A fluorescent molecular switch for room temperature operation based on oligonucleotide hybridization without labeling of probes or targets

Construction of label-free electrochemical aptasensor and logic circuit based on triple-stranded DNA molecular switch

BACKGROUND

Pesticide residues can cause chronic toxicity to the human body and lead to a series of diseases that damage the liver. Therefore, developing a highly sensitive, selective, and low-cost pesticide residues detection method is of great significance for protecting human health and safety. Nowadays, commonly used methods for pesticide residue detection include gas chromatography, high-performance liquid chromatography, and fluorescence sensing. These methods have some typical shortcomings, such as long sample pretreatment time, expensive instruments, and poor controllability. It was thought that a sensing platform based on electrochemical analysis method and functional DNA molecules can eliminate the above drawbacks.

RESULTS

Herein, this study developed a simple and label-free electrochemical aptasensor based on a triple-stranded DNA molecular switch. Acetamiprid (ACE) was served as the analytical model, and its binding with the aptamer opened the triple-stranded DNA molecular switch, resulting in the in-situ formation of G-quadruplex/hemin complexes on the electrode surface, obtaining a significantly enhanced electrochemical signal and achieving high specificity and label-free detection of ACE, with a detection limit as low as 4.67 × 10-3 nM (S/N = 3). In addition, due to the specific recognition between the aptamer and the target, the aptasensor effectively avoided the interference of other pesticides and exhibited good specificity. Moreover, benefiting from the pH-switchable of the triple-stranded DNA molecular switch and the programmability of DNA molecules, "OR" logic gate and "OR-INHIBIT" cascade logic circuit were successfully implemented.

SIGNIFICANCE

The proposed electrochemical aptasensor exhibited good accuracy and sensitivity in detecting acetamiprid in vegetable soil sample, indicating its practicality in the detection of pesticide residues in actual samples. Furthermore, the sensing system was reasonably programmed and successfully operated an "OR" logic gate and an "OR-INHIBIT" cascade logic circuit, demonstrating its potential application in intelligent sensing.

Optimization of a peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) method for the detection of bacteria and disclosure of a formamide effect

Despite the fact that fluorescence in situ hybridization (FISH) is a well-established technique to identify microorganisms, there is a lack of understanding concerning the interaction of the different factors affecting the obtained fluorescence. In here, we used flow cytometry to study the influence of three essential factors in hybridization - temperature, time and formamide concentration - in an effort to optimize the performance of a Peptide Nucleic Acid (PNA) probe targeting bacteria (EUB338). The PNA-FISH optimization was performed with bacteria representing different families employing response surface methodology. Surprisingly, the optimum concentration of formamide varied according to the bacterium tested. While hybridization on the bacteria possessing the thickest peptidoglycan was more successful at nearly 50% (v/v) formamide, hybridization on all other microorganisms appeared to improve with much lower formamide concentrations. Gram staining and transmission electron microscopy allowed us to confirm that the overall effect of formamide concentration on the fluorescence intensity is a balance between a harmful effect on the bacterial cell envelope, affecting cellular integrity, and the beneficial denaturant effect in the hybridization process. We also conclude that microorganisms belonging to different families will require different hybridization parameters for the same FISH probe, meaning that an optimum universal PNA-FISH procedure is non-existent for these situations.