Article
Biotechnology & Applied Microbiology
Vaclav Brazda, Otilia Porubiakova, Alessio Cantara, Natalia Bohalova, Jan Coufal, Martin Bartas, Miroslav Fojta, Jean-Louis Mergny
Summary: The study identified multiple potential G-quadruplex forming sequences in the G4-EA-H1N1 genomes, which could serve as potential therapeutic targets.
Article
Virology
Lu Lv, Leiliang Zhang
Summary: Monkeypox virus (MPXV), a member of Orthopoxvirus, has caused a Public Health Emergency of International Concern with a significant increase in cases and geographic range in 2022. This study aims to characterize the G-quadruplex (GQ) secondary structures encoded by MPXV and evaluate the binding and stabilization abilities of GQ ligands. The results demonstrate the presence of MPXV GQ and suggest GQs could be potential antiviral targets, providing a new approach for MPXV therapy.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Biochemical Research Methods
Marco Caterino, Katrin Paeschke
Summary: The nucleic acid structure known as G-quadruplex (G4) plays a significant role in nucleic acid-based mechanisms that impact cellular processes. DNA G4 is well-studied, while RNA G4 is gaining attention for its role in cellular homeostasis. Proper regulation of G4 structures within cells is crucial, and helicases are important in resolving them. However, only a few rG4 unwinding helicases have been identified and characterized so far.
Article
Biochemistry & Molecular Biology
Poulomi Das, Khac Huy Ngo, Fernaldo Richtia Winnerdy, Arijit Maity, Blaz Bakalar, Yves Mechulam, Emmanuelle Schmitt, Anh Tuan Phan
Summary: This study investigates the adaptability of left-handed G4 structures towards the presence of bulges, presenting the structural characteristics of left-handed G4s accommodating varying numbers of bulges. Bulges in left-handed G4s exhibit distinct features compared to those in right-handed G4s, and elucidation of the intricate structural details may enhance understanding of the potential roles and limitations of these unique structures.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Ye Teng, Ming Zhu, Zhidong Qiu
Summary: Repeat expansions are the main genetic cause of various neurodegeneration diseases. G-rich repeat sequences, such as CGG and GGGGCC, form functional G-quadruplexes and play important roles in bioprocesses. This review provides an overview of the contribution of G-quadruplex in repeat expansion disorders and summarizes the related mechanisms, including genetic instabilities, toxic RNA foci, and protein/peptide dysfunction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Ahyun Son, Veronica Huizar Cabral, Zijue Huang, Theodore J. Litberg, Scott Horowitz
Summary: Recent research has found that G-quadruplex (G4) nucleic acids are effective in preventing protein aggregation and improving protein folding in Escherichia coli. Through in vitro protein folding experiments, it was discovered that G4s can accelerate protein folding by rescuing kinetically trapped intermediates. Time-course folding experiments in E. coli further showed that G4s primarily enhance protein folding quality instead of preventing protein aggregation. This study suggests that nucleic acids and ATP-independent chaperones may play important roles in determining the folding fate of proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Elishiba Muturi, Fei Meng, Huan Liu, Mengwei Jiang, Hongping Wei, Hang Yang
Summary: The study found that functional PQSs in the ASFV genome, which can form stable G4s in the presence of K+ and be stabilized by G4 ligands such as NMM and PDS, could serve as potential targets for antiviral drugs. Experimental results showed that NMM and PDS can significantly suppress the expression of ASFV genes and inhibit the replication of ASFV in Porcine Alveolar Macrophages.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Ilaria Frasson, Valentina Pirota, Sara N. Richter, Filippo Doria
Summary: G-quadruplexes (G4s) are stable non-canonical structures in human cells that regulate key cellular processes. They can form high-order structures through multimerization, and play important roles in genome replication, transcription, and translation.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Rongxin Zhang, Yajun Liu, Xingxing Zhang, Ke Xiao, Yue Hou, Hongde Liu, Xiao Sun
Summary: The study profiles and depicts RNA G-quadruplexes in the human transcriptome using DMS-seq and bioinformatics pipeline, revealing their significant association with immune pathways and COVID-19-related gene sets. The bioinformatics analysis also suggests potential regulatory functions of G-quadruplexes on miRNA targeting at the whole transcriptome level. Moreover, G-quadruplexes are found to be depleted in putative, but not real, PAS-strong poly(A) sites, weakening their likelihood of being actual cleaved sites.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Cell Biology
Aaron Antcliff, Louise D. McCullough, Andrey S. Tsvetkov
Summary: G-Quadruplex (G4) DNA and RNA are secondary nucleic acid structures that play multiple roles in cellular processes. DHX36, a helicase, unwinds both G4 DNA and G4 RNA, regulating transcription, genomic stability, telomere maintenance, translation, and RNA metabolism in the process. This review explores the potential role of DHX36 in neuronal development and neurodegeneration, as well as discussing the possible functions of G4s and DHX36 in the aging brain.
