Article
Biology
Miho Kasuga, Hiromi Mutsuro-Aoki, Tadashi Ando, Koji Tamura
Summary: In this study, researchers investigated the conditions under which the class I ligase ribozyme retains ligation activity by removing partial structures and splitting. They found that the ligation activity can be maintained even when the ribozyme is split into two molecules. The study also identified the necessary duplex length for activity and explored the structural basis of the ribozyme's activity. These findings provide insight into the prebiotic synthesis of the class I ligase ribozyme.
Article
Biology
Hiromi Mutsuro-Aoki, Koji Tamura
Summary: The introduction of complementary loops allows nonfunctional RNAs to acquire dual functions, highlighting the versatility of kissing-loop interactions in RNA evolution.
Article
Biology
Kristian Kyle Le Vay, Elia Salibi, Basusree Ghosh, T. Y. Dora Tang, Hannes Mutschler
Summary: Condensed coacervate phases are important in modern cell biology and in origin-of-life studies and synthetic biology. A ligase ribozyme system was developed to concatenate short RNA fragments into long chains. The formation of coacervate microdroplets with the system enhances ribozyme rate and yield and imparts specific physical properties to the droplets.
Article
Biochemistry & Molecular Biology
V. Janett Olzog, Christiane Gaertner, Peter F. Stadler, Joerg Fallmann, Christina E. Weinberg
Summary: Self-cleaving ribozymes are catalytically active RNAs that are widely used in synthetic RNA devices and therapeutics. The targeted discovery of these ribozymes remains a challenge, but a new method called cyPhyRNA-seq has been developed to screen for ribozyme cleavage fragments. This approach allows for the global analysis of active self-cleaving ribozymes and has the potential to discover novel ribozymes in different organisms.
Article
Biochemistry & Molecular Biology
Sunny Sharma, Jun Yang, Selom K. Doamekpor, Ewa Grudizen-Nogalska, Liang Tong, Megerditch Kiledjian
Summary: Research on budding yeast has revealed that highly conserved 5'-3' exoribonucleases, Xrn1 and Rat1, physically interact with RNA 5' FAD caps and possess decapping activity. This activity was also found in human cells and in the bacterial enzyme RNase AM. The crystal structure of RNase AM provided details on the hydrolysis of the FAD cap. These findings suggest that 5'-3' exoribonucleases possess intrinsic hydrolysis and degradation activity towards noncanonical RNA caps.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Suvam Roy, Supratim Sengupta
Summary: The encapsulation of genetic material and formation of functionally diverse components inside compartments played a crucial role in the development of replicating protocells in an RNA world. Experimental evidence suggests that RNA replication inside lipid vesicles can lead to vesicular growth and division. The impact of such replication on the emergence of ribozymes inside protocells and their subsequent evolution remains uncertain.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Douglas Magde, Arvin Akoopie, Michael D. Magde, Ulrich F. Muller
Summary: In the early history of life, RNA may have had catalytic functions that have since disappeared. To explore this possibility, researchers conducted in vitro selection experiments to identify catalytically active RNAs. By using microfluidics to create nanodroplets for large-scale in emulsio selection experiments, they were able to produce stable emulsions ideal for their purposes.
Article
Chemistry, Organic
Wen-Chao Tu, Xing-Jie Zhang, Ying-Xin Zhao, Wei-Chi Chen, Xing-Yu Zhang, Chang-Lin Yang, Muhammad Aurang Zeb, Xiao-Li Li, Kaunda-Joseph Sakah, Rui-Han Zhang, Mei-Feng Liu, Wei-Lie Xiao
Summary: Compounds Wulfenioidins A-C (1-3), isolated from Orthosiphon wulfenioides, possess an unprecedented tricyclic skeleton with a 6/5-5 configuration and a unique spiro[4.4] nonane structure. Elucidation of their structures was achieved through X-ray diffraction, quantum chemical calculations, and extensive spectroscopic methods. Compound 3 exhibited potent inhibitory activity against the NLRP3 inflammasome and effectively blocked NLRP3 inflammasome-induced pyroptosis in J774A.1 cells by inhibiting caspase-1 activation, GSDMD-NT production, and IL-1 beta secretion.
