In order to obtain rigidity within the sugar moiety of nucleosides, the bicyclic pyrimidine derivatives of N,O-isoxazolidines were designed and synthesized by using 1,3-dipolar cycloaddition of Delta(1)-pyrrolidine-1-oxide and the appropriate vinyl-nucleobases.
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http://dx.doi.org/10.1016/j.bmcl.2004.11.048 | DOI Listing |
bioRxiv
January 2025
Department of Biochemistry & Molecular Biology, The University of Chicago; Chicago IL, 60637, USA.
Large serine integrases (LSIs) catalyze unidirectional site-specific DNA recombination reactions, yet those reactions are reversed by the presence of a cognate recombination directionality factor (RDF). Mechanistic understanding of directionality control has been hampered by a lack of structural information. Here, we use cryo-electron microscopy (cryo-EM) to determine the structures of six SPbeta integrase-DNA complexes along the integrative (-RDF) and excisive (+RDF) reaction pathways, at 4.
View Article and Find Full Text PDFChem Commun (Camb)
November 2024
Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA.
Conformationally constrained nucleotides, LNA or α-L-LNA, at the 5' terminus of the antisense strand impeded gene silencing of small interfering RNA (siRNA) by hindering phosphorylation, thereby deterring loading into the RNA-induced silencing complex. Installation of a phosphate mimic, ()-vinyl phosphonate (VP), improved activity considerably. Gene silencing was more efficient when the antisense strand of the siRNA was modified with 5'-VP-α-L-LNA, which adopts a C3'- (south) conformation, than when the antisense strand was modified with 5'-VP-LNA, which adopts a C3'- (north) pucker.
View Article and Find Full Text PDFChem Sci
August 2024
Key Laboratory of Colloid and Interface Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University Jinan 250100 People's Republic of China
Developing chiral molecular platforms that respond to external fields provides opportunities for designing smart chiroptical materials. Herein, we introduce a molecular clamp whose chiral properties can be turned on by photoactivation. Selective anion binding achieves rational tuning of the conformations and chiroptical properties of the clamp, including circular dichroism and circularly polarized luminescence.
View Article and Find Full Text PDFJ Am Chem Soc
September 2024
Department of Cellular and Molecular Pharmacology, University of California─San Francisco, San Francisco, California 94158, United States.
The development of electrophilic ligands that rapidly modify specific lysine residues remains a major challenge. Salicylaldehyde-based inhibitors have been reported to form stable imine adducts with the catalytic lysine of protein kinases. However, the targeted lysine in these examples is buried in a hydrophobic environment.
View Article and Find Full Text PDFChem Commun (Camb)
June 2024
Materials Innovation Factory and Department of Chemistry, University of Liverpool, 51 Oxford Street, Liverpool, L7 3NY, UK.
Organic cages can possess complex, functionalised cavities that make them promising candidates for synthetic enzyme mimics. Conformationally flexible, chemically robust structures are needed for adaptable guest binding and catalysis, but rapidly exchanging systems are difficult to resolve in solution. Here, we use low-cost calculations and high-throughput crystallisation to identify accessible conformers of a recently reported organic cage by 'locking' them in the solid state.
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