Production of Structured RNA Fragments by In Vitro Transcription and HPLC Purification

Y-switch: a spring-loaded synthetic gene switch for robust DNA/RNA signal amplification and detection

Nucleic acid tests (NATs) are essential for biomedical diagnostics. Traditional NATs, often complex and expensive, have prompted the exploration of toehold-mediated strand displacement (TMSD) circuits as an economical alternative. However, the wide application of TMSD-based reactions is limited by 'leakage'-the spurious activation of the reaction leading to high background signals and false positives. Here, we introduce the Y-Switch, a new TMSD cascade design that recognizes a custom nucleic acid input and generates an amplified output. The Y-Switch is based on a pair of thermodynamically spring-loaded DNA modules. The binding of a predefined nucleic acid target triggers an intermolecular reaction that activates a T7 promoter, leading to the perpetual transcription of a fluorescent aptamer that can be detected by a smartphone camera. The system is designed to permit the selective depletion of leakage byproducts to achieve high sensitivity and zero-background signal in the absence of the correct trigger. Using Zika virus (ZIKV)- and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-derived nucleic acid sequences, we show that the assay generates a reliable target-specific readout. Y-Switches detect native RNA under isothermal conditions without reverse transcription or pre-amplification, with a detection threshold as low as ∼200 attomole. The modularity of the assay allows easy re-programming for the detection of other targets by exchanging a single sequence domain. This work provides a low-complexity and high-fidelity synthetic biology tool for point-of-care diagnostics and for the construction of more complex biomolecular computations.

A smartphone-based fluorescent sensor for rapid detection of multiple pathogenic bacteria

In this study, we developed a fluorescent sensor for the sensitive detection of multiple pathogenic bacteria based on magnetic separation, fluorescent probes, and smartphone image processing. A microchannel device was assembled using high-transparency resin and 3D printing technology. This device was combined with a smartphone and an external lens to develop a fluorescent sensor for autonomous detection of multiple pathogenic bacteria. Three fluorescence probes with different fluorescence were synthesized from highly specific aptamers and tetraphenylethylene derivatives. These fluorescent probes can make Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa emit different colors of fluorescence. Using the enrichment performance of molecularly imprinted materials, separation and detection of bacteria can be achieved simultaneously. Finally, with the Red-Green-Blue (RGB) analysis functionality of a smartphone, real-time field detection was realized with a sensitivity of 102 CFU/mL and a detection time of 40 min. This work provides a simple, inexpensive, and real-time sensor for the detection of multiple pathogens in medical diagnostics, food testing, and environmental analyses.

Enzymatic incorporation of an isotope-labeled adenine into RNA for the study of conformational dynamics by NMR

Solution NMR spectroscopy is a well-established tool with unique advantages for structural studies of RNA molecules. However, for large RNA sequences, the NMR resonances often overlap severely. A reliable way to perform resonance assignment and allow further analysis despite spectral crowding is the use of site-specific isotope labeling in sample preparation. While solid-phase oligonucleotide synthesis has several advantages, RNA length and availability of isotope-labeled building blocks are persistent issues. Purely enzymatic methods represent an alternative and have been presented in the literature. In this study, we report on a method in which we exploit the preference of T7 RNA polymerase for nucleotide monophosphates over triphosphates for the 5’ position, which allows 5’-labeling of RNA. Successive ligation to an unlabeled RNA strand generates a site-specifically labeled RNA. We show the successful production of such an RNA sample for NMR studies, report on experimental details and expected yields, and present the surprising finding of a previously hidden set of peaks which reveals conformational exchange in the RNA structure. This study highlights the feasibility of site-specific isotope-labeling of RNA with enzymatic methods.