ORGANIC CHEMISTRY FRONTIERS
(2023)
Article
Biochemistry & Molecular Biology
Shuntaro Takahashi, Naoki Sugimoto
Summary: Nucleic acids (DNA and RNA) play a representative role in storing genetic information, with RNA acting as ribozymes that catalyze biochemical reactions. This study investigated the effects of high pressure and temperature on RNA replication, finding that pressure accelerated the replication activity at higher temperatures. Molecular crowding by concentrated polyethylene glycol enhanced the replication activity further, suggesting that the prebiotic conditions for the RNA world involved high pressure and temperatures in a crowded environment.
BIOPHYSICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Melissa van Duelmen, Nils Muthmann, Andrea Rentmeister
Summary: Eukaryotic mRNAs can be modified with site-specific chemo-enzymatic methods to enhance immune response, offering a potential strategy for future therapeutic applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Mst. Ayesha Siddika, Hiroki Oi, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa
Summary: In this study, the construction of larger RNA assemblies based on ribozyme was achieved through the use of RNA oligomerization technology. The addition of specific interacting units enabled the assembly of ribozyme dimer, open-chain oligomers, and branched oligomers.
Article
Chemistry, Multidisciplinary
Junya Akagi, Takahiro Yamada, Kumi Hidaka, Yoshihiko Fujita, Hirohide Saito, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa
Summary: Ribozymes are attractive platforms for constructing nanoscale objects with biological functions. In this study, a dimeric form of the Tetrahymena group I ribozyme was designed and analyzed biochemically and observed directly by atomic force microscopy. The formation of the ribozyme dimer triggered trans-splicing reactions, resulting in a fluorescent RNA aptamer as the trans-splicing product.
APPLIED SCIENCES-BASEL
(2021)
Article
Biology
Xavier Portillo, Yu-Ting Huang, Ronald R. Breaker, David P. Horning, Gerald F. Joyce
Summary: A study has shown that through evolution, an RNA polymerase ribozyme underwent significant structural changes to develop a new tertiary structural element that improved catalytic activity. The evolving population stabilized the new structure, leading to the discovery of a new fitness locale and the potential for further enhancement of polymerase activity.
Article
Chemistry, Multidisciplinary
Yao Wang, Yueyao Wang, Dongfan Song, Xin Sun, Ze Zhang, Xintong Li, Zhe Li, Hanyang Yu
Summary: TNA is considered a potential RNA progenitor, and T8-6 is an RNA ligase TNA enzyme that catalyzes specific reactions and can be used to prepare functional RNAs, providing a new molecular tool for biotechnology.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemical Research Methods
Charis Du Cheyne, Yao Chen, Jurgen De Craene, Olivier Thas, Ward De Spiegelaere
Summary: Accurate tools for measuring RNA integrity are crucial for reliable gene expression data. A triplex dPCR 3':5' assay has been developed as a rapid and simple alternative to RT-qPCR for assessing RNA integrity in equine samples. This assay not only provides a straightforward analysis of mRNA integrity, but also its quantity.
ANALYTICAL BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Luigi D'Ascenzo, Filip Leonarski, Quentin Vicens, Pascal Auffinger
Article
Biochemistry & Molecular Biology
Luigi D'Ascenzo, Quentin Vicens, Pascal Auffinger
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemistry & Molecular Biology
Quentin Vicens, Estefania Mondragon, Francis E. Reyes, Philip Coish, Paul Aristoff, Judd Berman, Harpreet Kaur, Kevin W. Kells, Phil Wickens, Jeeffery Wilson, Robert C. Gadwood, Heinrich J. Schostarez, Robert K. Suto, Kenneth F. Blount, Robert T. Batey
ACS CHEMICAL BIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Quentin Vicens, Xavier Coumoul, Jean-Luc Souciet
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION
(2019)
Editorial Material
Biochemistry & Molecular Biology
Quentin Vicens
Article
Biochemistry & Molecular Biology
Rachel A. Jones, Anna-Lena Steckelberg, Quentin Vicens, Matthew J. Szucs, Benjamin M. Akiyama, Jeffrey S. Kieft
Summary: During flavivirus infection, cells generate sfRNAs that interfere with antiviral pathways, with conserved nucleotides supporting a unique fold through specific tertiary interactions. By studying xrRNA from Tamana bat virus (TABV), researchers discovered that different sequences and interactions can achieve the same overall architecture, providing insight into the diversity of this type of RNA and informing searches for undiscovered xrRNAs in viruses and beyond.
