous NMR detection of the two competing ions. (3) Na+ ions are found to locate in the diagonal T4 loop region of the G-quadruplex formed by two strands of d(G4T4G4). This is the first time that direct NMR evidence has been found for alkali metal ion binding to the diagonal T4 loop in solution. We propose that the loop Na+ ion is located above the terminal G-quartet, coordinating to four guanine O6 atoms from the terminal G-quartet and one O2 atom from a loop thymine base and one water molecule. This Na+ ion coordination is supported by quantum chemical calculations on 23Na chemical shifts. Variable-temperature 23Na NMR results have revealed that the channel and loop Na+ ions in d(G4T4G4) exhibit very different ion mobilities. The loop Na+ ions have a residence lifetime of 220 micros at 15 degrees C, whereas the residence lifetime of Na+ ions residing inside the G-quadruplex channel is 2 orders of magnitude longer. (4) We have found direct 23Na NMR evidence that mixed K+ and Na+ ions occupy the d(G4T4G4) G-quadruplex channel when both Na+ and K+ ions are present in solution. (5) The high spectral resolution observed in this study is unprecedented in solution 23Na NMR studies of biological macromolecules. Our results strongly suggest that multinuclear NMR is a viable technique for studying ion binding to G-quadruplex DNA.     

Visualization of dynamic conformational switching of the G-quadruplex in a DNA nanostructure

We herein report the real-time observation of G-quadruplex formation by monitoring the G-quadruplex-induced global change of two duplexes incorporated in a DNA nanoscaffold. The introduced G-rich strands formed an interstrand (3 + 1) G-quadruplex structure in the presence of K(+), and the formed four-stranded structure was disrupted by removal of K(+). These conformational changes were visualized in a nanoscaffold in real-time with fast-scanning atomic force microscopy.     

Anion induced conformational switch of a macrocyclic amide receptor

Isophthalic acid-based macrocyclic tetraamide 4 shows considerable conformational change during anion binding. In the solid state and in solution the free receptor exists in nonbonding, closed conformation stabilized by two intramolecular hydrogen bonds. Upon anion complexation, the receptor switches to a conformation with convergent arrangement of hydrogen bond donors. The conformational switch is evidenced by 2D NMR and X-ray analyses of the free ligand and its Cl⁻ complex.     

A regenerated electrochemical biosensor for label-free detection of glucose and urea based on conformational switch of i-motif oligonucleotide probe

Improving the reproducibility of electrochemical signal remains a great challenge over the past decades. In this work, i-motif oligonucleotide probe-based electrochemical DNA (E-DNA) sensor is introduced for the first time as a regenerated sensing platform, which enhances the reproducibility of electrochemical signal, for label-free detection of glucose and urea. The addition of glucose or urea is able to activate glucose oxidase-catalyzed or urease-catalyzed reaction, inducing or destroying the formation of i-motif oligonucleotide probe. The conformational switch of oligonucleotide probe can be recorded by electrochemical impedance spectroscopy. Thus, the difference of electron transfer resistance is utilized for the quantitative determination of glucose and urea. We further demonstrate that the E-DNA sensor exhibits high selectivity, excellent stability, and remarkable regenerated ability. The human serum analysis indicates that this simple and regenerated strategy holds promising potential in future biosensing applications.     

Luminescence detection of cysteine based on Ag-mediated conformational change of terbium ion-promoted G-quadruplex

In this work, we developed a simple and sensitive method for the detection of cysteine (Cys) by employing terbium ion (Tb³⁺)-promoted G-qudraplex (G4/Tb) as a luminescent probe, which is based on Ag⁺-mediated conformational change of G4/Tb. Due to Ag⁺ is able to compete with Tb³⁺ to bind guanine at G4, the presence of Ag⁺ can lead to the formation of G4/Tb–Ag⁺ complex and disrupt the structure of G4/Tb. Meanwhile, the binding of Ag⁺ with G4/Tb will also cause the alteration of the excited state of G4 and more efficient energy transfer from G4 to Tb³⁺, enhancing the luminescence of G4/Tb. However, upon the addition of Cys, Ag⁺ will be released from G4/Tb–Ag⁺ complex because of the high affinity of Cys to Ag⁺. This results in the re-formation of the conformation of G4/Tb and the decrease of the luminescence of G4/Tb. So, Ag⁺-enhanced luminescence of G4/Tb is associated with its conformational transformation. As a luminescent probe for Cys, G4/Tb not only shows excellent selectivity and sensitivity with a detection limit of 20 nM, but also possesses the features of simple preparation, easy reproducibility, and eliminating the interferences from background fluorescence. We envision that the presented strategy might provide new insight into the biosensing applications of lanthanide complex.     

Self-organized fluorescent nanosensors for ratiometric Pb2+ detection

Silica nanoparticles (60 nm diameter) doped with fluorescent dyes and functionalized on the surface with thiol groups have been proved to be efficient fluorescent chemosensors for Pb2+ ions. The particles can detect a 1 microM metal ion concentration with a good selectivity, suffering only interference from Cu2+ ions. Analyte binding sites are provided by the simple grafting of the thiol groups on the nanoparticles. Once bound to the particles surface, the Pb2+ ions quench the emission of the reporting dyes embedded. Sensor performances can be improved by taking advantage of the ease of production of multishell silica particles. On one hand, signaling units can be concentrated in the external shells, allowing a closer interaction with the surface-bound analyte. On the other, a second dye can be buried in the particle core, far enough from the surface to be unaffected by the Pb2+ ions, thus producing a reference signal. In this way, a ratiometric system is easily prepared by simple self-organization of the particle components.     

Conformational conversion of DNA G-quadruplex induced by a cationic porphyrin

The interactions between cationic meso-tetrakis(4-(N-methylpyridiumyl))porphyrin (TMPyP4) and the G-quadruplex (G4) of human telomeric single-strand oligonucleotide d(TTAGGG)₂ (S12) have been investigated by means of circular dichroism (CD), UV–visible absorption and fluorescence spectroscopies. It is found that TMPyP4 can preferentially induce the conformational conversion of the G4 structure from the parallel type to the parallel/antiparallel mixture in the presence of K⁺, and that it can directly induce the formation of antiparallel G4 structure from the single-strand oligonucleotide S12 in the absence of K⁺. Furthermore, the comparable experiments of TMPyP4 with two single-strand oligonucleotides S6 d(TTAGGG) and S24 d(TAGGG(TTAGGG)₃T) in the absence of K⁺ show that TMPyP4 can also induce the formation of antiparallel G4 from S24 but not from S6, indicating that the end-loops of the G4 structure are the key factors for the formation of G4 induced by TMPyP4.