Article
Chemistry, Multidisciplinary
Todd N. Poe, Sarah Molinari, Samantha Justiniano, Grace M. McLeod, Thomas E. Albrecht-Schonzart
Summary: Three Ln(II) 18-crown-6 complexes were synthesized and characterized, showing differences in crystal structure, molecular packing, and spectroscopic features. Distinct absorption and photoluminescence behaviors were observed, setting them apart from other similar systems.
CRYSTAL GROWTH & DESIGN
(2022)
Article
Biology
Shuntaro Takahashi, Sudipta Bhowmik, Shinobu Sato, Shigeori Takenaka, Naoki Sugimoto
Summary: The relationship between G4 structures and DNA replication was studied, and it was found that different ligands have different effects on the topology of G4. Some ligands can inhibit the replication of G4 with anti-parallel topology, while others selectively inhibit G4 with anti-parallel and hybrid topology. The experiments suggest that native human telomere G4 is more flexible than the modified sequence and can interact with ligands.
Review
Genetics & Heredity
MaryElizabeth Stein, Kristin A. Eckert
Summary: Genome instability, especially in cancer cells, is associated with DNA structures like G-quadruplexes and oxidative damage caused by chronic inflammation. Maintaining stability in the genome requires specialized DNA polymerases to handle challenges posed by G4 structures and unrepaired lesions from inflammation. Inflammation's impact on gene regulation and mutagenesis through G4 structures requires further investigation for a better understanding of genome instability mechanisms.
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, Multidisciplinary
Anirban Basu
Summary: The crown ether 18-crown-6 has the potential to suppress fibrillation in lysozyme and decrease the protein's β-sheet content, thus inhibiting the formation of amyloid fibrils. These findings can be utilized to develop more effective anti-amyloidogenic agents.
NEW JOURNAL OF CHEMISTRY
(2023)
Article
Chemistry, Physical
Irina A. Kuz'mina, Mariia A. Kovanova, Anna S. Udalova
Summary: The Gibbs free energies and enthalpies of transfer and dissolution of dibenzo-18-crown-6 ether in different solvent mixtures were determined in this study. The solvent composition was found to have limited impact on the solvation state of the crown ether, and a compensation effect between enthalpy and entropy contributions was observed. The resolvation of the crown ring oxygen atoms was identified as the main factor influencing the thermodynamic characteristics of the solvation process.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Multidisciplinary
Elena Merzlyakova, Silke Wolf, Sergei Lebedkin, Lkhamsuren Bayarjargal, B. Lilli Neumeier, Daniel Bartenbach, Christof Holzer, Wim Klopper, Bjoern Winkler, Manfred Kappes, Claus Feldmann
Summary: A series of transition metal crown-ether coordination compounds were synthesized using ionic liquids, showing both conventional and unusual structural motifs. Some of these compounds exhibit outstanding photoluminescence properties, with high quantum yields observed for compounds like ZnI2, Mn2I4 (18-crown-6)(2), EuBr2, and EuI2. The optical properties and structural features of these compounds were characterized through various analytical techniques, revealing unique and efficient luminescent behavior.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Thermodynamics
Olga A. Zakurdaeva, Irina O. Kuchkina, Tikhon S. Kurkin, Sergey V. Nesterov
Summary: The thermal stability of macrocyclic complexes with alkaline earth metal salts was studied in this research. The size of the cation and anion was found to affect the stability, with Ba2+ < Sr2+ < Ca2+ and Cl- < Br- ≈ I-. The complexes with CaCl2, SrBr2, and SrI2 exhibited a two-stage destruction mechanism, suggesting the coexistence of two conformationally nonequivalent forms of the macrocycles.
JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY
(2023)
Article
Genetics & Heredity
Vaclav Brazda, Natalia Bohalova, Richard P. Bowater
Summary: With improved sequencing methods, the new end-to-end assembly of human chromosome 8 has revealed a greater presence of non-B DNA structures than previously estimated, indicating their potential importance has been underestimated. As sequencing technologies continue to advance, similar discoveries may arise across the genomes of various organisms.
Article
Chemistry, Multidisciplinary
Snehasis Dutta, Trilochan Gadly, Amey P. Wadawale, Mayur Darekar, Sulekha Mukhopadhay, Sunil K. Ghosh, Birija S. Patro
Summary: This paper presents a novel method for the synthesis and purification of DTBDB18C6, as well as the heterogeneous catalytic hydrogenation of DTBDB18C6 to DTBDCH18C6. The synthesis of DTBDB18C6 was successfully scaled up to a 5 kg scale, and the purification process was developed and scaled up to a 300 g scale. The hydrogenation of DTBDB18C6 to DTBDCH18C6 was achieved with a rhodium on alumina catalyst, and the addition of K+ ions in the reaction mixture enhanced the reaction yield to 75%. The synthesized DTBDCH18C6 exhibited high distribution coefficients for the extraction of strontium.
