Aptamer-guided site-specific covalent coupling of nucleic acids to intact proteins

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Aptamer-guided site-specific covalent coupling of nucleic acids to an intact protein

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Selective RNA Labeling by RNA-Compatible Type II Restriction Endonuclease and RNA-Extending DNA Polymerase

© 2022 by the authors.RNAs not only offer valuable information regarding our bodies but also regulate cellular functions, allowing for their specific manipulations to be extensively explored for many different biological and clinical applications. In particular, rather than temporary hybridization, permanent labeling is often required to introduce functional tags to target RNAs; however, direct RNA labeling has been revealed to be challenging, as native RNAs possess unmodifiable chemical moieties or indefinable dummy sequences at the ends of their strands. In this work, we demonstrate the combinatorial use of RNA-compatible restriction endonucleases (REs) and RNA-extending polymerases for sequence-specific RNA cleavage and subsequent RNA functionalization. Upon the introduction of complementary DNAs to target RNAs, Type II REs, such as AvrII and AvaII, could precisely cut the recognition site in the RNA-DNA heteroduplexes with exceptionally high efficiency. Subsequently, the 3′ ends of the cleaved RNAs were selectively and effectively modified when Therminator DNA polymerase template-dependently extended the RNA primers with a variety of modified nucleotides. Based on this two-step RNA labeling, only the target RNA could be chemically labeled with the desired moieties, such as bioconjugation tags or fluorophores, even in a mixture of various RNAs, demonstrating the potential for efficient and direct RNA modifications.11Nsciescopu

Detection and beyond: challenges and advances in aptamer-based biosensors

Beyond traditional needs of biosensors such as high sensitivity and selectivity for analyte detection, newly emerging requirements including a real-time detection ability and in-field applicability have been gradually emphasized to address clinical and environmental availability. Highly programmable, synthetic aptamers that can specifically recognize a broad range of targets have the potential to fulfill these requirements; cooperative binding to target molecules achieves a significant increase in sensitivity, and binding-induced structure-switching enables target detection even in complex mixtures. Due to the availability of chemical synthesis and functional modifications, these artificial ligand materials are easily installed in many devices, and the amenability to modularization allows the aptamer-based biosensors to diversify detectable targets and signaling processes. In this review, we highlight current progress in the development of aptamer-based, next-generation biosensors including new types of field-effect transistors, electrochemical detectors, and microfluidic devices. As the nucleic acid aptamers have been rapidly generated by various in vitro selection techniques, the use of the versatile nanostructures is expected to expand further to include in-field and real-time biosensors.11Nscopu

Catalytic RNA, ribozyme, and its applications in synthetic biology

Ribozymes are functional RNA molecules that can catalyze biochemical reactions. Since the discovery of the first catalytic RNA, various functional ribozymes (e.g., self-cleaving ribozymes, splicing ribozymes, RNase P, etc.) have been uncovered, and their structures and mechanisms have been identified. Ribozymes have the advantage of possessing features of “RNA” molecules; hence, they are highly applicable for manipulating various biological systems. To fully employ ribozymes in a broad range of biological applications in synthetic biology, a variety of ribozymes have been developed and engineered. Here, we summarize the main features of ribozymes and the methods used for engineering their functions. We also describe the past and recent efforts towards exploiting ribozymes for effective and novel applications in synthetic biology. Based on studies on their significance in biological applications till date, ribozymes are expected to advance technologies in artificial biological systems.This work was supported by the National Research Foundation of Korea (NRF) grant (NRF-2017R1C1B3012050) and the Global Research Laboratory Program (NRF-2016K1A1A2912829) funded by the Korea government (Ministry of Science and ICT). Also, this research was supported by Basic Science Research Program funded by the Ministry of Education (2018R1A6A3A11045727).Peer reviewe

Severe Fever with Thrombocytopenia Syndrome Virus in Ticks in the Republic of Korea

Severe fever with thrombocytopenia syndrome virus (SFTSV) is a zoonotic, tick-borne RNA virus of the genus Bandavirus (Family Phenuiviridae), mainly reported in China, Japan, and the Republic of Korea (Korea). For the purpose of this study, a total of 3,898 adult and nymphal ticks of species Haemaphysalis longicornis (94.2%), Haemaphysalis flava (5.0%), Ixodes nipponensis (0.8%), and 1 specimen of Ixodes ovatus, were collected from the Deogyusan National Park, Korea, between April 2016 and June 2018. A single-step reverse transcriptase-nested PCR was performed, targeting the S segment of the SFTSV RNA. Total infection rate (IR) of SFTSV in individual ticks was found to be 6.0%. Based on developmental stages, IR was 5.3% in adults and 6.0% in nymphs. The S segment sequences obtained from PCR were divided into 17 haplotypes. All haplotypes were phylogenetically clustered into clades B-2 and B-3, with 92.7% sequences in B-2 and 7.3% in B-3. These observations indicate that the Korean SFTSV strains were closer to the Japanese than the Chinese strains. Further epidemiological studies are necessary to better understand the characteristics of the Korean SFTSV and its transmission cycle in the ecosystem.N

Direct strain correlations at the single-atom level in three-dimensional core-shell interface structures

Nanomaterials with core-shell architectures are prominent examples of strain-engineered materials, where material properties can be designed by fine-tuning the misfit strain at the interface. Here, we elucidate the full 3D atomic structure of Pd@Pt core-shell nanoparticles at the single-atom level via atomic electron tomography. Full 3D displacement fields and strain profiles of core-shell nanoparticles were obtained, which revealed a direct correlation between the surface and interface strain. It also showed clear Poisson effects at the scale of the full nanoparticle as well as the local atomic bonds. The strain distributions show a strong shape-dependent anisotropy, whose nature was further corroborated by molecular statics simulations. From the observed surface strains, the surface oxygen reduction reaction activities were predicted. These findings give a deep understanding of structure-property relationships in strain-engineerable core-shell systems, which could pave a new way toward direct control over the resulting catalytic properties.Comment: Main manuscript: 30 pages, 4 figures, 73 references || Supplementary info: 26 pages, 26 figures, 1 table, 15 reference

Metastable hexagonal close-packed palladium hydride in liquid cell TEM

Metastable phases-kinetically favoured structures-are ubiquitous in nature1,2. Rather than forming thermodynamically stable ground-state structures, crystals grown from high-energy precursors often initially adopt metastable structures depending on the initial conditions, such as temperature, pressure or crystal size1,3,4. As the crystals grow further, they typically undergo a series of transformations from metastable phases to lower-energy and ultimately energetically stable phases1,3,4. Metastable phases sometimes exhibit superior physicochemical properties and, hence, the discovery and synthesis of new metastable phases are promising avenues for innovations in materials science1,5. However, the search for metastable materials has mainly been heuristic, performed on the basis of experiences, intuition or even speculative predictions, namely 'rules of thumb'. This limitation necessitates the advent of a new paradigm to discover new metastable phases based on rational design. Such a design rule is embodied in the discovery of a metastable hexagonal close-packed (hcp) palladium hydride (PdHx) synthesized in a liquid cell transmission electron microscope. The metastable hcp structure is stabilized through a unique interplay between the precursor concentrations in the solution: a sufficient supply of hydrogen (H) favours the hcp structure on the subnanometre scale, and an insufficient supply of Pd inhibits further growth and subsequent transition towards the thermodynamically stable face-centred cubic structure. These findings provide thermodynamic insights into metastability engineering strategies that can be deployed to discover new metastable phases. © 2022. The Author(s), under exclusive licence to Springer Nature Limited.11Nsciescopu