Label-free fluorescent and electrochemical biosensors based on defective G-quadruplexes

Fluorescence/electrochemical dual-mode strategy for Golgi protein 73 detection based on molybdenum disulfide/ferrocene/palladium nanoparticles and nitrogen-doped graphene quantum dots

Golgi protein 73 (GP73) is a new serum marker associated with early diagnosis and postoperative assessment of hepatocellular carcinoma (HCC). Herein, an electrochemical/fluorescence dual-signal biosensor was designed for determination of GP73 based on molybdenum disulfide/ferrocene/palladium nanoparticles (MoS2-Fc-PdNPs) and nitrogen-doped graphene quantum dots (NGQDs). GP73 aptamer (Apt) was labeled with NGQDs to form the NGQDs-Apt fluorescence probe. MoS2-Fc-PdNPs served not only as the fluorescence quencher but also as electrochemical enhancer. The sensing platform (NGQDs-Apt/MoS2-Fc-PdNPs) was formed based on the fluorescence resonance energy transfer (FRET) mechanism. In the presence of GP73, the specific binding of NGQDs-Apt to GP73 interrupted FRET, restoring the fluorescence of NGQDs-Apt at λex/em = 348/438 nm and enhancing the oxidation current of Fc in MoS2-Fc-PdNPs at 0.04 V through differential pulse voltammetry (DPV). Under the optimal conditions, the DPV current change and fluorescence recovery have a good linear relationship with GP73 concentration from 1.00 to 10.0 ng/mL. The calibration equation for the fluorescence mode was Y1 = (0.0213 ± 0.00127)X + (0.0641 ± 0.00448) and LOD was 0.812 ng/mL (S/N = 3). The calibration equation of the electrochemical mode was Y2 = (3.41 ± 0.111)X + (1.62 ± 0.731), and LOD of 0.0425 ng/mL (S/N = 3). The RSDs of fluorescence mode and electrochemical mode after serum detection were 1.62 to 5.21% and 0.180 to 6.62%, respectively. By combining the electrochemical and fluorescence assay, more comprehensive and valuable information for GP73 was provided. Such dual-mode detection platform shows excellent reproducibility, stability, and selectivity and has great application potential.

A novel self-cleaning electrochemical biosensor integrating copper porphyrin-derived metal-organic framework nanofilms, G-quadruplex, and DNA nanomotors for achieving cyclic detection of lead ions

A self-cleaning electrochemical biosensor based on two-dimensional Cu-porphyrin (Cu-TCPP) metal-organic framework nanofilms, novel super G-quadruplex (G4), and DNA nanomotors was developed for the cyclic detection of Pb²⁺ ions. The Cu-TCPP framework with inherent peroxidase activity can create an ultra-thin nanofilm that functioned as a carrier to support the metastable G4 comprising four individual DNA strands. The introduction of Pb²⁺ and the intercalation of hemin can help it to form stable G4-hemin DNAzymes, which exhibits strong catalytic H₂O₂ reduction activity, and its number will be directly related to the amount of the introduced Pb²⁺. Moreover, a DNA nanomotor system is introduced to achieve cyclic detection, and the addition of the fuel DNA strands enables G4 to perform a "complete-dissociation-complete" process for achieving self-cleaning of the electrode interface and the cycle detection of Pb²⁺. The synergistic effects of Cu-TCPP and G4-hemin DNAzymes, which exhibits efficient and catalytic H₂O₂ reduction, enhance the performance of the electrochemical sensing system. The linear range of this sensor to Pb²⁺ is 5 nM-5 μM, and the detection limit is 1.7 nM. Compared with the best system in reported studies, its linear range is five times wider and its detection limit is lower than the previously lowest one. Taking advantage of the Pb²⁺ stabilized G4, the proposed sensor can selectively detect Pb²⁺ in the presence of other metal ions. The results presented herein comprise a valuable reference for constructing DNA nanoelectronic devices and establish sensitive and cyclic detection of the target and preparing of self-cleaning electrode interfaces.

