The chemical structure of the mercury-mediated T-T pair (T-Hg(I)I-T) was determined with (15)N NMR spectroscopy. In order to determine the chemical structure of the T-Hg(I)I-T pair, (15)N-(15)N J-coupling across a metal center (2JNN) was employed. Notably, this is the first observation of (2)J(NN) in a biological macromolecule (DNA duplex). This pairing mode was found to be a irregular metal ion-binding mode for DNA and RNA molecules, in which imino proton-metal exchange processes are included. Accordingly, (2)J(NN) is highly important for the determination of the chemical structures of metal-mediated base pairs.
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http://dx.doi.org/10.1093/nass/nrm038 | DOI Listing |
J Phys Chem B
January 2025
Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4.
Despite the remarkable resistance of the nucleic acid phosphodiester backbone to degradation affording genetic stability, the P-O bond must be broken during DNA repair and RNA metabolism, among many other critical cellular processes. Nucleases are powerful enzymes that can enhance the uncatalyzed rate of phosphodiester bond cleavage by up to ∼10-fold. Despite the most well accepted hydrolysis mechanism involving two metals (M to activate a water nucleophile and M to stabilize the leaving group), experimental evidence suggests that some nucleases can use a single metal to facilitate the chemical step, a controversial concept in the literature.
View Article and Find Full Text PDFChemistry
December 2024
Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 28/30, 48149, Münster, Germany.
Two artificial imidazole-derived nucleobases, Im (3H-imidazo[4,5-f]quinolin-5-ol) and Im (imidazole-4-carboxylate), were introduced into short DNA duplexes to systematically investigate their thermal stability upon metal ion coordination. Metal-mediated base pairs are formed with the 3d metal ions Co, Ni and Zn, as well as with the lanthanoid ions Eu and Sm, which induce a thermal stabilization of up to 8 °C upon binding. The latter are the first lanthanoid-mediated base pairs involving only four donor atoms that result in a significant duplex stabilization.
View Article and Find Full Text PDFTop Curr Chem (Cham)
October 2024
Department of Chemistry, Ramananda Centenary College, Laulara, Purulia, West Bengal, India, 723151.
Epoxides are class of cyclic ether and have been extensively used in petrochemicals and pharmaceuticals industries as raw materials. Due to this reasons, development of the synthetic strategy of epoxides are getting enormous interest among the research chemists. In terms of "development of the synthetic strategy", the use of a catalyst, especially, Schiff base-based complex is of potential interest due to alternative easy routes and significant advances in metal-mediated pathways giving rise to diverse degree of substrate-reagent interactions.
View Article and Find Full Text PDFOrg Biomol Chem
November 2024
Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
While Mn ions are well-established for reducing the fidelity of DNA polymerases, leading to the misincorporation of nucleotides, our investigation of the effects of metal ions revealed a contrasting role of Zn. Here, we demonstrate that Zn ions enhance the fidelity of DNA polymerases (the 3' → 5' exonuclease-deficient Klenow fragment and Taq DNA polymerase) by suppressing misincorporation during primer extension reactions. Remarkably, Zn ions inhibit both intrinsic misincorporation and Mn-induced misincorporation of nucleotides.
View Article and Find Full Text PDFJ Inorg Biochem
January 2025
Key Laboratory of Applied Surface and Colloid Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China. Electronic address:
DNA hybrid catalysts are constructed by embedding active metal species into the chiral scaffolds of DNA, which have been successfully applied to some important aqueous-phase enantioselective transformations. Owing to simple components and inherent chirality, nucleotide hybrid catalysts are emerging in response to soving the unclear locations of catalytic centers and the plausible catalytic mechanisms in DNA-based asymmetric catalysis. However, the tertiary structure of nucleotides lacks tunability, severely impeding further design of nucleotide hybrid catalysts for potential applications.
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