Article
Biochemical Research Methods
Masanobu Nagano, Sosuke Nakano, Keitaro Yoshimoto
Summary: This study presents a method for identifying deoxyguanines (dGs) that form antiparallel G4 using optical spectroscopy, called dG-to-dT scanning. By comparing the spectra at all dG positions, the most strongly involved dGs in forming antiparallel G4 can be determined. This method provides a simple and robust approach for understanding the formation of de novo antiparallel G4.
ANALYTICAL BIOCHEMISTRY
(2022)
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
Chemistry, Multidisciplinary
Iva Kejnovska, Petr Stadlbauer, Lukas Trantirek, Daniel Renciuk, Martin Gajarsky, Daniel Krafcik, Jan Palacky, Klara Bednarova, Jiri Sponer, Jean-Louis Mergny, Michaela Vorlickova
Summary: Guanine quadruplexes (G4s) are noncanonical forms of nucleic acids that are frequently found in genomes. The stability of G4s depends on the number of G-tetrads. Experiment and theoretical approaches have shown that a solitary two-tetrad parallel DNA G4 is not thermodynamically stable and requires additional interactions through capping residues.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Analytical
Wen Lei, Jun Hu, Hong-Yuan Chen, Jing-Juan Xu
Summary: Accurate measurements of G-quadruplexes (G4s) and their interactions with metal ions and ligands under physiological conditions are crucial for understanding their biological roles and developing antitumor drugs. This study demonstrated for the first time that G4 ions can be directly released from common biochemical buffers and analyzed using mass spectrometry without non-specific adduction. The intermediate complexes of G4s with mixed di-cation coordination were successfully observed, and their structures were revealed by circular dichroism spectra.
ANALYTICAL CHEMISTRY
(2022)
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
Biochemistry & Molecular Biology
Sabrina Dallavalle, Luce M. Mattio, Roberto Artali, Loana Musso, Anna Avino, Carme Fabrega, Ramon Eritja, Raimundo Gargallo, Stefania Mazzini
Summary: The study revealed the DNA binding properties of curaxin CBL0137 with G-quadruplex, providing insights for the design of novel selective DNA-targeting curaxin analogues.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Medicinal
Weronika Kotkowiak, Carolina Roxo, Anna Pasternak
Summary: This article analyzed and compared the physicochemical and biological properties of G-quadruplex forming oligonucleotides in RNA and DNA series. The intermolecular G-quadruplexes vary in loop length, number of G-tetrads, and homogeneity of the core. The study found that slight variations in sequence can cause changes in G-quadruplex properties. DNA G-quadruplexes are less thermally stable than RNA counterparts, more topologically diversified, and better candidates as inhibitors of cancer cells proliferation. The most efficient antiproliferative activity was observed for two DNA G-quadruplexes with unperturbed core and lower content of thymidine residues within the loops, reducing cell viability up to 65% and 33% for HeLa and MCF-7 cell lines, respectively.
ACS MEDICINAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Medicinal
Weronika Kotkowiak, Carolina Roxo, Anna Pasternak
Summary: This article analyzes and compares the physicochemical and biological properties of sequence-related G-quadruplex forming oligonucleotides in RNA and DNA series. The intermolecular G-quadruplexes vary in loop length, number of G-tetrads, and homogeneity of the core. The study finds that even slight variations in sequence can cause changes in G-quadruplex properties. DNA G-quadruplexes are less thermally stable than RNA counterparts but are more effective as inhibitors of cancer cell proliferation.
ACS MEDICINAL CHEMISTRY LETTERS
(2023)
Review
Pharmacology & Pharmacy
Andrea Criscuolo, Ettore Napolitano, Claudia Riccardi, Domenica Musumeci, Chiara Platella, Daniela Montesarchio
Summary: G-quadruplexes are important targets for anticancer/antiviral therapies. Over 3000 small-molecule ligands have been described, which exert their activity by damaging telomeres or altering gene expression in cancer cells and viruses. Detailed knowledge on the interactions between ligands and G-quadruplexes has been obtained through NMR and crystallographic studies.
