Article
Chemistry, Physical
Lu-Qi Tao, Guanya Wang, Peng Hou, Jiahao Liu, Xianping Chen
Summary: In this article, the adsorption characteristics of single DNA nucleobases and hydrogen-bonded base pairs on monolayer bismuthene were investigated using density functional theory (DFT). The results showed that the interaction strength between adenine, cytosine, guanine, thymine and bismuthene followed the order G > C > A > T, with adsorption energies of 0.83 eV, 0.69 eV, 0.65 eV, and 0.59 eV, respectively. Bismuthene demonstrated potential for selective detection of the four bases due to their distinguishable energy levels. The study also revealed the physisorption nature of the interactions and the importance of a single oxygen atom in stronger interactions with C/G.
APPLIED SURFACE SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Nikita Brodyagin, Aubrey L. Maryniak, Ilze Kumpina, John M. Talbott, Martins Katkevics, Eriks Rozners, James A. MacKay
Summary: Peptide nucleic acids (PNA) with extended isoorotamides containing nucleobases (I-o) were designed to bind A-U base pairs in double-stranded RNA. Isothermal titration calorimetry and UV thermal melting experiments showed improved affinity for A-U using the Io scaffold in PNA, with PNAs having four sequential Io extended nucleobases maintaining high binding affinity.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Hidetaka Torigoe, Jiro Kondo, Fumihiro Arakawa
Summary: Metal ion-nucleic acid interactions are important for nucleic acid structure and biological activity and have applications in nanotechnology. Hg2+ binds specifically to a T-T mismatched base pair in DNA. Metal ions can enhance DNA damage caused by DNA-damaging agents, but their interactions with damaged DNA are less well known.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)
Article
Chemistry, Physical
Bernhard Kretz, David A. Egger
Summary: In this study, it is suggested that using time-dependent density functional theory with optimally tuned range-separated hybrid functionals can accurately obtain excited-state molecular geometries, particularly in cases involving complex excited-state potential energy surfaces with local and charge-transfer excitations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Analytical
Tong-Tong Ji, Neng-Bin Xie, Jiang-Hui Ding, Min Wang, Xia Guo, Ying-Ying Chen, Si-Yu Yu, Yu-Qi Feng, Bi-Feng Yuan
Summary: A new member of the uracil-DNA glycosylase family enzyme (UdgX-H109S) was characterized to selectively cleave uracil-containing single-stranded and double-stranded DNA. Based on this, an enzymatic cleavage-mediated extension stalling (ECES) method was developed for locus-specific detection and quantification of uracil in genomic DNA. The ECES method was proven to be accurate and reproducible in the quantification of uracil in genomic DNA from biological and clinical samples, with a significant decrease in uracil level observed in breast cancer tissues.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Philipp Innig Aguion, John Kirkpatrick, Teresa Carlomagno, Alexander Marchanka
Summary: Knowledge of RNA structure, whether in isolation or in complex, is crucial for understanding cellular processes. Solid-state NMR has been used to study high molecular-weight complexes, and recent developments in H-1 detection at fast MAS rates have overcome sensitivity and resolution limitations, allowing for more efficient analysis of RNA structures in protein-RNA complexes of any size.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Briana T. A. Boychuk, Sarah P. Meyer, Stacey D. Wetmore
Summary: This study generates a comprehensive dataset of accurate binding energies between group I metals and nucleic acids. By testing various computational methods and analyzing the results, the most accurate methods are determined. These findings are important for understanding the role of group I metals in the environment and human biology, designing metal sensors, developing biomaterials, and improving computational methods for studying metal-nucleic acid interactions.
FRONTIERS IN CHEMISTRY
(2023)
Article
Chemistry, Physical
Nicholas M. Gravina, James C. Gumbart, Harold D. Kim
Summary: This study investigates the interactions between DNA sticky ends using the coarse-grained oxDNA model, finding that the orientation of double-stranded DNA (dsDNA) segments affects the time required for the sticky ends to bind. Specifically, the binding time is fastest when the helical axes of duplexes are pointing toward each other and the sticky ends protrude from the farthest two points.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Review
Biochemistry & Molecular Biology
Robert Doerrenhaus, Philip K. Wagner, Stephanie Kath-Schorr
Summary: Nucleic acid chemistry is constantly evolving to meet the demand for novel nucleotide modifications and artificial building blocks. This review focuses on the development and applications of unnatural base pairs in expanding the genetic alphabet. Recent advancements in nature-like artificial base pairs as well as synthetic methods for acquiring C-glycosidic nucleotides are presented. The feasibility of synthesis plays a vital role in the successful utilization of unnatural base pairs and is thoroughly discussed.
BIOLOGICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Asyeh Barkhoda, Alireza Nowroozi, Mohammad Reza Housaindokht
Summary: In this study, several models were proposed to estimate the energy of individual hydrogen bonds in traditional base pairs. The computational results showed that the energy in the first method is higher and the NHN interactions are stronger. Additionally, the calculated individual HB energies of the base pairs are similar to the compliance constant model.
STRUCTURAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
M. T. Rodgers, Yakubu S. Seidu, E. Israel
Summary: Modifications at the 2'-position of nucleic acids can fine-tune their conformational characteristics and stability. Among these modifications, 2'-O-methylation and 2',2'-difluorination enhance base-pairing interactions and stability of i-motif structures.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Chemistry, Physical
Evan L. Jones, Alan J. Mlotkowski, Sebastien P. Hebert, H. Bernhard Schlegel, Christine S. Chow
Summary: Modified nucleobases play essential structural and biological roles in RNA, but their characteristics are still poorly understood. This study determined the pK(a) values of modified nucleobases using ab initio quantum mechanical calculations, providing insights into their structural and energetic impacts within nucleic acids.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Analytical
Mengmeng He, Yusuke Sato, Seiichi Nishizawa
Summary: Compared to DNA-selective dyes, RNA-selective dyes are less developed due to the challenges of achieving RNA selectivity. This study introduces thiazole orange (TO) as a promising fluorogenic dye for live cell imaging of nucleolar RNA. The regioisomer 2TO shows even better selectivity and performance, with significant improvement in brightness and selectivity for RNA in both solution and living cells, compared to TO derivatives carrying different substituents.
Article
Chemistry, Physical
Alan J. Mlotkowski, H. Bernhard Schlegel, Christine S. Chow
Summary: The study used ab initio quantum mechanical calculations to estimate pKa values of aza- and deaza-modified nucleobases. The B3LYP density functional with the 6-31+G(d,p) basis set and an implicit-explicit solvent model were employed. A comparison with experimental data was conducted, and adjustment factors were applied to improve the accuracy of pKa predictions.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Biochemical Research Methods
Wojciech Jankowski, Marcin Hoffmann, Paulina Polrul, Magdalena Franska
Summary: This study focused on the protonated dimers of cytosine and its nucleoside, using experimental and quantum mechanics methods to investigate their gas-phase stabilities. The results showed that substitution of sugar moiety at N1 cytosine atom decreased the stability of the protonated dimers, and the deoxycytidine dimer was more stable than the cytidine dimer. Quantum chemical calculations suggested that a cytosine aminohydroxy tautomer may play a role in the formation of protonated cytosine-cytosine nucleoside dimers.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2023)
Article
Chemistry, Multidisciplinary
Prajyot Jayadev Nagtilak, Manoj V. Mane, Supreeth Prasad, Luigi Cavallo, Dean J. Tantillo, Manmohan Kapur
Summary: This study reports the reactivity of propargyl alcohols as Three-Carbon Synthons in a Rh(III)-catalyzed C-H functionalization. This method allows for the efficient synthesis of diverse molecular frameworks, with good functional group tolerance and unique regioselectivity.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Multidisciplinary Sciences
Long Huang, Marcin Szewczyk, Rajesh Kancherla, Bholanath Maity, Chen Zhu, Luigi Cavallo, Magnus Rueping
Summary: In this study, stereodivergent allylic C(sp(3))-H bond arylations were successfully developed through a systematic investigation of the direction and degree of stereoselectivity in the cross-coupling process. Unlike the typical photosensitized geometrical isomerization of alkenes, the catalytic reaction demonstrated the feasibility of switching the C-C double bond stereoselectivity through ligand control and steric and electronic effects.
NATURE COMMUNICATIONS
(2023)
Article
Immunology
Nahid Akhtar, Jorge Samuel Leon Magdaleno, Suryakant Ranjan, Atif Khurshid Wani, Ravneet Kaur Grewal, Romina Oliva, Abdul Rajjak Shaikh, Luigi Cavallo, Mohit Chawla
Summary: In this study, a multi-epitope vaccine candidate targeting C. dubliniensis secreted aspartyl proteinases (SAP) proteins was designed using an immunoinformatics approach. Computational tools were utilized to predict epitopes and determine their potential for allergic reactions, antigenicity, toxicity, and ability to elicit immune responses. Eight epitopes were predicted and linked with adjuvants for the development of the final vaccine candidate. Computational immune simulations confirmed the strong immunogenicity of the designed immunogen. Molecular docking and molecular dynamics simulation analyses showed stable interactions between the vaccine candidate and the human toll-like receptor 5 (TLR5). Immune simulations further supported the promising candidature of the designed vaccine, calling for further in vivo investigation.
