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1. Single-molecule fluorescence detection of a tricyclic nucleoside analogue

   https://doi.org/10.1039/D0SC03903A  

   Samaan, George N.; Wyllie, Mckenzie K.; Cizmic, Julian M.; Needham, Lisa-Maria; Nobis, David; Ngo, Katrina; Andersen, Susan; Magennis, Steven W.; Lee, Steven F.; Purse, Byron W. (February 2021, Chemical Science)

   null (Ed.)

   Fluorescent nucleobase surrogates capable of Watson–Crick hydrogen bonding are essential probes of nucleic acid structure and dynamics, but their limited brightness and short absorption and emission wavelengths have rendered them unsuitable for single-molecule detection. Aiming to improve on these properties, we designed a new tricyclic pyrimidine nucleoside analogue with a push–pull conjugated system and synthesized it in seven sequential steps. The resulting C -linked 8-(diethylamino)benzo[ b ][1,8]naphthyridin-2(1 H )-one nucleoside, which we name ABN, exhibits ε 442 = 20 000 M −1 cm −1 and Φ em,540 = 0.39 in water, increasing to Φ em = 0.50–0.53 when base paired with adenine in duplex DNA oligonucleotides. Single-molecule fluorescence measurements of ABN using both one-photon and two-photon excitation demonstrate its excellent photostability and indicate that the nucleoside is present to > 95% in a bright state with count rates of at least 15 kHz per molecule. This new fluorescent nucleobase analogue, which, in duplex DNA, is the brightest and most red-shifted known, is the first to offer robust and accessible single-molecule fluorescence detection capabilities. 

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2. Tailoring amorphous boron nitride for high-performance two-dimensional electronics

   https://doi.org/10.1038/s41467-024-48429-4  

   Chen, Cindy Y; Sun, Zheng; Torsi, Riccardo; Wang, Ke; Kachian, Jessica; Liu, Bangzhi; Rayner, Gilbert B; Chen, Zhihong; Appenzeller, Joerg; Lin, Yu-Chuan; et al (December 2024, Nature Communications)

   Abstract Two-dimensional (2D) materials have garnered significant attention in recent years due to their atomically thin structure and unique electronic and optoelectronic properties. To harness their full potential for applications in next-generation electronics and photonics, precise control over the dielectric environment surrounding the 2D material is critical. The lack of nucleation sites on 2D surfaces to form thin, uniform dielectric layers often leads to interfacial defects that degrade the device performance, posing a major roadblock in the realization of 2D-based devices. Here, we demonstrate a wafer-scale, low-temperature process (<250 °C) using atomic layer deposition (ALD) for the synthesis of uniform, conformal amorphous boron nitride (aBN) thin films. ALD deposition temperatures between 125 and 250 °C result in stoichiometric films with high oxidative stability, yielding a dielectric strength of 8.2 MV/cm. Utilizing a seed-free ALD approach, we form uniform aBN dielectric layers on 2D surfaces and fabricate multiple quantum well structures of aBN/MoS₂and aBN-encapsulated double-gated monolayer (ML) MoS₂field-effect transistors to evaluate the impact of aBN dielectric environment on MoS₂optoelectronic and electronic properties. Our work in scalable aBN dielectric integration paves a way towards realizing the theoretical performance of 2D materials for next-generation electronics. 

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3. 5-Dihydroxyboryluridine enhances cytosolic penetration of antisense oligonucleotides

   https://doi.org/10.1039/d3cc01945d  

   Kavoosi, Sam; Deprey, Kirsten; Kritzer, Joshua A; Islam, Kabirul (July 2023, Chemical Communications)

   Boronic acid functionalized synthetic antisense oligonucleotides demonstrate enhanced cellular uptake and biological activity, constituting a novel approach for delivery of therapeutic oligonucleotides. 

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4. Digital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs

   https://doi.org/10.1126/sciadv.adi4997  

   Tayyab, Muhammad; Barrett, Donal; van Riel, Gijs; Liu, Shujing; Reinius, Björn; Scharfe, Curt; Griffin, Peter; Steinmetz, Lars M.; Javanmard, Mehdi; Pelechano, Vicent (September 2023, Science Advances)

   Fast and accurate detection of nucleic acids is key for pathogen identification. Methods for DNA detection generally rely on fluorescent or colorimetric readout. The development of label-free assays decreases costs and test complexity. We present a novel method combining a one-pot isothermal generation of DNA nanoballs with their detection by electrical impedance. We modified loop-mediated isothermal amplification by using compaction oligonucleotides that self-assemble the amplified target into nanoballs. Next, we use capillary-driven flow to passively pass these nanoballs through a microfluidic impedance cytometer, thus enabling a fully compact system with no moving parts. The movement of individual nanoballs is detected by a change in impedance providing a quantized readout. This approach is flexible for the detection of DNA/RNA of numerous targets (severe acute respiratory syndrome coronavirus 2, HIV, β-lactamase gene, etc.), and we anticipate that its integration into a standalone device would provide an inexpensive (<$5), sensitive (10 target copies), and rapid test (<1 hour). 

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5. Non‐Chromatographic Purification of Synthetic RNA Using Bio‐Orthogonal Chemistry

   https://doi.org/10.1002/cpz1.247  

   He, Muhan; Wu, Xunshen; Mao, Song; Haruehanroengra, Phensinee; Khan, Irfan; Sheng, Jia; Royzen, Maksim (September 2021, Current Protocols)

   Abstract Solid‐phase synthesis of RNA oligonucleotides over 100 nt in length remains challenging due to the complexity of purification of the target strands from the failure sequences. This article describes a non‐chromatographic procedure that will enable routine solid‐phase synthesis and purification of long RNA strands. The optimized five‐step process is based on bio‐orthogonal inverse electron demand Diels‐Alder chemistry betweentrans‐cyclooctene (TCO) and tetrazine (Tz), and entails solid‐phase synthesis of RNA on a photo‐labile support. The target oligonucleotide strands are selectively tagged with Tz while on‐support. After photocleavage from the solid support, the target oligonucleotide strands can be captured and purified from the failure sequences using immobilized TCO. The approach can be applied for purification of 76‐nt long tRNA and 101‐nt long sgRNA for CRISPR experiments. Purity of the isolated oligonucleotides should be evaluated using gel electrophoresis, while functional fidelity of the sgRNA should be confirmed using CRISPR‐Cas9 experiments. © 2021 Wiley Periodicals LLC. Basic Protocol: Five‐step non‐chromatographic purification of synthetic RNA oligonucleotides Support Protocol 1: Synthesis of the components that are required for the non‐chromatographic purification of long RNA oligonucleotides. Support Protocol 2: Solid‐phase RNA synthesis 

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