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
Biochemistry & Molecular Biology
Valeria Libera, Francesca Ripanti, Caterina Petrillo, Francesco Sacchetti, Javier Ramos-Soriano, Maria Carmen Galan, Giorgio Schiro, Alessandro Paciaroni, Lucia Comez
Summary: Guanine-rich DNA sequences can form non-canonical nucleic acid structures called G-quadruplexes (G4s), which have implications in various fields. Ligands that interact with G4s have attracted attention for their potential in medical therapies and nanodevice applications. This study investigates the manipulation of the secondary structure of a human telomeric G4 sequence by two photosensitive ligands, demonstrating their different effects on G4 unfolding and stabilization.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
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)
Article
Multidisciplinary Sciences
Junyeop Lee, Keewon Sung, So Young Joo, Jun-Hyeon Jeong, Seong Keun Kim, Hyunsook Lee
Summary: The dynamic interaction between BRCA2 and telomeric G-quadruplex (G4) plays a crucial role in telomere replication. Binding of BRCA2 remodels telomeric G4 structure, allowing the restart of stalled replication forks driven by G4 and preventing telomere breakdown.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Wei Long, Bo-Xin Zheng, Ying Li, Xuan-He Huang, Dan-Min Lin, Cui-Cui Chen, Jin-Qiang Hou, Tian-Miao Ou, Wing-Leung Wong, Kun Zhang, Yu-Jing Lu
Summary: This study reports a new approach of designing small molecules based on a non-selective thiazole orange scaffold to target G4 structures with improved selectivity. The ligands establish multi-site interactions with flanking residues and loops of the G4 motif, and demonstrate antitumor activity in cancer cells.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Dana Beseiso, Erin Chen, Sawyer E. McCarthy, Kailey N. Martin, Elizabeth P. Gallagher, Joanne Miao, Liliya A. Yatsunyk
Summary: G-quadruplexes (GQs) are DNA structures composed of stabilized G-tetrads. This study investigates telomeric DNA variants from Tetrahymena thermophila and solves the crystal structure of two variants, revealing new GQ structures. The results expand our understanding of telomeric repeats and GQs in general.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Maja Marusic, Hisae Tateishi-Karimata, Naoki Sugimoto, Janez Plavec
Article
Chemistry, Multidisciplinary
Stacey L. Edwards, Vasanthanathan Poongavanam, Jagat R. Kanwar, Kislay Roy, Kristine M. Hillman, Neerati Prasad, Rikke Leth-Larsen, Michael Petersen, Maja Marusic, Janez Plavec, Jesper Wengel, Rakesh N. Veedu
CHEMICAL COMMUNICATIONS
(2015)
Review
Biochemical Research Methods
Lorenzo Baronti, Hampus Karlsson, Maja Marusic, Katja Petzold
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2018)
Article
Chemistry, Multidisciplinary
Sabina Bozic Abram, Maja Marusic, Martina Lenarcic Zivkovic, Jasna Brcic, Janez Plavec
CROATICA CHEMICA ACTA
(2018)
Article
Biochemistry & Molecular Biology
Selimcan Azizoglu, Riza Kizilel, Maja Marusic, Ibrahim Halil Kavakli, Burak Erman, Seda Kizilel
JOURNAL OF MOLECULAR RECOGNITION
(2013)
Article
Biochemistry & Molecular Biology
Maja Marusic, Rakesh N. Veedu, Jesper Wengel, Janez Plavec
NUCLEIC ACIDS RESEARCH
(2013)
Review
Biochemistry & Molecular Biology
Maja Marusic, Judith Schlagnitweit, Katja Petzold
Article
Biochemistry & Molecular Biology
Maja Marusic, Janez Plavec
Article
Biochemistry & Molecular Biology
Sara Lago, Matteo Nadai, Emanuela Ruggiero, Martina Tassinari, Maja Marusic, Beatrice Tosoni, Ilaria Frasson, Filippo M. Cernilogar, Valentina Pirota, Filippo Doria, Janez Plavec, Gunnar Schotta, Sara N. Richter
Summary: Well-differentiated liposarcoma is a malignant neoplasm characterized by amplification of the MDM2 gene region, and targeting the MDM2 G-quadruplex can promote apoptosis in cancer cells. The research suggests that this approach may be beneficial for treating WDLPS and other tumors seeking to restore wild-type p53.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Emanuela Ruggiero, Enrico Lavezzo, Marco Grazioli, Irene Zanin, Maja Marusic, Janez Plavec, Sara N. Richter, Stefano Toppo
Summary: Viruses have highly conserved multiple A tracts in their genomes which, although unable to form quadruplex structures, induce polymerase pausing and may play a significant role in viral translation.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Medicinal
Emanuela Ruggiero, Ilaria Frasson, Elena Tosoni, Matteo Scalabrin, Rosalba Perrone, Maja Marusic, Janez Plavec, Sara N. Richter
Summary: The fused in liposarcoma (FUS) protein has been found to selectively bind and stabilize the least stable and bulged G-quadruplex (G4) structure in HIV-1 LTR, leading to down-regulation of viral transcription. This study reveals the complexity and dynamics of HIV-1 LTR G4s, highlighting their significance as potential targets for antiviral therapies.
ACS INFECTIOUS DISEASES
(2022)
Article
Multidisciplinary Sciences
Hannes Feyrer, Cenk Onur Gurdap, Maja Marusic, Judith Schlagnitweit, Katja Petzold
Summary: Solution NMR spectroscopy is a valuable tool for studying the structure of RNA molecules, but large RNA sequences often face resonances overlap. This study presents an enzymatic method for site-specific isotope labeling of RNA to overcome this challenge and successfully conduct NMR studies. The method also reveals previously hidden conformational exchange in the RNA structure.
Article
Biochemistry & Molecular Biology
Maja Marusic, Maria Toplishek, Janez Plavec
Summary: Recent research has shown that RNA plays a more significant role in cellular processes regulation than previously anticipated. Understanding the structure of specific RNAs, how the structure changes to accommodate different functional roles, and how RNA interacts with other biomolecules and changes its fold are important for a complete representation of RNA's involvement in cellular processes. Nuclear magnetic resonance (NMR) spectroscopy is a collection of methods and approaches that provide insights into various structural aspects of RNAs. This review focuses on the recent advances in viral, long non-coding, regulatory, and four-stranded RNAs, with a particular emphasis on detecting dynamic sub-states and the impact of chemical modifications on RNA's function.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Maja Marusic, Lea Hosnjak, Petra Krafcikova, Mario Poljak, Viktor Viglasky, Janez Plavec
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2017)