REACTION CHEMISTRY & ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Zhe Shen, Ruiling Zheng, Huamao Yang, Sunhui Xing, Xiangxiang Jin, Hao Yan, Jufan Zhu, Yanan Mei, Feng Lin, Xiaohui Zheng
Summary: This study explores the biological effects of G-quadruplex stabilizer Tetra-Pt(bpy) in telomerase-positive cancer cells, revealing its ability to accelerate telomere shortening, inhibit cell proliferation, induce senescence, decrease cell migration, and suppress FAK transcription. Tetra-Pt(bpy) also shows potential as a novel chemotherapeutic agent for targeting telomerase-positive cancer cells.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Ying Ma, Yang Yang, Jingyu Xin, Lingfeng He, Zhigang Hu, Tao Gao, Feiyan Pan, Zhigang Guo
Summary: Reactive oxygen species (ROS) are highly oxidative molecules that induce DNA damage and affect gene expression. This study identified a novel RNA G-quadruplex (rG4) sequence in the 5' untranslated region (5' UTR) of FEN1 mRNA. Under oxidative stress, ROS can oxidize the G bases in the G4-forming sequence, disrupting the structure of G-quadruplex. Additionally, a novel rG4-binding protein hnRNPA1 was identified and shown to play a role in regulating FEN1 expression. Overall, this study reveals a novel role for rG4 in translational control under oxidative stress.
Article
Chemistry, Multidisciplinary
Zibin Zhang, Yu Yao, Lang He, Tao Hong, Shijun Li, Feihe Huang, Peter J. Stang
Summary: Coordination-driven self-assembly was utilized to construct two metallacycles using a dicarboxylate-functionalized dibenzo-18-crown-6 in combination with either a 0 degrees anthracene-based clip-type acceptor or a 60 degrees phenanthrene-based acceptor. The angularities of these components enabled the formation of a [2 + 2] rectangle and a [3 + 3] triangle, respectively. The synthesis, characterization, and host-guest chemistry of the two metallacycles were described and supported by 31P{1H}, 1H NMR spectra, and electrospray mass spectrometry. (c) 2022 Published by Elsevier B.V. on behalf of Chinese Chemical Society and Institute of Materia Medica, Chinese Academy of Medical Sciences.
CHINESE CHEMICAL LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Yi-Rong Li, Yun-Fang Zhang, Yuan-Yuan Tang, Han-Yue Zhang
Summary: We discovered that [(histamine)(18-crown-6)(2)][BF4](2) is a high-temperature host-guest inclusion complex that exhibits decent piezoelectric properties and potential ferroelectricity. This work provides a new idea for constructing host-guest inclusion piezoelectrics.
CHEMICAL COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Sam Y. Thompson, Lauren A. Devenney, Dmitry S. Yufit, John S. O. Evans
Summary: In this study, the temperature and thermal history dependence of polymorphic phase transitions in the multiaxial molecular ferroelectric 18-crown-6 oxonium tetrachloro-gallium(III) were explored. The structures of two previously suggested polymorphs (D and Y) were solved from high-temperature powder diffraction data, and a new polymorph (X) was identified using low-temperature powder diffraction data. Another polymorph (W) that can form on cooling was also discovered. The ferroelectric properties of the various polymorphs were rationalized based on the structural findings.
CRYSTAL GROWTH & DESIGN
(2023)
Article
Biochemistry & Molecular Biology
R. Aaron Rogers, Madeline R. Meyer, Kayla M. Stewart, Gabriela M. Eyring, Aaron M. Fleming, Cynthia J. Burrows
Summary: The study investigated the pH stability of i-motifs (iM) formed under slightly acidic conditions in DNA-rich sequences, focusing on the effects of different experimental techniques and thermal changes. Results showed that iM analysis methods could impact the pH(T) parameter measured, and hysteresis was observed in both pH(T) and T(m) values.
Article
Chemistry, Multidisciplinary
Aaron M. Fleming, Michael B. Chabot, Ngoc L. B. Nguyen, Cynthia J. Burrows
Summary: The research found that 8-oxoguanine (dOG) is the most reactive in nucleosides, and the native nucleoside dG is higher or similar in reactivity to 5mdC or m(6)A; competition of oxidant in both single- and double-stranded DNA confirmed that dG is favorably oxidized.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Rodrigo Galindo-Murillo, Lauren Winkler, Jingwei Ma, Fatjon Hanelli, Aaron M. Fleming, Cynthia J. Burrows, Thomas E. Cheatham
Summary: This study investigates the specific ligand recognition of abasic sites in G-quadruplex using riboflavin and guanine as examples. The results show that riboflavin can only stabilize abasic site-containing G-quadruplex in the presence of an adjacent OG-modified base.
Article
Biology
Aaron M. Fleming, Cynthia J. Burrows
Summary: The article discusses the oxidation of guanine in DNA caused by ionizing radiation or the Fenton reaction, focusing on the formation of various oxidized lesions including 8-oxo-7,8-dihydroguanine (OG) and 5-carboxamido-5-formamido-2-iminohydantoin (2Ih). It compares the pathways and biological consequences of guanine oxidation induced by hydroxyl radicals with endogenous oxidative stress, emphasizing the potential impact on mutagenesis and epigenetics.
