Article
Chemistry, Multidisciplinary
Lukas M. Stratmann, Yury Kutin, Muege Kasanmascheff, Guido H. Clever
Summary: DNA G-quadruplexes have a tendency to form higher-order structures, and square-planar Cu(pyridine)(4) complexes are used as rigid spin labels to detect dimeric structures and measure intermolecular distances via pulsed dipolar EPR spectroscopy. Different spatial dimensions of G-quadruplex dimers and new binding modes of well-known G-quadruplex binders were discovered in this study. The transition metal labeling approach combined with pulsed EPR spectroscopy opens new possibilities for examining structures of non-covalent DNA aggregates.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Microbiology
Almaz Nigatu Tesfahun, Marina Alexeeva, Migle Tomkuviene, Aysha Arshad, Prashanna Guragain, Arne Klungland, Saulius Klimasauskas, Peter Ruoff, Svein Bjelland
Summary: Mis-insertion by DNA polymerase III can lead to all possible non-cognate base pairs in DNA, resulting in base substitutions if not corrected by exonuclease or mismatch repair. In vitro evidence suggests that the C.C mismatch can be processed by base excision repair initiated by E. coli formamidopyrimidine-DNA glycosylase (Fpg). Fpg may play a role in resolving C.C and other pyrimidine.pyrimidine mismatches, increasing survival at the expense of some mutagenesis.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Xiaoqian Wei, Shaojia Song, Weiyu Song, Yating Wen, Weiqing Xu, Yifeng Chen, Zhichao Wu, Ying Qin, Lei Jiao, Yu Wu, Meng Sha, Jiajia Huang, Xiaoli Cai, Lirong Zheng, Liuyong Hu, Wenling Gu, Miharu Eguchi, Toru Asahi, Yusuke Yamauchi, Chengzhou Zhu
Summary: This study used spin state engineering to enhance the catalytic performance of Fe single-atom nanozymes through the introduction of Pd nanoclusters. The spin-rearranged FeNC-Pd-NC showed improved peroxidase-like activity and achieved an ultralow detection limit in the colorimetric detection of prostate-specific antigen.
Review
Chemistry, Multidisciplinary
Hana Dohnalova, Filip Lankas
Summary: The review article discusses recent developments in modeling the mechanical properties of DNA in its B-form, using various models and molecular dynamics simulations. The models are illustrated and critically examined using MD data and Amber force fields.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Karen Zagorski, Tommy Stormberg, Mohtadin Hashemi, Anatoly B. Kolomeisky, Yuri L. Lyubchenko
Summary: The interplay between the mechanical properties of double-stranded and single-stranded DNA plays an important role in genetic processes. In this study, DNA nanorings were designed to investigate the stretching effect of double-stranded DNA on single-stranded DNA. The results showed that the stretching effect was consistent with theoretical estimates. Furthermore, time-lapse observations revealed dynamic behavior of the DNA rings, allowing for the formation of various morphologies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Simon L. Schumann, Simon Kotnig, Yury Kutin, Maria Drosou, Lukas M. Stratmann, Yana Streltsova, Alexander Schnegg, Dimitrios A. Pantazis, Guido H. Clever, Muege Kasanmascheff
Summary: In this study, the structure and conformational flexibility of a unimolecular GQ were investigated using electron-nuclear double resonance (ENDOR) experiments combined with Cu(II) and fluorine labeling. The successful application of the 19F-ENDOR methodology at 34 GHz overcame the limitations of higher-frequency spectrometers, providing both sensitivity and orientational resolution. This integrated study enhances our understanding of GQs and expands the methodological toolbox for studying other macromolecules.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Physical
Jawaher Mosrati, Ali M. Abdel-Mageed, Thanh Huyen Vuong, Reni Grauke, Stephan Bartling, Nils Rockstroh, Hanan Atia, Udo Armbruster, Sebastian Wohlrab, Jabor Rabeah, Angelika Brueckner
Summary: Cu single-atom catalysts supported on CeO2-TiO2 were prepared using a sol-gel method and showed high efficiency and stability in CO oxidation. Spectroscopic methods such as infrared, electron paramagnetic resonance, and X-ray photoelectron spectroscopy revealed the mechanism of action and structure-reactivity relationships.
