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
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
Biochemistry & Molecular Biology
Valeria Libera, Federico Bianchi, Barbara Rossi, Francesco D'Amico, Claudio Masciovecchio, Caterina Petrillo, Francesco Sacchetti, Alessandro Paciaroni, Lucia Comez
Summary: This study found that during the thermal melting process of G4 structure, the hydrogen-bonded network of water molecules undergoes rearrangement, which is closely related to the DNA rearrangement. Understanding the structural properties of the solvent can contribute to a better understanding of the interaction between G4s and ligands.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
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
Chemistry, Organic
Jonathan Alvarez-Garcia, Victor Rubio-Pisabarro, Luis Garcia-Rio, Maria Magdalena Cid
Summary: Proton transfer equilibria play a key role in various biological and pharmaceutical processes. The behavior of chiral pyrido-cyclophanes in the presence of different acids was studied, revealing double protonation and formation of cascade ion-pairs. Water presence promoted the crystallization of intermediates not corresponding to those in solution, and proton transfer from acid to pyridine was found to occur regardless of acid's pKa. The hydrogen position after proton transfer equilibria was elucidated by diagnostic signals in ECD of cascade complexes.
ORGANIC CHEMISTRY FRONTIERS
(2023)
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)
Article
Chemistry, Physical
Tom Miclot, Cecilia Hognon, Emmanuelle Bignon, Alessio Terenzi, Marco Marazzi, Giampaolo Barone, Antonio Monari
Summary: This study presents the first calculated G4 structure of the RG-1 RNA sequence in the SARS-CoV-2 genome, demonstrating its stability and potential interaction with G4 ligands inhibiting viral protein translation. The findings highlight the importance of RNA G4 structures in modulating viral biological activities.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Multidisciplinary
David Pal, Celine Besnard, Adiran de Aguirre, Amalia I. Poblador-Bahamonde, Gennaro Pescitelli, Jerome Lacour
Summary: Hydrogen bonding plays a significant role in chemical reactions, conformation, and stereochemistry. This study introduces a novel dye, tetranitrofluorenone oximate, which can visually detect hydrogen-bond donating species and quickly determine the strength of hydrogen bonding by monitoring hypsochromic shifts. The molecule also exhibits atropisomeric conformations, and enantiopure bis-thioureas are found to be the most effective hydrogen bond donors for chiral induction, as demonstrated by electronic circular dichroism and time-dependent density functional theory calculations. Furthermore, bis-thioureas are used as chiral reagents in asymmetric 1,3-dipolar cycloadditions, with the electronic circular dichroism sensing of stereoinduction serving as an indirect method to select the most effective hydrogen bond donor for asymmetric synthesis.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Allison M. Williams, Raghav R. Poudyal, Philip C. Bevilacqua
Summary: This study found that eukaryotic biological concentrations of spermine can induce microaggregation of three-tiered G-rich sequences, while higher spermine concentrations can even induce aggregation of purely two-tiered structures. The formation of microaggregates has implications for the stability and functional roles of G-rich nucleic acid structures in vivo.
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
Chemistry, Medicinal
Simona Marzano, Giulia Miglietta, Rita Morigi, Jessica Marinello, Andrea Arleo, Monica Procacci, Alessandra Locatelli, Alberto Leoni, Bruno Pagano, Antonio Randazzo, Jussara Amato, Giovanni Capranico
Summary: This study investigates the interplay between G4 affinity/selectivity, cytotoxicity, and immune gene activation in the search for new anticancer drugs. The researchers found that G4 affinity is critical for immune gene activation, but high cytotoxic potency interferes with it. The balance between G4 stabilization and cytotoxicity determines the level of immune gene activation in cancer cells, suggesting a new rationale for discovering effective anticancer G4 ligands based on low cell-killing potency and high immune stimulation.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Ahmed M. Rozza, Imre Bako, Julianna Olah
Summary: Solvation plays a crucial role in maintaining the structure and function of biomolecules. In this study, the hydration patterns of DNA with different base pairings were investigated using molecular dynamics simulation and topological analysis of the hydrogen bond network. It was found that HG base pairing increased the solvation of the major groove and disrupted the water structure in the minor groove, which could contribute to the recognition of specific DNA binding proteins.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Multidisciplinary
Tom Miclot, Camille Corbier, Alessio Terenzi, Cecilia Hognon, Stephanie Grandemange, Giampaolo Barone, Antonio Monari
Summary: This study demonstrated the crucial role of the stability of G-quadruplex in telomeric DNA in resisting oxidative stress and as an inhibitor of telomerase, an enzyme overexpressed in most cancers associated with oxidative stress. The combined experimental and computational investigation utilized circular dichroism, cellular immunofluorescence assays, and molecular dynamics simulations to identify these roles.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Inorganic & Nuclear
Marko Nuskol, Petar Sutalo, Ivan Kodrin, Mojca Cakic Semencic
Summary: The study demonstrates the potential of the ferrocene chromophore to translate chiral information stored in l-Ala and transmitted through an achiral sequence into a characteristic signal in circular dichroism spectra. The findings suggest the possibility of designing ferrocene-based probes to determine the screw-sense preference of short peptides.