Article
Chemistry, Multidisciplinary
Benon P. Maliszewski, Tahani A. C. A. Bayrakdar, Perrine Lambert, Lama Hamdouna, Xavier Trivelli, Luigi Cavallo, Albert Poater, Marek Belis, Olivier Lafon, Kristof Van Hecke, Dominic Ormerod, Catherine S. J. Cazin, Fady Nahra, Steven P. Nolan
Summary: In this study, the catalytic activity of a series of platinum(II) pre-catalysts with N-heterocyclic carbene (NHC) ligands in the alkene hydrosilylation reaction is reported. The structural and electronic properties of these catalysts are fully characterized using X-ray diffraction analysis and nuclear magnetic resonance spectroscopy (NMR). A structure-activity relationship within this group of pre-catalysts is established, and mechanistic insights into the catalyst activation step are provided. One of the complexes shows exceptional catalytic performance, achieving a turnover number (TON) of 970,000 and a turnover frequency (TOF) of 40,417 h(-1) at 1 ppm catalyst loading. Furthermore, a solvent-free and open-to-air alkene hydrosilylation protocol with efficient platinum removal (reducing residual Pt from 582 ppm to 5.8 ppm) is disclosed.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Yu Cao, Ekaterina Toshcheva, Walid Almaksoud, Rafia Ahmad, Tatsuya Tsumori, Rohit Rai, Ya Tang, Luigi Cavallo, Hiroshi Kageyama, Yoji Kobayashi
Summary: In this study, we demonstrate the robust ammonia synthesis activity of the nitride hydride compound Ca3CrN3H, which activates dinitrogen through active sites where calcium provides the primary coordination environment. DFT calculations indicate that an associative mechanism is favored, unlike the dissociative mechanism found in traditional Ru or Fe catalysts. This work showcases the potential of alkaline earth metal hydride catalysts and other related 1D hydride/electrides for ammonia synthesis.
Article
Chemistry, Physical
Yuqi Wang, Zhen Cao, Zheng Ma, Gang Liu, Haoran Cheng, Yeguo Zou, Luigi Cavallo, Qian Li, Jun Ming
Summary: We detected the presence of weak solvent-solvent interactions in electrolytes using nuclear magnetic resonance and found that these interactions play a significant role in stabilizing the electrolytes, which is a novel discovery. By studying the role of ethylene carbonate (EC) solvent in lithium-ion battery electrolyte, we found that EC can stabilize linear carbonate solvent electrolyte, particularly diethyl carbonate (DEC), through weak intermolecular interactions, enhancing the energy difference between the orbitals of the Li+(EC)(x)(DEC)(y) complex and demonstrating strong capability against reduction. Our findings were further confirmed in other metal ion batteries (e.g., Na+, K+), highlighting the importance of electrolyte design and deeper understanding of battery performance.
ACS ENERGY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Honghong Liang, Zheng Ma, Yuqi Wang, Fei Zhao, Zhen Cao, Luigi Cavallo, Qian Li, Jun Ming
Summary: This study achieves reversible lithium-ion (de)intercalation in a propylene carbonate (PC)-based electrolyte containing a fluoroether by tuning the solvent-solvent interaction, providing an opportunity to enhance the compatibility of PC-based electrolytes with graphite anodes.