Article
Chemistry, Analytical
Soching Luikham, A. Mavani, Jhimli Bhattacharyya
Summary: Insights into the binding efficacy and thermodynamic aspects of the interaction between Harmane and AT and GC hairpin duplex-DNAs have been obtained in this study. The binding constants indicate a specific and noncooperative intercalation binding mode. Thermodynamic analysis reveals an exothermic binding process with positive entropy and negative enthalpy changes. Salt-dependent studies suggest the involvement of nonpolyelectrolytic and hydrophobic forces. Ligand-induced structural perturbation of DNA structures has been observed.
Article
Multidisciplinary Sciences
Gou Takahashi, Daiki Kondo, Minato Maeda, Yuji Morishita, Yuichiro Miyaoka
Summary: This study utilized the Single Particle isolation System to analyze genome editing outcomes in individual human cultured cells, revealing a binary nature of genome editing induction and providing a new strategy for analyzing genome editing outcomes in single cells.
Article
Chemistry, Multidisciplinary
Nicolo Zuin Fantoni, Zara Molphy, Sinead O'Carroll, Georgia Menounou, George Mitrikas, Marios G. Krokidis, Chryssostomos Chatgilialoglu, John Colleran, Anna Banasiak, Martin Clynes, Sandra Roche, Suainibhe Kelly, Vickie McKee, Andrew Kellett
Summary: A series of copper(II) artificial metallo-nucleases (AMNs) were reported, demonstrating their DNA damaging properties and in-vitro cytotoxicity against human-derived pancreatic cancer cells. Among these, the Cu-DPA-DPPZ complex showed the strongest DNA binding and intercalation effects, exhibiting promising anticancer activity surpassing the clinical platinum(II) drug oxaliplatin in in-vitro results.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Daniele Rosa-Gastaldo, Andrea Dalla Valle, Tommaso Marchetti, Luca Gabrielli
Summary: A new family of duplex-forming recognition encoded oligomers was developed with the ability of sequence selective duplex formation and template directed synthesis. The duplex formation and assembly properties were studied by F-19 and H-1 NMR experiments. The use of dynamic combinatorial chemistry demonstrated the templated synthesis of complementary oligomers. The H-bond recognition played a key role in discriminating mutated donor monomers. The combination of sequence-selective duplex formation and template effect makes this system a promising target for further studies.
Review
Geochemistry & Geophysics
Maryam Hooshyari, Monica Casale
Summary: This study successfully identified different types of base stocks in engine oils using NIR and EEM spectroscopies coupled with chemometrics, showing potential for classification and prediction, as well as non-destructive characterization of base oils in engine oils.
