Article
Virology
Han Wan, Rebecca L. Adams, Brett D. Lindenbach, Anna Marie Pyle
Summary: Researchers have reported a complete secondary structure map of the HCV RNA genome, revealing its folding in the cellular context and demonstrating the importance of many structures in the virus life cycle. Furthermore, this work provides a resource for future studies aimed at identifying therapeutic targets and conducting further mechanistic studies on this important human pathogen.
JOURNAL OF VIROLOGY
(2022)
Article
Biophysics
Gianmarco Lazzeri, Cristian Micheletti, Samuela Pasquali, Pietro Faccioli
Summary: By applying an enhanced path-sampling method to RNA, we successfully simulate the folding process and resolve the challenges of developing realistic force fields and sampling rare conformational transitions. The folding landscape of RNA is found to be more frustrated compared to small proteins with similar size and architecture. The predicted folding mechanisms of RNA are consistent with experiments and existing models. This method provides a promising platform to accurately study atomistic RNA folding trajectories and preserve sequence information.
BIOPHYSICAL JOURNAL
(2023)
Article
Multidisciplinary Sciences
Baocheng Liu, Yao He, Yaqiang Wang, He Song, Z. Hong Zhou, Juli Feigon
Summary: This study reveals the structure of human telomerase and its interaction with TPP1. The binding of TPP1 to TERT activates telomerase activity. Additionally, the study found that elements in TERT and TER involved in template and telomeric DNA handling are structurally similar to those in Tetrahymena telomerase, providing unique insights into the mechanism of telomerase activity.
Review
Biochemistry & Molecular Biology
Maria Rubtsova, Olga Dontsova
Summary: Telomerase RNA plays a crucial role in maintaining telomere length in eukaryotic cells and has functions beyond its role as a template for telomeric repeat synthesis and structural scaffold for telomerase. Investigation into its biogenesis and turnover, as well as structural data, has revealed additional functions of telomerase RNA not directly related to telomerase activity.
Article
Biochemical Research Methods
Mubarak Umar, Chun-Yin Chan, Chun Kit Kwok
Summary: The RNA G-quadruplex (rG4)-SELEX method generates L-RNA aptamers to target rG4 structures, effectively suppressing G-quadruplex-mediated interactions. This Protocol Extension improves aptamer discovery speed, showcasing the utility of L-RNA aptamers. The detailed procedure expands the current rG4 toolkit, facilitating exploration of innovative rG4-related applications.
Article
Biochemistry & Molecular Biology
Tatiana Pakhomova, Maria Moshareva, Daria Vasilkova, Timofey Zatsepin, Olga Dontsova, Maria Rubtsova
Summary: Telomerase RNA (hTR) undergoes distinct pathways and cellular localization during its biogenesis, resulting in different functions. ZFC3H1, specifically, participates in the biogenesis of hTR by being involved in the polyadenylated RNA degradation mechanism. These findings are crucial for understanding the generation of hTR and exploring potential therapeutic targets.
Review
Biochemistry & Molecular Biology
Jian Qin, Chantal Autexier
Summary: Telomere maintenance is crucial for genome integrity and replicative capacity in eukaryotic cells. Telomerase, composed of a reverse transcriptase and an RNA component, catalyzes telomere synthesis. While the sequence and structural domains of human telomerase RNA (hTR) have been extensively characterized, the regulation of hTR transcription, maturation, and localization remains not fully understood. This review focuses on recent breakthroughs in uncovering the mechanisms of hTR maturation and localization.
Article
Chemistry, Physical
Adam K. Nijhawan, Arnold M. Chan, Darren J. Hsu, Lin X. Chen, Kevin L. Kohlstedt
Summary: This perspective discusses the integration of experimental signals with molecular dynamics models to refine protein ensemble structures. It explores the use of experimental restraints in disordered protein systems and proposes strategies to find kinetic pathways between refined structures.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Multidisciplinary
Diana Muller, Irene Bessi, Christian Richter, Harald Schwalbe
Summary: The folding kinetics of RNA G4 and DNA G4 differ significantly during K+-induced folding, mainly due to differences in their folded conformations, especially regarding the chi angle preferences. Modified DNA G4 can achieve faster folding kinetics and monomorphic conformations similar to RNA G4 by adjusting the chi angle.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Multidisciplinary Sciences
Benjamin W. Wormald, Nicolas Moser, Nandita M. deSouza, Katerina-Theresa Mantikas, Kenny Malpartida-Cardenas, Ivana Pennisi, Thomas E. J. Ind, Katherine Vroobel, Melpomeni Kalofonou, Jesus Rodriguez-Manzano, Pantelis Georgiou
Summary: This study demonstrates the efficacy of a handheld Lab-on-Chip device for detecting cervical cancer from biopsy samples. The device uses ISFET sensors and LAMP assays to amplify and detect HPV DNA and hTERT mRNA. The results show that these markers can be used for cervical cancer detection in tissue samples.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Mojtaba Mortazavi, Masoud Torkzadeh-Mahani, Mehdi Rahimi, Mahmood Maleki, Safa Lotfi, Ali Riahi-Madvar
Summary: The impact of synonymous mutations on the thermostability of luciferase was investigated. It was found that synonymous mutations can slightly increase the thermal stability of the mutant enzyme, possibly by altering the translation rate and causing slight structural changes. The results suggest that thermostability mainly originates from hydrophobic interactions.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Multidisciplinary Sciences
Anna Hojka-Osinska, Aleksander Chlebowski, Joanna Grochowska, Ewelina P. Owczarek, Kamila Affek, Kamila Klosowska-Kosicka, Roman J. Szczesny, Andrzej Dziembowski
Summary: Processive exoribonucleases play a crucial role in RNA decay and have complex genetic interactions with diverse pathways of RNA metabolism. Functional differences between nuclear DIS3 and cytoplasmic DIS3L in RNA metabolism were identified in human cells.
Article
Chemistry, Physical
Xiaojun Xu, Lei Jin, Liangxu Xie, Shi-Jie Chen
Summary: This article describes an alternative approach to predicting cotranscriptional RNA folding by zooming in and out of the RNA folding energy landscape. The application of this approach to specific RNAs shows promising results and provides new insights into biologically significant conformational switches and pathways.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
Tingting Han, Yu-Qian Geng, Min Zhang, Yue Cao, Jun-Jie Zhu
Summary: In this study, ultrathin tetraphenylethylene-active tris(bipyridine)ruthenium(II) derivative nanosheets were synthesized through a protein-assisted self-assembly strategy, realizing aggregation-induced enhanced electrochemiluminescence (ECL) and excellent water-dispersion. The proposed method serves as a highly sensitive biosensor for the detection of human telomerase RNA.
Article
Medicine, Research & Experimental
Farkhad Maksudov, Evgenii Kliuchnikov, Daniel Pierson, M. L. Ujwal, Kenneth A. Marx, Arani Chanda, Valeri Barsegov
Summary: This article investigates the structure-function relationships of PMOs, which are therapeutic RNA mimicking molecules. By utilizing various techniques, such as circular dichroism and molecular dynamics simulations, the solution structures of PMOs were determined. The study reveals that PMOs adopt non-canonical, partially helical, and stable folded structures, and exhibit thermodynamic stability and concentration-dependent viscosity properties.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)