INTERNATIONAL JOURNAL OF RADIATION BIOLOGY
(2022)
Article
Chemistry, Organic
Aaron M. Fleming, Songjun Xiao, Michael B. Chabot, Cynthia J. Burrows
Summary: This study found that common fluorescent dyes can act as photosensitizers to oxidize nucleic acids, but with slow rates and low overall yield. This is unlikely to affect most experiments studying nucleic acids, but may have an impact on experiments with long exposures to high-intensity lights, such as sequencing-by-synthesis experiments using fluorescence as the readout.
JOURNAL OF PHYSICAL ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Michael B. Chabot, Aaron M. Fleming, Cynthia J. Burrows
Summary: Ozonolysis of guanosine leads to the formation of 2Ih nucleoside and trace amounts of Sp. We propose an unconventional ozone mechanism based on literature precedent, which involves the incorporation of one oxygen atom from O3 to form 2Ih and the release of singlet oxygen that is responsible for Sp formation. Experimental evidence using the stabilizing solvent D2O and isotope labeling supports this mechanism and reveals the challenges of working with 2Ih and the context effects on the half-life of the 2Ih glycosidic bond.
CHEMICAL RESEARCH IN TOXICOLOGY
(2022)
Letter
Biology
Cynthia Burrows, Aaron Fleming
INTERNATIONAL JOURNAL OF RADIATION BIOLOGY
(2023)
Article
Chemistry, Organic
Michael B. Chabot, Aaron M. Fleming, Cynthia J. Burrows
Summary: Exposure of DNA to oxidants results in modification of the guanine heterocycle, forming the mutagenic 2Ih lesion. Previously believed to exist in a single structure, we have discovered that under biological conditions, 2Ih can reversibly close to an intermediate and open into a newly discovered regioisomer.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Organic
Aaron M. Fleming, Songjun Xiao, Cynthia J. Burrows
Summary: The differential reactions of pseudouridine (Psi) and 5-methylcytidine (m(5)C) with NaHSO3 at pH 5 were used to locate their positions in RNA. The study found that NaHSO3 was unique in achieving quantitative yields compared to other reagents. The reaction selectivity of pseudouridine with NaHSO3 was supported by the reaction rate constants at pH 7. Additionally, the Psi derivative N1-methylpseudouridine in mRNA vaccines formed ribose adducts through a similar reaction with bisulfite.
Article
Biochemistry & Molecular Biology
Shereen A. Howpay Manage, Aaron M. Fleming, Hsiao-Nung Chen, Cynthia J. Burrows
Summary: This study provides a quantitative survey of cysteine oxidation to sulfenic acid in APE1 and demonstrates how this modification affects APE1's function towards the NEIL3 gene promoter G4. The research suggests that cysteine oxidation to sulfenic acid enhances APE1's affinity for G4 during oxidative stress, but attenuates its endonuclease activity.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Analytical
Aaron M. Fleming, Renee Tran, Carla A. Omaga, Shereen A. Howpay Manage, Cynthia J. Burrows, John C. Conboy
Summary: This study used SHG to measure the binding interaction between the DNA repair enzyme APE1 and the VEGF promoter G4 folds with AP sites, demonstrating that the interaction is ordered and specific. This resolves the question of how APE1 engages G4 folds with gene regulatory features.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Aaron M. Fleming, Cynthia J. Burrows
Summary: Direct RNA sequencing using a commercial nanopore platform was utilized to sequence RNA molecules with uridine (U), pseudouridine (psi) or N1-methylpseudouridine (m(1)psi) in various contexts. The base calling data for psi and m(1)psi differed from U, allowing their detection. The study examined the selection of UTP, psi TP, or m(1)psi TP by T7 RNA polymerase in different adjacent sequence contexts, finding a significant dependency on sequence context.
NUCLEIC ACIDS RESEARCH
(2023)
Editorial Material
Cell Biology
Aaron M. Fleming, Cynthia J. Burrows
Summary: In the study of DNA modifications, the disciplines of epigenetics and of DNA damage and repair have traditionally been separate. However, it is now recognized that epigenetic modifications require DNA repair pathways for erasure and recent discoveries have shown that oxidative DNA damage can affect gene expression, blurring the lines between these two areas.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Cynthia J. Burrows, Shereen A. Howpay Manage, Aaron M. Fleming, Hsiao-Nung Chen
Summary: This study quantitatively investigated cysteine oxidation to sulfenic acid in APE1 and how this modified form affects APE1's binding to the NEIL3 gene promoter G4; the results suggest that cysteine oxidation can enhance G4 binding but reduce endonuclease activity in APE1, potentially triggering a switch from base excision repair to transcriptional modulation.
ACS CHEMICAL BIOLOGY
(2022)
Meeting Abstract
Environmental Sciences
Jackson I. Gargaro, Cynthia Burrows, Aaron Fleming
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
(2022)