EUROPEAN JOURNAL OF INORGANIC CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Hsiao-Chieh Tsai, Ching-Hong Huang, Ling-Hsien Tu
Summary: Islet amyloid polypeptide (IAPP) is a polypeptide hormone co-secreted with insulin by pancreatic beta-cells. It tends to aggregate into soluble oligomers, which are considered one of the hallmarks of type II diabetes. This study successfully grafted the aggregation-induced emission molecule TPE onto IAPP, allowing real-time monitoring of IAPP oligomer formation and potential application in the diagnosis of T2D.
BIOPHYSICAL CHEMISTRY
(2024)
Article
Biochemistry & Molecular Biology
Aristeidis Papagiannopoulos, Aggeliki Sklapani, Nikolaos Spiliopoulos
Summary: This study presents a method for preparing Hb-based nanoparticles (NPs) using a fully biocompatible approach. These NPs have a spherical structure with a diameter ranging from 50 to 100 nm, and can form electrostatic complexes with CS at pH 4. The NPs can be pH-tunable and stable in solutions with high salt content, making them suitable for nanodelivery of nutrients and drugs.
BIOPHYSICAL CHEMISTRY
(2024)
Article
Biochemistry & Molecular Biology
Andrey V. Struts, Alexander V. Barmasov, Steven D. E. Fried, Kushani S. K. Hewage, Suchithranga M. D. C. Perera, Michael F. Brown
Summary: This article summarizes and reviews the osmotic stress studies of G-protein-coupled receptor rhodopsin. It is found that water plays an important role in the activation of the receptor, with at least 80 water molecules entering the receptor in the transition to the active state. If water influx is prevented, the functional transition of the receptor is reversed. These findings reveal the phenomenon of solvent swelling in the activation mechanism of rhodopsin, with water acting as an allosteric modulator of function for rhodopsin-like receptors in lipid membranes.
BIOPHYSICAL CHEMISTRY
(2024)
Article
Biochemistry & Molecular Biology
Maria Chiara Saija, Adela Melcrova, Wojciech Pajerski, Itay Schachter, Matti Javanainen, Marek Cebecauer, Lukasz Cwiklik
Summary: We used molecular dynamics simulations to investigate the effects of palmitoylation on a transmembrane peptide in different lipid environments. The study found that palmitoylation reduces the peptide's impact on membrane thickness, particularly in lipid-ordered and boundary environments. The hydrophobic palmitoyl chains on the peptide did not significantly affect membrane hydration. Interestingly, the boundary membrane environment was found to be highly compatible with the palmitoylated peptide. These findings have important implications for understanding cell signaling, membrane organization, and optimizing lipid membrane-based drug delivery systems.
BIOPHYSICAL CHEMISTRY
(2024)
Article
Biochemistry & Molecular Biology
Achanta Rishisree, Brayer Mallory, Karnaukhova Elena, Jankovic Teodora, Zdunic Gordana, Savikin Katarina, Jeremic Aleksandar
Summary: Pomegranate peel, ironwort, and chokeberry leaf extracts exhibit anti-aggregative and antitoxic properties against human amylin. They can prevent amyloidosis and cell loss in patients with Type 2 Diabetes Mellitus.
BIOPHYSICAL CHEMISTRY
(2024)