Engineering base-excised aptamers for highly specific recognition of adenosine

The DNA aptamer for adenosine and ATP has been used as a model system for developing analytical biosensors. For practical reasons, it is important to distinguish adenosine from ATP, although this has yet to be achieved despite extensive efforts made on selection of new aptamers. We herein report a strategy of excising an adenine nucleotide from the backbone of a one-site adenosine aptamer, and the adenine-excised aptamer allowed highly specific binding of adenosine. Cognate analytes including AMP, ATP, guanosine, cytidine, uridine, and theophylline all failed to bind to the engineered aptamer according to the SYBR Green I (SGI) fluorescence spectroscopy and isothermal titration calorimetry (ITC) results. Our A-excised aptamer has two binding sites: the original aptamer binding site in the loop and the newly created one due to base excision from the DNA backbone. ITC demonstrated that the A-excised aptamer strand can bind to two adenosine molecules, with a K_d of 14.8 ± 2.1 μM at 10 °C and entropy-driven binding. Since the wild-type aptamer cannot discriminate adenosine from AMP and ATP, we attributed this improved specificity to the excised site. Further study showed that these two sites worked cooperatively. Finally, the A-excised aptamer was tested in diluted fetal bovine serum and showed a limit of detection of 46.7 μM adenosine. This work provides a facile, cost-effective, and non-SELEX method to engineer existing aptamers for new features and better applications.

The DNA aptamer for adenosine and ATP has been used as a model system for developing analytical biosensors.

Studying the excited electronic states of guanine rich DNA quadruplexes by quantum mechanical methods: main achievements and perspectives

Calculations are providing more and more useful insights into the interaction between light and DNA quadruplexes.

Comprehensive Study of Guanine Excited State Relaxation and Photoreactivity in G-quadruplexes

G-quadruplexes (G4) are four-stranded DNA/RNA structures playing a key role in many biological functions and promising for nanotechnology applications. Here, combining theoretical calculations and multiscale time-resolved fluorescence, we describe, for the first time, an ensemble of photoactivated processes involving the guanines of the G4 core. We use as showcase the G4 formed by the human telomeric sequence GGG(TTAGGG)₃ in the presence of Na⁺ ions. According to quantum mechanical/molecular mechanics calculations, the hyperchromism at the red part of the absorption spectrum, typical of G4 structures, arises mainly from the inner Na⁺ ions. Various relaxation pathways, leading to excited states localized on individual bases, neutral excimers, and excited charge transfer states between two guanines or a guanine and a thymine in the loop, are mapped. Their fingerprints are detected in the fluorescence anisotropies and the fluorescence decays, spanning five decades of time. Finally, a reaction funnel leading to guanine dimerization is identified.

Facile detection of melamine by a FAM-aptamer-G-quadruplex construct

The development of a novel method for melamine detection that uses a FAM-aptamer-G-quadruplex construct due to the efficient quenching ability of an aptamer-linked G-quadruplex is reported herein. The construct, which is labeled with the fluorescent dye 6-carboxyfluorescein (FAM), consists of two parts: a melamine-binding aptamer and a G-rich sequence that can form a G-quadruplex structure. Because of the specific recognition of melamine by the T-rich aptamer, this aptamer folds into a hairpin structure in the presence of melamine, which draws the G-quadruplex closer to the FAM fluorophore, leading to the quenching of the fluorescence of FAM. Thus, a highly sensitive and selective fluorescence strategy for assaying melamine was established. Under optimal conditions, the fluorescence quenching is proportional to the concentration of melamine within the range 10-90 nM, and the method has a detection limit of 6.32 nM. Further application of the method to plastic cup samples suggested that it permitted recoveries of between 97.15% ± 1.02 and 101.92% ± 2.07. The detected amounts of melamine spiked into the plastic cup samples and the corresponding amounts measured by HPLC were in good accordance, indicating that this fluorescent method is reliable and practical. Owing to its high sensitivity, excellent selectivity, and convenient procedure, this strategy represents a promising alternative method of melamine screening. Graphical abstract.