SURVEYS IN GEOPHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Amedeo Capobianco, Alessandro Landi, Andrea Peluso
Summary: Molecular dynamics simulations and quantum mechanical/molecular mechanics methods predict that short, single-stranded DNA oligonucleotides adopt conformations similar to crystallographic B-DNA in solution. Single strands rich in adjacent purine nucleobases have more regular arrangements, and poly-thymine single strands also retain helical structure in solution.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Medicinal
Federica Battistini, Alba Sala, Adam Hospital, Modesto Orozco
Summary: The properties of DNA duplex have been accurately described using molecular dynamics simulations, but there lacks equivalent simulations for RNA duplex which is usually represented as a rigid rod. In this study, a massive simulation effort was conducted to derive the properties of RNA duplex and a simplified model for long RNA duplexes. Despite high chemical similarity, the local and global elastic properties of DNA and RNA duplexes are significantly different. Statement about the relative flexibility or stability of both polymers is meaningless and a detailed description depending on the sequence and deformation type should be used.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Multidisciplinary Sciences
Daniel W. Conroy, Yu Xu, Honglue Shi, Nicole Gonzalez Salguero, Rudra N. Purusottam, Matthew D. Shannon, Hashim M. Al-Hashimi, Christopher P. Jaroniec
Summary: The majority of base pairs in DNA follow the canonical Watson-Crick geometry, but they can also adopt alternative Hoogsteen conformations which are important for biological function and mechanism. This study demonstrates that multidimensional dynamic nuclear polarization-enhanced solid-state NMR can be used as a spectroscopic tool to observe and distinguish between Watson-Crick and Hoogsteen base pairs in various DNA systems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Marcel Heinz, Nicole Erlenbach, Lukas S. Stelzl, Grace Thierolf, Nilesh R. Kamble, Snorri Th Sigurdsson, Thomas F. Prisner, Gerhard Hummer
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemical Research Methods
Patrick T. Judge, Erika L. Sesti, Nicholas Alaniva, Edward P. Saliba, Lauren E. Price, Chukun Gao, Thomas Halbritter, Snorri Th Sigurdsson, George B. Kyei, Alexander B. Barnes
JOURNAL OF MAGNETIC RESONANCE
(2020)
Article
Biochemistry & Molecular Biology
Haraldur Y. Juliusson, Snorri Th. Sigurdsson
Article
Chemistry, Multidisciplinary
Sucharita Mandal, Snorri Th Sigurdsson
CHEMISTRY-A EUROPEAN JOURNAL
(2020)
Article
Chemistry, Multidisciplinary
Alberto Collauto, Soeren von Buelow, Dnyaneshwar B. Gophane, Subham Saha, Lukas S. Stelzl, Gerhard Hummer, Snorri T. Sigurdsson, Thomas F. Prisner
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2020)
Article
Biochemistry & Molecular Biology
Dimitrios G. Anastasakis, Alexis Jacob, Parthena Konstantinidou, Kazuyuki Meguro, Duncan Claypool, Pavol Cekan, Astrid D. Haase, Markus Hafner
Summary: CLIP methods, particularly PAR-CLIP, allow for the interrogation of direct protein-RNA interactions and gene regulatory networks. This technique utilizes photoreactive nucleosides to crosslink interacting molecules, offering a high sensitivity and specificity in pinpointing RNA binding sites.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Frederic Mentink-Vigier, Thierry Dubroca, Johan Van Tol, Snorri Th Sigurdsson
Summary: Bis-nitroxide radicals are commonly used as polarizing agents to enhance the sensitivity of solid-state NMR experiments. The relative orientation of the nitroxide moieties plays a critical role in efficient polarization transfer, influenced by the degree of substitution on the urea bridge connecting the two nitroxides. Different substitutions affect the distance between g-tensors, impacting the polarization performance and build-up times.
JOURNAL OF MAGNETIC RESONANCE
(2021)
Article
Chemistry, Organic
Anna-Lena Johanna Segler, Snorri Th Sigurdsson
Summary: The synthesis and characterization of rigid spin labels for DNA and RNA were reported, with single-crystal X-ray crystallography and continuous-wave EPR spectra analysis. The results showed that these labels are nonperturbing of duplex structure.
JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Genetics & Heredity
Brona Brejova, Kristina Borsova, Viktoria Hodorova, Viktoria Cabanova, Lenka Reizigova, Evan D. Paul, Pavol Cekan, Boris Klempa, Jozef Nosek, Tomas Vinar
Summary: SARS-CoV-2 mutants with H69/V70 deletion emerged in six lineages, including the B.1.1.7 variant. Samples from Slovakia showed a significant presence of the B.1.258 variant, which circulated in Central Europe before the arrival of B.1.1.7.