Article
Multidisciplinary Sciences
Ilias Georgakopoulos-Soares, Guillermo E. Parada, Hei Yuen Wong, Ragini Medhi, Giulia Furlan, Roberto Munita, Eric A. Miska, Chun Kit Kwok, Martin Hemberg
Summary: This study reveals the enrichment of G4 motifs near splice junctions, suggesting their regulatory role in RNA stability and splicing. G4 motifs play important roles in exon skipping and inclusion, and are associated with multiple RNA binding proteins. Furthermore, G4 motifs show strong enrichment at splice sites in mammals and birds, indicating the evolutionary conservation of this splice regulatory mechanism.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Sara Illodo, Cibran Perez-Gonzalez, Ramiro Barcia, Flor Rodriguez-Prieto, Wajih Al-Soufi, Mercedes Novo
Summary: Guanine quadruplexes (G4s) are four-stranded structures formed within guanine-rich DNA and RNA sequences that play a crucial role in biological processes. The recent discovery of G4 structures within mitochondrial DNA has brought significant advancements to the field. This study investigates the relevant G4 structures formed within CSB II and reveals the stability differences among different sequences.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Analytical
Xu Lu, Xianhua Wu, Shi Kuang, Chunyang Lei, Zhou Nie
Summary: This study established a G4 probe design strategy and developed ThT-NA, a red fluorescent benzothiazole derivative for detecting and imaging G4 structures in living cells and tissue samples. ThT-NA shows excellent photophysical properties and can reveal the distribution of RNA G4 in cells and differentiate the cell cycle by monitoring changes in RNA G4 folding.
ANALYTICAL CHEMISTRY
(2022)
Review
Genetics & Heredity
Fangyuan Li, Jiang Zhou
Summary: Non-coding RNAs (ncRNAs), particularly lncRNAs and miRNAs, play a significant role in gene expression regulation, and their interplay with proteins and other RNAs is mediated by higher-order structures such as RNA G-quadruplexes (rG4s). The formation of rG4s, which are predicted in guanine-rich sequences, is closely associated with various human diseases. Understanding the dynamic balance between rG4s and RNA stem-loop/hairpin structures, as well as the interaction between ncRNAs and interactors, is crucial for modulating gene expression and disease progression. The folding of ncRNAs into the appropriate three-dimensional structure is of critical importance and opens up new therapeutic possibilities for diseases associated with potential-G4-containing-ncRNAs.