Article
Biochemistry & Molecular Biology
Anna-Lena Steckelberg, Quentin Vicens, David A. Costantino, Jay C. Nix, Jeffrey S. Kieft
Article
Microbiology
Matthew J. Szucs, Parker J. Nichols, Rachel A. Jones, Quentin Vicens, Jeffrey S. Kieft
Article
Multidisciplinary Sciences
Parker J. Nichols, Shaun Bevers, Morkos Henen, Jeffrey S. Kieft, Quentin Vicens, Beat Vogeli
Summary: The study demonstrates the binding of Z alpha protein to various RNA sequences and adoption of Z-RNA conformation, specifically with non-CpG sequences. This work contributes to proposing a model of how Z alpha could influence the RNA binding specificity of ADAR1.
NATURE COMMUNICATIONS
(2021)
Editorial Material
Biochemistry & Molecular Biology
Alan Herbert, Sergey Karapetyan, Maria Poptsova, Karen M. Vasquez, Quentin Vicens, Beat Vogeli
Summary: The biological function of left-handed Z-DNA and Z-RNA conformations, once controversial, is now supported by evidence of their association with disease outcomes and genetic instability, potentially leading to diseases such as cancer, and their role in inducing cell death during viral infection. The ABZ2021 meeting showcased cutting-edge science in this field and plans to reconvene in 2022.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Quentin Vicens, Jeffrey S. Kieft
Summary: Recent events have brought RNA research into the spotlight, igniting a new passion for understanding the diverse functions and structure of RNA. However, there is a misunderstanding of the foundational characteristics of RNA structure, often viewed as a single floppy strand. The purpose of this article is to help adjust mental models, better utilize RNA structural information, and provide suggestions for future efforts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Steve L. Bonilla, Quentin Vicens, Jeffrey S. Kieft
Summary: This study used cryo-EM to visualize a long-lived misfolded state in the folding pathway of Tetrahymena thermophila group I intron, revealing its structure and providing insights into RNA folding. The misfolded state contains incorrectly crossed strands, causing mispositioning of a critical catalytic domain that requires extensive refolding. The findings of this study have important implications for understanding RNA folding pathways.
Review
Biochemistry & Molecular Biology
Jeffrey B. Krall, Parker J. Nichols, Morkos A. Henen, Quentin Vicens, Beat Vogeli
Summary: Despite structural differences, both A-RNA and B-DNA adopt similar left-handed Z-conformations. RNA and DNA differ in their ability to adopt the Z-conformation in terms of hydration shells, chemical modifications, and junction structures. This review explores the similarities and differences of Z-DNA and Z-RNA, and extends the principles of Z-DNA to Z-RNA, taking into account the inherent differences of nucleic acids.
Review
Biochemistry & Molecular Biology
Parker J. Nichols, Jeffrey B. Krall, Morkos A. Henen, Beat Vogeli, Quentin Vicens
Summary: Z-RNA is a higher-energy, left-handed conformation of RNA with unknown function. Recent studies suggest that Z-RNA may play regulatory roles in the immune response. This article discusses the recognition of Z-RNA features in cellular RNAs, particularly retroelements, by a family of winged helix proteins, and their impact on host defense. The article also highlights the functional losses caused by mutations to specific Z-contacting amino acids. Knowledge gaps in this field are identified, and addressing them would greatly advance research in this area.
Article
Biochemistry & Molecular Biology
Quentin Vicens, Jeffrey S. Kieft
Summary: Viral RNA genomes may be small, but they make up for it in complexity with elements like xrRNAs, which resist degradation and play diverse roles during infection. Studies suggest that xrRNAs, found in a variety of RNA viruses, could be a crucial strategy for virus evolution and pathogenicity regulation.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
