Article
Multidisciplinary Sciences
Yu Sun, Laura Abriola, Rachel O. Niederer, Savannah F. Pedersen, Mia M. Alfajaroe, Valter Silva Monteiro, Craig B. Wilen, Ya-Chi Ho, Wendy Gilbert, Yulia Surovtseva, Brett D. Lindenbach, Junjie U. Guo
Summary: The study found that merafloxacin can inhibit -1 PRF activity of SARS-CoV-2 and is similarly effective on other betacoronaviruses.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Anna A. Mikkelsen, Feng Gao, Elizabeth Carino, Sayanta Bera, Anne E. Simon
Summary: Plus-strand RNA viruses often use -1 programmed ribosomal frameshifting to maximize their coding capacity. This study discovered six tertiary interactions associated with the FSE of citrus yellow vein associated virus, which covers three-quarters of the genomic RNA. Two long-distance interactions connect sequences on opposite sides of the critical FSE central stem, destabilizing the FSE and potentially allowing ribosome progression through a disrupted upstream FSE.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Shuting Yan, Qiyao Zhu, Jenna Hohl, Alex Dong, Tamar Schlick
Summary: The frameshifting RNA element (FSE) in coronaviruses (CoVs) plays a crucial role in regulating the viral protein production and is considered as a potential drug candidate. By analyzing the conformational landscapes of FSEs with increasing sequence lengths, researchers have identified competing stems and topological changes that contribute to frameshifting efficiency. This study provides insights into the structural evolution of FSEs and the potential for therapeutic interventions against a broad spectrum of CoVs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Multidisciplinary
Tamar Schlick, Qiyao Zhu, Abhishek Dey, Swati Jain, Shuting Yan, Alain Laederach
Summary: The FSE of SARS-CoV-2 is a promising target for Covid-19 therapy, but its structures and mechanisms pose challenges. Research suggests that the FSE may adopt multiple conformations, including the 3-stem H-type and HL-type pseudoknots, as well as the unknotted 3-way junction RNA. These findings advance our understanding of the virus frameshifting process and lifecycle, indicating potential avenues for therapeutic intervention.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Virology
Chris H. Hill, Ian Brierley
Summary: Protein synthesis is a crucial process for gene expression, and programmed ribosomal frameshifting is a strategy used by RNA viruses to control the levels of viral proteins. Recent studies have revealed the structural diversity and complexity of this mechanism.
ANNUAL REVIEW OF VIROLOGY
(2023)
Article
Multidisciplinary Sciences
Gabriel Demo, Howard B. Gamper, Anna B. Loveland, Isao Masuda, Christine E. Carbone, Egor Svidritskiy, Ya-Ming Hou, Andrei A. Korostelev
Summary: The study found that the ribosome and EF-G cooperate to induce +1 frameshifting during tRNA-mRNA translocation.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Howard Gamper, Yujia Mao, Isao Masuda, Henri McGuigan, Gregor Blaha, Yuhong Wang, Shoujun Xu, Ya-Ming Hou
Summary: By utilizing the high-efficiency +1-frameshifting SufB2 tRNA, it was discovered that there are two explorations of +1 frameshifting in one elongation cycle of protein synthesis, with the majority occurring during translocation from the A site to the P site. This research demonstrates that the ribosome itself plays a critical role in determining changes in the reading frame, providing insights into the mechanistic parallel of +1 frameshifting with -1 frameshifting.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Howard Gamper, Yujia Mao, Isao Masuda, Henri McGuigan, Gregor Blaha, Yuhong Wang, Shoujun Xu, Ya-Ming Hou
Summary: The study investigates the mechanism of +1 frameshifting during translation using the SufB2 tRNA with an extra nucleotide in the anticodon loop. It reveals that +1 frameshifting occurs twice in one elongation cycle, with the majority of the shift happening during translocation from the A site to the P site, and a fraction occurring within the P site upon A site occupancy in the +1 frame. This work suggests that the ribosome itself plays a crucial role in determining the reading frame changes during protein synthesis.