Article
Biochemistry & Molecular Biology
Arijit Das Sharma, Ravneet Kaur Grewal, Suresh Gorle, Andres Felipe Cuspoca, Vikas Kaushik, Abdul Rajjak Shaikh, Luigi Cavallo, Mohit Chawla
Summary: Gastrointestinal diarrhea, mainly caused by rotavirus, is a highly contagious disease with high mortality rates, especially in developing countries. The available vaccines have limited efficacy and there are risks associated with vaccination. Therefore, the development of alternative vaccines is necessary.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Sonam Kumari, Jorge S. Leon Magdaleno, Ravneet Kaur Grewal, Manik Prabhu Narsing Rao, Abdul Rajjak Shaikh, Luigi Cavallo, Mohit Chawla, Manoj Kumar
Summary: This study focuses on the bioprospecting of native soil microbes from the undisturbed environment in Netarhat, India, with the potential for biomass digestion. Metagenomic analysis revealed the dominance of Actinobacteria among the bacterial species and the presence of a large number of carbohydrate enzyme families.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Jorge Samuel Leon Magdaleno, Ravneet K. Grewal, Jose L. Medina-Franco, Romina Oliva, Abdul Rajjak Shaikh, Luigi Cavallo, Mohit Chawla
Summary: Sialyl Lewis X (sLe(x)) antigen, upregulated by fucosyltransferase 6 (FUT6), plays a crucial role in promoting metastasis in human colorectal, lung, prostate, and oral cancers. However, the lack of experimental structures for FUT6 hinders the development of its inhibitors. In this study, we employed in silico techniques to identify potential FUT6 inhibitors and found three natural compounds with comparable binding affinity to experimentally tested inhibitors. Molecular dynamics simulations further indicated the stability of these compounds, suggesting their potential as natural alternatives for FUT6 inhibition.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2023)
Article
Biochemical Research Methods
Grzegorz Chojnowski, Rafal Zaborowski, Marcin Magnus, Sunandan Mukherjee, Janusz M. Bujnicki
Summary: RNA Masonry is a computer program and web service that automates the process of modeling RNA 3D structures. It assembles RNA fragments into plausible models that meet user-provided constraints and small-angle X-ray scattering data. The method is illustrated with benchmarks and its application to structural studies of viral RNAs with SAXS restraints.
Review
Chemistry, Multidisciplinary
Bholanath Maity, Sayan Dutta, Luigi Cavallo
Summary: C-sp3-C cross-coupling, a dream reaction in the chemical community, can be achieved by activating C-sp3-H bonds through visible light-induced transition metal-catalysis under mild reaction conditions. However, this research area is still in its early stages due to the chemical and technical complexity of this catalysis. Complementary experimental and theoretical mechanistic studies are essential for rational advances, as each approach alone is inadequate to clarify the operative mechanisms. In this tutorial review, we summarize representative experimental and computational mechanistic studies, highlighting the weaknesses, strengths, and synergies between the two approaches.
CHEMICAL SOCIETY REVIEWS
(2023)
Article
Chemistry, Inorganic & Nuclear
Sofie M. P. Vanden Broeck, Nikolaos V. V. Tzouras, Marina Saab, Kristof Van Hecke, Busra Dereli, Ida Ritacco, Luigi Cavallo, Georgios C. C. Vougioukalakis, Pierre Braunstein, Steven P. P. Nolan, Andreas A. A. Danopoulos, Catherine S. J. Cazin
Summary: The 4-RN-1,3-Ar-2-imidazolium salt, R = iPr, tBu, Ar = Mes, Dipp, underwent metalation by Au-I at the C2-, C5-, and 4-RN positions, depending on the reactants and conditions used. A rare direct rearrangement of the Au-I aminide to an abnormal imidazol-5-ylidene Au-I complex was also observed, which may involve TfO- facilitated H+ transfer, according to a DFT study.
DALTON TRANSACTIONS
(2023)
Article
Chemistry, Inorganic & Nuclear
Ekaterina A. Martynova, Marco Zuccarello, Domenic Kronenberg, Marek Belis, Agnieszka Czapik, Ziyun Zhang, Kristof Van Hecke, Marcin Kwit, Olivier Baudoin, Luigi Cavallo, Steven P. Nolan
Summary: Green and sustainable access to chiral and achiral gold-IBiox complexes is achieved through a simple and air-tolerant synthesis method using a green solvent. The catalytic activity of these complexes in the hydroamination of alkynes is examined, and their steric protection of the gold center is compared with commonly encountered NHCs using the %V-bur model.
DALTON TRANSACTIONS
(2023)
Article
Chemistry, Physical
Bo Li, Liang Yi, Bholanath Maity, Jiaqi Jia, Yuqin Shen, Xiang-Yu Chen, Luigi Cavallo, Magnus Rueping
Summary: Noncovalent interactions, particularly halogen bonding, play a crucial role in organic synthesis and catalysis, including the synthesis of organoselenium compounds. By utilizing the reaction balance between an electron donor-acceptor complex and Ph2Se2, the halogen bonding interaction facilitates the formation of C-Se bonds through the capture of alkyl radicals. This synthetic strategy has been successfully applied in the transformation of various carboxylic acids, natural products, drugs, and alpha-selenoamino acids.