The structure of the complex formed by naphthyridine carbamate dimer (NCD) binding to CGG repeat sequences in DNA, associated with fragile X syndrome, has been elucidated using N-labeled NCD and H-N HSQC. In a fully saturated state, two NCD molecules consistently bind to each CGG/CGG unit, maintaining a 1 : 2 binding stoichiometry.
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Enhancing Binding Affinity to CGG/CGG Triad: Optimizing Naphthyridine Carbamate Dimer Derivatives with Varied Linker Lengths.
ChemMedChem
October 2024
Department of Regulatory Bioorganic Chemistry, SANKEN, The University of Osaka, 8-1 Mihogaoka, Ibaraki, 567-0047, Japan.
This study examines the binding properties of six naphthyridine carbamate dimer (NCD) derivatives with varying linker lengths to the CGG/CGG triad, a non-canonical DNA structure linked to repeat expansion disorders. By altering the linker length from 2 to 4 methylene groups, we found changes in thermal stability of the ligand-bound complexes while maintaining a consistent 2 : 1 binding stoichiometry. Among the derivatives, CC23 showed superior binding affinity compared to the parent molecule CC33 (NCD).
View Article and Find Full Text PDFNMR analysis of N-labeled naphthyridine carbamate dimer (NCD) to contiguous CGG/CGG units in DNA.
Chem Commun (Camb)
March 2024
Department of Regulatory Bioorganic Chemistry, SANKEN, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan.
The structure of the complex formed by naphthyridine carbamate dimer (NCD) binding to CGG repeat sequences in DNA, associated with fragile X syndrome, has been elucidated using N-labeled NCD and H-N HSQC. In a fully saturated state, two NCD molecules consistently bind to each CGG/CGG unit, maintaining a 1 : 2 binding stoichiometry.
View Article and Find Full Text PDFRh(III)-Catalyzed C-H Activation of Benzamides and Chemodivergent Annulation with Benzoxazinanones: Substrate Controlled Selectivity.
Org Lett
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School of Chemistry and Chemical Engineering, Shaanxi Normal University (SNNU), Xi'an 710062, China.
Decarboxylative annulation of propargyl carbamates with benzamides has been realized via rhodium-catalyzed C-H bond activation under mild conditions, delivering two distinct classes of heterocycles in high efficiency and selectivity under substrate control. This protocol provides a direct synthetic method for the preparation of functionalized 1,8-naphthyridines and isoindolinones.
View Article and Find Full Text PDFInhibitory Effects of Mismatch Binding Molecules on the Repair Reaction of Uracil-Containing DNA.
Biochemistry
November 2022
Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan.
The stable R-loop formed during transcription induces enzyme-mediated deamination of cytosine, and the uracil in the DNA produced activates the base excision repair (BER) pathway. DNA cleavage involved in the BER pathway is thought to be one of the possible causes of trinucleotide repeat instability. Here, we performed an in vitro assay to investigate the effect of a DNA-binding small molecule, naphthyridine carbamate dimer (NCD), on BER enzyme reactions.
View Article and Find Full Text PDFNMR determination of the 2:1 binding complex of naphthyridine carbamate dimer (NCD) and CGG/CGG triad in double-stranded DNA.
Nucleic Acids Res
September 2022
Department of Regulatory Bioorganic Chemistry, SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
Trinucleotide repeat (TNR) diseases are caused by the aberrant expansion of CXG (X = C, A, G and T) sequences in genomes. We have reported two small molecules binding to TNR, NCD, and NA, which strongly bind to CGG repeat (responsible sequence of fragile X syndrome) and CAG repeat (Huntington's disease). The NMR structure of NA binding to the CAG/CAG triad has been clarified, but the structure of NCD bound to the CGG/CGG triad remained to be addressed.
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