JOURNAL OF MOLECULAR MEDICINE-JMM
(2023)
Article
Biochemistry & Molecular Biology
Yaqin Li, Yance Zhu, Yue Wang, Yi Feng, Dongliang Li, Shuai Li, Panpan Qin, Xia Yang, Lu Chen, Jun Zhao, Chao Zhang, Yongtao Li
Summary: Porcine epidemic diarrhea virus (PEDV) is a significant threat to the global pig industry, but there is a lack of accurate targets for anti-PEDV drugs. This study identified G-quadruplex structures in the PEDV genome and showed that G4-specific compounds can inhibit the virus at the replication and protein expression stages. These findings provide new insights into developing antiviral drugs targeting PEDV RNA G-quadruplexes.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Multidisciplinary Sciences
Marta Szabat, Tomasz Pedzinski, Tomasz Czapik, Elzbieta Kierzek, Ryszard Kierzek
Review
Biochemistry & Molecular Biology
Marta Szabat, Ryszard Kierzek
Article
Biochemistry & Molecular Biology
Agnieszka Ludwikow, Agata Ciesla, Anna Kasprowicz-Maluski, Filip Mitula, Malgorzata Tajdel, Lukasz Galganski, Piotr A. Ziolkowski, Piotr Kubiak, Arleta Maleck, Aneta Piechalak, Marta Szabat, Alicja Gorska, Maciej Dabrowski, Izabela Ibragimow, Jan Sadowski
Article
Multidisciplinary Sciences
Marta Szabat, Dorota Gudanis, Weronika Kotkowiak, Zofia Gdaniec, Ryszard Kierzek, Anna Pasternak
Article
Multidisciplinary Sciences
Marta Szabat, Elzbieta Kierzek, Ryszard Kierzek
SCIENTIFIC REPORTS
(2018)
Article
Biochemistry & Molecular Biology
Marta Szabat, Martina Prochota, Ryszard Kierzek, Elzbieta Kierzek, David H. Mathews
Summary: RNA folding free energy change parameters are used to predict RNA secondary structure and design RNA sequences. This study derived a full set of nearest neighbor terms for RNA including N-6-methyladenosine (m(6)A) and tested the model using optical melting experiments. The results showed that the parameters for m(6)A are as accurate as those for A, and the refined parameter set enables prediction of RNA secondary structures with m(6)A.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Elzbieta Kierzek, Xiaoju Zhang, Richard M. Watson, Scott D. Kennedy, Marta Szabat, Ryszard Kierzek, David H. Mathews
Summary: This study addresses the issue of predicting the secondary structure of RNA with covalently modified nucleotides. The researchers developed software and determined thermodynamic parameters to enable the prediction of secondary structure for sequences containing N-6-methyladenosine (m(6)A). The study also revealed the effects of N-6-methylation on folding stability in different contexts.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Maria Nalewaj, Marta Szabat
Summary: The relationship between conserved structural motifs and their biological function in the virus replication cycle is a subject of interest to researchers worldwide. Understanding RNA structure is crucial for understanding RNA function, making technological advancements in high-throughput RNA structure analysis and development of new methods highly important. In this mini review, the authors discuss the structural elements of viral genomes and methods used for RNA structure prediction and characterization. Examples from recent literature, including studies on SARS-CoV-2 and IAV, are highlighted to emphasize the importance of understanding viral genome architecture in discovering the structure-function relationship and potential antiviral therapeutics.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Immunology
Amanda Fabra-Garcia, Sophia Hailemariam, Roos M. de Jong, Kirsten Janssen, Karina Teelen, Marga van de Vegte-Bolmer, Geert-Jan van Gemert, Danton Ivanochko, Anthony Semesi, Brandon McLeod, Martijn W. Vos, Marloes H. C. de Bruijni, Judith M. Bolscher, Marta Szabat, Stefanie Vogt, Lucas Kraft, Sherie Duncan, Moses R. Kamya, Margaret E. Feeney, Prasanna Jagannathan, Bryan Greenhouse, Koen J. Dechering, Robert W. Sauerwein, C. Richter King, Randall S. MacGill, Teun Bousema, Jean-Philippe Julien, Matthijs M. Jore
Summary: Malaria transmission-blocking vaccines aim to induce antibodies that interrupt parasite development in mosquitoes, providing a tool for malaria control. We isolated and characterized 81 human monoclonal antibodies specific to the Pfs48/45 protein, a leading vaccine candidate. Potent antibodies targeting specific domains achieved high transmission-reducing activity. Co-crystal structures identified protective epitopes, providing insight for refined vaccine design.
Review
Microbiology
Marta Szabat, Dagny Lorent, Tomasz Czapik, Maria Tomaszewska, Elzbieta Kierzek, Ryszard Kierzek