NUCLEIC ACIDS RESEARCH
(2021)
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)
Review
Microbiology
Wesley D. Penn, Suchetana Mukhopadhyay
Summary: The constrained nature of viral genomes has allowed -1 Programmed Ribosomal Frameshifting (-1 PRF) to thrive. Traditional assays often overlook the impact of genomic and cellular context on -1 PRF, while sequence elements proximal to the Minimal Frameshifting Element (MFE) can significantly affect -1 PRF rates. Additionally, cellular context such as tRNA abundance, miRNAs, and immune response elements can also impact -1 PRF.
Article
Multidisciplinary Sciences
Howard Gamper, Haixing Li, Isao Masuda, D. Miklos Robkis, Thomas Christian, Adam B. Conn, Gregor Blaha, E. James Petersson, Ruben L. Gonzalez, Ya-Ming Hou
Summary: The study investigates the translation of quadruplet codons by a +1-frameshifting tRNA SufB2, revealing that SufB2 initially uses triplet anticodon-codon pairing in the 0-frame to decode the quadruplet codon before shifting to the +1-frame during tRNA-mRNA translocation. The frameshifting mechanism of SufB2 involves perturbation of a crucial ribosome conformational change, highlighting the potential for engineering specific ribosome conformational changes to enhance genome recoding efficiency.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Xia Zhou, Zhihua Du, Xiaolan Huang
Summary: Researchers have proposed a computational method to identify a certain kind of long-range intra-molecular RNA-RNA interactions involving loop nucleotides of a hairpin loop. Using this method, they discovered a potential long-range intra-molecular RNA-RNA interaction within HIV-1 genomic mRNA. The interaction is mediated by a kissing loop structure between two stem-loops of the previously reported secondary structure of the entire HIV-1 genome.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Jing-Jie Su, Xing-liang Xu, Ting-Ting Sun, Yu Shen, Yan Wang
Summary: By using a helix-based transition rate model and master equation, the study investigated the refolding and cotranscriptional folding processes of RNA pseudoknots, revealing differences in final states and intermediates between refolding and cotranscriptional folding. These findings provide insights into the cotranscription folding of hTR pseudoknot with different rates.
CHEMICAL PHYSICS LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Jiahui Zhang, Ashkan Fakharzadeh, Christopher Roland, Celeste Sagui
Summary: Friedreich's ataxia is associated with noncanonical nucleic acid structures that emerge when GAA:TTC repeats in the FXN gene expand beyond a critical number of repeats. In this study, an in silico investigation of all possible triplexes formed by attaching a third RNA strand to an RNA:RNA or DNA:DNA duplex was conducted. The results provide insights into the stability and structural characteristics of triplexes based on the GAA and TTC/UUC sequences, contributing to the understanding of trinucleotide repeats and the triggers for expansion.
Article
Biochemistry & Molecular Biology
Xiaolan Huang, Zhihua Du
Summary: Pseudoknots play important roles in RNA viruses, such as stimulating ribosomal frameshifting or stop codon readthrough. Recent studies have confirmed the significance of three-stemmed pseudoknots in SARS-CoV-2 and related coronaviruses. Additional complex pseudoknots with various structural elements have also been identified, expanding our understanding of their regulatory functions in different virus families.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Maike M. K. Hansen, Sabine Paffenholz, David Foschepoth, Hans A. Heus, Julian Thiele, Wilhelm T. S. Huck
Article
Nanoscience & Nanotechnology
