The unfolding of G-quadruplexes and its adverse effect on DNA-gold nanoparticles-based sensing system

Development of a fluorescent DNA sensor for dual detection of heavy metal ions utilising DAPI in distinct buffers

The DNA-based biosensor utilises a thymine/guanine(T/G)-rich ODN-4 scaffold with 4',6-diamidino-2-phenylindole(DAPI) as a fluorescent emissary to monitor mercury/lead(Hg(II)/Pb(II)) ions simultaneously. Key to its bifocal detection capability is the twin unbound cytosine(C) bases strategically bridging the G-quadruplex and T-rich sequences, enabling their synergistic interplay. It facilitates the recognition of Hg(II)/Pb(II) ions, characterised by high specificity, and effectively mitigates interference from silver(Ag(I)). The G-quadruplex, guided by the C bases, induces a conformational transition in T-Hg(II)-T complexes, resulting in intense fluorescence. Pb(II) causes a spatial shift in the G-quadruplex, relaxing the T-Hg(II)-T base pairs and attenuating the fluorescence signal. The ODN-4 exhibits a robust, linear correlation with Hg(II) concentration (4.09 nmol/L to 1000 nmol/L) and Pb(II) concentration (3.22 nmol/L to 5 μmol/L). Recovery rates in milk, tap water, and rice water specimens with both ions validate method accuracy (Hg(II): 95.19% to 104.68%, Pb(II): 98.20% to 103.46%). It holds promising prospects for practical food analysis.

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.

Secondary Structure-Dependent Physicochemical Interaction of Oligonucleotides with Gold Nanorod and Photothermal Effect for Future Applications: A New Insight

We investigate the physicochemical interactions of gold nanorod (GNR) with single-stranded, double-stranded, and hairpin DNA structures to improve the biological compatibility as well as the therapeutic potential, including the photothermal effect of the conjugates. Studies have demonstrated that different DNA secondary structures, containing thiol group, have different patterns of physicochemical interaction. Conjugation efficiency of paired oligonucleotides are significantly higher than that of oligonucleotides with naked bases. Furthermore, hairpin-shaped DNA structures are most efficient in terms of conjugation and increased dispersion, with least interference on GNR near-infrared absorbance and photothermal effect. Our conjugation method can successfully exchange the overall coating of the GNR, attaching the maximum number of DNA molecules, thus far reported. Chemical mapping depicted uniform attachment of thiolated DNA molecules without any topological preference on the GNR surface. Hairpin DNA-coated GNR are suitable for intracellular uptake and remain dispersed in the cellular environment. Finally, we conjugated GNR with 5-fluoro-2'-deoxyuridine-containing DNA hairpin and the conjugate demonstrated significant cytotoxic activity against human cervical cancer cell line (KB). Thus, hairpin DNA structures could be utilized for optimal dispersion and photothermal effect of GNR, along with the delivery of cytotoxic nucleotides, developing the concept of multimodality approach.

A SERS/fluorescence dual-mode nanosensor based on the human telomeric G-quadruplex DNA: Application to mercury (II) detection

DNA-metal nanoparticle conjugates have been increasingly exploited for sensing purposes over the past decades. However, most of the existing strategies are operated with canonical DNA structures, such as single-stranded forms, stem-loop structures, and double helix structures. There is intense interest in the development of nano-system based on high order DNA secondary structures. Herein, we propose a SERS/fluorescence dual-mode nanosensor, where the signal transduction mechanism is based on the conformational switching of the human telomeric G-quadruplex DNA. The nanosensor exhibits excellent SERS/fluorescence responses to the complementary strands of G-quadruplexes. Based on T-Hg(2+)-T coordination chemistry, this sensor is effectively applied to determination of Hg(2+) in buffer solution and real samples. It achieves a limit of detection (LOD) as low as 1ppt, which is ~100 times more sensitive than conventional optical sensors. We anticipate that the proposed G-quadruplex-based nanosensor could be applied to the analysis of other metal ions and small molecules in environmental samples and biological systems.

An ultrasensitive label-free assay of 8-hydroxy-2'-deoxyguanosine based on the conformational switching of aptamer

We developed a highly sensitive label-free assay of 8-hydroxy-2'-deoxyguanosine (8-OHdG) using 8-OHdG-aptamer (Apt) as the recognition element. The Apt was adsorbed onto the surface of gold nanoparticles (AuNPs), which prevents them from aggregating under high-salt conditions. Upon addition of 8-OHdG, the conformation of the Apt changes to form a G-quadruplex structure, which leads to the aggregation of the AuNPs along with the increase of the resonance light scattering intensity. The mechanism of 8-OHdG that induces Apt to form G-quadruplexes structure was studied by circular dichroism. The response signals linearly correlated with the concentration of 8-OHdG ranging from 90.8pM to 14.1nM with a detection limit of 27.3pM, which is much lower than that obtained by other methods. This method does not need any label steps and sophisticated equipment. The application for detection of 8-OHdG in real samples further demonstrated its reliability. This strategy would be helpful for developing a universal analytical method by simply replacing corresponding aptamers for various target molecules.