Fluorescent trimethyl-substituted naphthyridine as a label-free signal reporter for one-step and highly sensitive fluorescent detection of DNA in serum samples

A novel fluorescent platform of DNA-stabilized silver nanoclusters based on exonuclease III amplification-assisted detection of Salmonella Typhimurium

A novel fluorescent platform of DNA-stabilized silver nanoclusters (DNA-AgNCs) has been developed based on exonuclease III (Exo III) amplification-assisted for simple and sensitive detection of Salmonella Typhimurium (S. Typhimurium). The platform was designed by using magnetic beads, aptamer, its complementary DNA, hairpin probe (HP), Exo III, AgNO₃, and NaBH₄. The functionalized HP contained a cytosine-rich oligonucleotide loop (C-rich loop), which served as an effective template for the chemical reduction of Ag⁺ with NaBH₄ to synthesize DNA-AgNCs. In the presence of S. Typhimurium, the C-rich loop was converted into an open form of ssDNA by the recycle digestion of Exo III, leading to a corresponding decrease in fluorescence intensity. Based on the fluorescence changes of the formed DNA-AgNCs, the sensitive detection of S. Typhimurium was achieved. Under the optimal conditions, a wide linear relationship was observed in the concentration of S. Typhimurium ranging from 4.6 × 10² to 4.6 × 10⁷ cfu mL^-1 with the limit of detection (LOD) being 82 cfu mL^-1. The method showed good selectivity for detecting S. Typhimurium. In addition, the platform could be used for the detection of S. Typhimurium in milk samples. The LOD reached 6.6 × 10² cfu mL^-1 with a good linear range, indicating that the method had excellent practicability in complex food samples.

A hairpin probe-mediated DNA circuit for the detection of the mecA gene of Staphylococcus aureus based on exonuclease III and DNAzyme-mediated signal amplification

A simple, highly sensitive biosensor for S. aureus detection is becoming increasingly important in human health and safety. In this work, a hairpin probe-mediated DNA circuit for the detection of the mecA gene of S. aureus was reported cascading Exo III-assisted cycling signal amplification and the DNAzyme-mediated cleavage reaction. In the presence of the target mecA gene, the recognition and hybridization between HP1 and mecA can trigger Exo III and DNAzyme-mediated signal amplification and further release numerous ATMND, resulting in an enhanced fluorescence response, which serves as a response signal for the fluorescence detection of mecA gene. This biosensor enables the sensitive and specific detection of the mecA gene, showing a linear response ranging from 1 fM to 1 nM with a detection limit of 0.5 fM. Moreover, this fluorescence assay has been applied for the analysis of clinical samples with satisfactory recovery. Importantly, this universal platform can be further extended for the analysis of other targets by alternating the corresponding recognition unit, which holds much promise in point-of-care testing for bacterial analysis.

Hairpin DNA-Mediated isothermal amplification (HDMIA) techniques for nucleic acid testing

Nucleic acid detection is of great importance in a variety of areas, from life science and clinical diagnosis to environmental monitoring and food safety. Unfortunately, nucleic acid targets are always found in trace amounts and their response signals are difficult to be detected. Amplification mechanisms are then practically needed to either duplicate nucleic acid targets or enhance the detection signals. Polymerase chain reaction (PCR) is one of the most popular and powerful techniques for nucleic acid analysis. But the requirement of costly devices for precise thermo-cycling procedures in PCR has severely hampered the wide applications of PCR. Fortunately, isothermal molecular reactions have emerged as promising alternatives. The past decade has witnessed significant progress in the research of isothermal molecular reactions utilizing hairpin DNA probes (HDPs). Based on the nucleic acid strand interaction mechanisms, the hairpin DNA-mediated isothermal amplification (HDMIA) techniques can be mainly divided into three categories: strand assembly reactions, strand decomposition reactions, and strand creation reactions. In this review, we introduce the basics of HDMIA methods, including the sensing principles, the basic and advanced designs, and their wide applications, especially those benefiting from the utilization of G-quadruplexes and nanomaterials during the past decade. We also discuss the current challenges encountered, highlight the potential solutions, and point out the possible future directions in this prosperous research area.