Maike M. K. Hansen, Lenny H. H. Meijer, Evan Spruijt, Roel J. M. Maas, Marta Ventosa Rosquelles, Joost Groen, Hans A. Heus, Wilhelm T. S. Huck
NATURE NANOTECHNOLOGY
(2016)
Article
Chemistry, Multidisciplinary
Jian Yang, Yasuhito Shimada, Rene C. L. Olsthoorn, B. Ewa Snaar-Jagalska, Herman P. Spaink, Alexander Kros
Article
Chemistry, Multidisciplinary
Swapneel R. Deshpande, Roel Hammink, Rajat K. Das, Frank H. T. Nelissen, Kerstin G. Blank, Alan E. Rowan, Hans A. Heus
ADVANCED FUNCTIONAL MATERIALS
(2016)
Review
Chemistry, Physical
Frank H. T. Nelissen, Marco Tessari, Sybren S. Wijmenga, Hans A. Heus
PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
(2016)
Article
Biochemical Research Methods
Maike M. K. Hansen, Marta Ventosa Rosquelles, Maaruthy Yelleswarapu, Roel J. M. Maas, Aafke J. van Vugt-Jonker, Hans A. Heus, Wilhelm T. S. Huck
ACS SYNTHETIC BIOLOGY
(2016)
Article
Chemistry, Multidisciplinary
Jian Yang, Azadeh Bahreman, Geert Daudey, Jeroen Bussmann, Rene C. L. Olsthoorn, Alexander Kros
ACS CENTRAL SCIENCE
(2016)
Article
Nanoscience & Nanotechnology
Esra te Brinke, Joost Groen, Andreas Herrmann, Hans A. Heus, German Rivas, Evan Spruijt, Wilhelm T. S. Huck
NATURE NANOTECHNOLOGY
(2018)
Article
Biochemical Research Methods
Clara L. van Emmerik, Ivana Gachulincova, Vincenzo R. Lobbia, Mark A. Daniels, Hans A. Heus, Abdenour Soufi, Frank H. T. Nelissen, Hugo van Ingen
ANALYTICAL BIOCHEMISTRY
(2020)
Article
Biochemical Research Methods
Mahesh A. Vibhute, Mark H. Schaap, Roel J. M. Maas, Frank H. T. Nelissen, Evan Spruijt, Hans A. Heus, Maike M. K. Hansen, Wilhelm T. S. Huck
ACS SYNTHETIC BIOLOGY
(2020)
Article
Chemistry, Medicinal
Frank H. T. Nelissen, Wenny J. M. Peeters, Timo P. Roelofs, Anika Nagelkerke, Paul N. Span, Hans A. Heus
Summary: The study used 3D Cell-SELEX to generate aptamers for specific binding and treatment of breast cancer cells, identifying ten abundant aptamer families with specific structures that selectively bind to SKBR3 cells. The aptamer polymers showed specific binding and efficient internalization into SKBR3 spheroids, and drug-loaded polymers were effective in killing SKBR3 breast cancer cells. This innovative approach holds promise for diagnosing and treating breast cancer.
Article
Biochemical Research Methods
Andrei Sakai, Christopher R. Deich, Frank H. T. Nelissen, Aafke J. Jonker, Daniela M. de C. Bittencourt, Christopher P. Kempes, Kim S. Wise, Hans A. Heus, Wilhelm T. S. Huck, Katarzyna P. Adamala, John Glass
Summary: This article describes attempts to use a Mycoplasma bacterium-based CFE system for cell-free gene expression, but found persistently high ribonuclease activity in the lysates, leading to failure of gene expression. Further investigation revealed that Mycoplasma cells have surface-associated RNase activity, though it is not clear which gene encodes the RNase.
Article
Chemistry, Multidisciplinary
Zhaobao Zhang, Chunling Tang, Roel Hammink, Frank H. T. Nelissen, Hans A. Heus, Paul H. J. Kouwer
Summary: T-cell acute lymphoblastic leukemia leads to an imbalance of immature white blood cells in the bone marrow, with significant undesired side effects associated with traditional chemotherapy treatment. Decorating polyisocyanopeptide scaffolds with the aptamer sgc8c has shown to inhibit proliferation through G0/G1-phase arrest, providing a potential avenue for future therapeutic strategies.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Swapneel R. Deshpande, Roel Hammink, Frank H. T. Nelissen, Alan E. Rowan, Hans A. Heus
Article
Chemistry, Multidisciplinary
Liping Qiu, Florian Wimmers, Jorieke Weiden, Hans A. Heus, Jurjen Tel, Carl G. Figdor
CHEMICAL COMMUNICATIONS
(2017)