Article
Chemistry, Multidisciplinary
Rania Harrabi, Thomas Halbritter, Fabien Aussenac, Ons Dakhlaoui, Johan van Tol, Krishna K. Damodaran, Daniel Lee, Subhradip Paul, Sabine Hediger, Frederic Mentink-Vigier, Snorri Th Sigurdsson, Gael De Paepe
Summary: Efficiently polarizing proton-dense molecular solids through dynamic nuclear polarization (DNP) solid-state NMR has been a great challenge. In this study, we introduce a new polarizing agent, cAsymPol-POK, which shows outstanding performance in polarizing biomolecular assemblies and organic microcrystals at high magnetic fields and fast magic angle spinning frequencies. Simulation and experimental results demonstrate the compatibility of cAsymPol-POK with challenging biomolecular applications and its ability to rapidly acquire crucial structural data of pharmaceutical drugs at natural isotopic abundance.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Oncology
Natalia Birknerova, Veronika Mancikova, Evan David Paul, Jan Matyasovsky, Pavol Cekan, Vladimir Palicka, Helena Parova
Summary: Liquid biopsy is a promising alternative to tissue biopsies, offering real-time detection and monitoring of tumor properties. It has significant implications for the diagnosis and prognosis of advanced stage head and neck cancer patients.
Article
Chemistry, Physical
Adam N. Smith, Rania Harrabi, Thomas Halbritter, Daniel Lee, Fabien Aussenac, Patrick C. A. van der Wel, Sabine Hediger, Snorri Th. Sigurdsson, Gael De Paepe
Summary: We demonstrate a technique for acquiring multidimensional solid-state NMR 13C-13C correlation spectra of biomolecular assemblies and microcrystalline organic molecules at natural isotopic abundance using only milligram quantities of sample. This technique combines fast Magic Angle Spinning, low-power dipolar recoupling, and dynamic nuclear polarization with AsymPol biradicals as polarizing agents. These experiments are crucial for structural characterization as they provide information on short-and long-range distances. We showcase the effectiveness of this approach on various sample types, including polyglutamine fibrils involved in Huntington's disease and microcrystalline ampicillin, a small antibiotic molecule.
SOLID STATE NUCLEAR MAGNETIC RESONANCE
(2023)
Article
Chemistry, Multidisciplinary
Andrei A. Kuzhelev, Vasyl Denysenkov, Iram M. Ahmad, Olga Yu. Rogozhnikova, Dmitry Trukhin, Elena G. Bagryanskaya, Victor M. Tormyshev, Snorri Th. Sigurdsson, Thomas F. Prisner
Summary: Dynamic nuclear polarization (DNP) is an effective method for enhancing the sensitivity of nuclear magnetic resonance (NMR) experiments. This study demonstrates that DNP can achieve over 50 times enhancement in viscous liquids using narrow-line polarizing agents and a microwave/RF double-resonance probehead. The results show potential applications of this new DNP approach for chemistry and biology, as demonstrated by the hyperpolarized 1H NMR spectra of tripeptides, triglycine, and glypromate in glycerol-d8.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Johanna Becker-Baldus, Alexei Yeliseev, Thomas T. Joseph, Snorri Th. Sigurdsson, Lioudmila Zoubak, Kirk Hines, Malliga R. Iyer, Arjen van den Berg, Sam Stepnowski, Jon Zmuda, Klaus Gawrisch, Clemens Glaubitz
Summary: Tremendous progress has been made in determining the structures of G-protein coupled receptors (GPCRs) and their complexes, but understanding their activation and signaling remains challenging due to protein dynamics. In this study, dynamic nuclear polarization (DNP)-enhanced magic angle spinning nuclear magnetic resonance was used to study the conformational ensemble of cannabinoid receptor 2 (CB2) at specific sites. The results showed that the conformational space of the protein backbone differs in different parts of the receptor, and a site in TM7 is sensitive to the ligand nature, while a site in ICL3 always exhibits large conformational freedom.
Article
Chemistry, Multidisciplinary
Sucharita Mandal, Snorri Th. Sigurdsson
CHEMICAL COMMUNICATIONS
(2020)