Symmetric exponential amplification reaction-based DNA nanomachine for the fluorescent detection of nucleic acids

By introducing palindromic sequences into the classical exponential amplification reaction (EXPAR), we constructed a new palindromic fragment-incorporated multifunctional hairpin probe (P-HP)-mediated symmetric exponential amplification reaction (S-EXPAR), to significantly reduce the background signal caused by inherent nonspecific amplification. A G-triplex/ThT complex was used as the signal reporter for the proposed label-free DNA nanomachine. The P-HP consists of five functional regions: a C-rich region (C), a target DNA recognition region (T′), two nicking sites (X′) and a palindromic fragment (P). When target DNA (T) hybridizes with P-HP, the palindromic fragment at the 3′ end of P-HP is fully exposed. Then, the P-HP/T duplexes hybridize with each other through the exposed P, and EXPAR occurs automatically and continuously on both sides of P under the synergistic effect of polymerase and nicking endonuclease. This is called the S-EXPAR assay. In this system, one T converts to a large number of G-triplex fragments, which can combine with ThT within a short time. The G-triplex/ThT complexes formed act as the signal reporter in a label-free and environmentally friendly format. In this way, the limit of detection of this method is as low as 10 pM with a dynamic response range of 10 pM to 300 nM. In addition, this method can detect other nucleic acids by simply changing the T′ region of the P-HP. Thus, the proposed DNA nanomachine is a potential alternative method for nucleic acid detection.

This label-free and ultra-low background signal DNA nanomachine was based on P-HP mediated S-EXPAR and the G-triplex/ThT complex.

Label-free and highly sensitive fluorescence detection of lead(ii) based on DNAzyme and exonuclease III-assisted cascade signal amplification

A Pb²⁺ biosensor has been constructed based on Exo III-assisted cascade signal amplification using 2-amino-5,6,7-trimethyl-1,8-naphthyridine as the signal indicator.

Ultrasensitive aptamer biosensor for arsenic (III) detection based on label-free triple-helix molecular switch and fluorescence sensing platform

Arsenic ion is a well-known harmful heavy element widely existing in the environment. Arsenic pollution occurring frequently has become increasing a serious worldwide threat to human health and the environment. The development of sensitive and reliable methods to detect As³⁺ in water is of great importance to biochemical research and monitoring applications. Herein, a label-free fluorescence sensing platform was elaborately designed for As³⁺ monitoring using exonuclease III (Exo III)-assisted cascade target recycling amplification strategy. The triple-helix molecular switch was employed as the sensing element and 2-amino-5,6,7-trimethyl-1,8-naphthyridine was used as the signal indicator. The resulting biosensor is simple, ultrasensitive, and exhibits a limit of detection of 5 ng/L with high selectivity. Meanwhile, the proposed sensor is successfully applied to determination of As³⁺ in practical sample analysis (tap water, lake water and pond water). The results shown herein have important implications in the development of new fluorescent sensors for the fast, easy, and selective detection and quantification of As³⁺ in water samples. More importantly, the proposed platform can be extended to detect other heavy metal ions with newly designed triple-helix molecular switch, as well as pesticide residue, antibiotic residues, and biomarkers by using aptamer sequences.

Ultrasensitive DNA detection based on target-triggered rolling circle amplification and fluorescent poly(thymine)-templated copper nanoparticles

An ultrasensitive DNA detection method is developed based on target-triggered rolling circle amplification coupled with fluorescent poly(thymine)-templated copper nanoparticles.

A universal aptameric biosensor: Multiplexed detection of small analytes via aggregated perylene-based broad-spectrum quencher

A universal aptameric system based on the taking advantage of double-stranded DNA/perylene diimide (dsDNA/PDI) as the signal probe was developed for multiplexed detection of small molecules. Aptamers are single-stranded DNA or RNA oligonucleotides which are selected in vitro by a process known as systematic evolution of ligands by exponential enrichment. In this work, we synthesized a new kind of PDI and reported this aggregated PDI could quench the double-stranded DNA (dsDNA)-labeled fluorophores with a high quenching efficiency. The quenching efficiencies on the fluorescence of FAM, TAMRA and Cy5 could reach to 98.3%±0.9%, 97.2%±0.6% and 98.1%±1.1%, respectively. This broad-spectrum quencher was then adopted to construct a multicolor biosensor via a label-free approach. A structure-switching-triggered enzymatic recycling amplification was employed for signal amplification. High quenching efficiency combined with autocatalytic target recycling amplification afforded the biosensor with high sensitivity towards small analytes. For other targets, changing the corresponding aptamer can achieve the goal. The quencher did not interfere with the catalytic activity of nuclease. The biosensor could be manipulated with similar sensitivity no matter in pre-addition or post-addition manner. Moreover, simultaneous and multiplexed analysis of several small molecules in homogeneous solution was achieved, demonstrating its potential application in the rapid screening of multiple biotargets.