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Competitive binding studies of the nucleosomal histone targeting drug, [Ru(η-p-cymene)Cl(pta)] (RAPTA-C), with oligonucleotide-peptide mixtures.
J Inorg Biochem
January 2023
Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne CH-1015, Switzerland. Electronic address:
Protein crystallography and biochemical assays reveal that the organometallic drug, [Ru(η-p-cymene)Cl(pta)] (RAPTA-C), preferentially binds to nucleosomal histone proteins in chromatin. To better understand the binding mechanism we report here a mass spectrometric-based competitive binding study between a model peptide from the acidic patch region of the H2A histone protein (the region where RAPTA-C is known to bind) and an oligonucleotide. In contrast to the protein crystallography and biochemical assays, RAPTA-C preferentially binds to the oligonucleotide, confirming that steric factors, rather than electronic effects, primarily dictate binding of RAPTA-C to histone proteins within the nucleosome.
View Article and Find Full Text PDFHelix 69 of Escherichia coli 23S ribosomal RNA as a peptide nucleic acid target.
Biochimie
July 2017
Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland. Electronic address:
A fragment of 23S ribosomal RNA (nucleotides 1906-1924 in E. coli), termed Helix 69, forms a hairpin that is essential for ribosome function. Helix 69 forms a conformationally flexible inter-subunit connection with helix 44 of 16S ribosomal RNA, and the nucleotide A1913 of Helix 69 influences decoding accuracy.
View Article and Find Full Text PDFOptimizing tissue-specific antisense oligonucleotide-peptide conjugates.
Methods Mol Biol
July 2012
Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
Cell-targeting peptides which improve tissue-specific delivery of antisense oligonucleotides (AONs) are a new exciting "next-generation" potential AON therapy. New peptides are regularly developed which increase targeting and cell penetration for the AON treatment of mRNA misregulated diseases. Optimization of these peptide conjugate AONs requires systematic treatment and methods of analysis.
View Article and Find Full Text PDF4-Pregnen-21-ol-3,20-dione-21-(4-bromobenzenesulfonate) (NSC 88915) and related novel steroid derivatives as tyrosyl-DNA phosphodiesterase (Tdp1) inhibitors.
J Med Chem
November 2009
Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is an enzyme that catalyzes the hydrolysis of 3'-phosphotyrosyl bonds. Such linkages form in vivo when topoisomerase I (Top1) processes DNA. For this reason, Tdp1 has been implicated in the repair of irreversible Top1-DNA covalent complexes.
View Article and Find Full Text PDFSynthesis of oligonucleotide-peptide conjugates carrying the c-myc peptide epitope as recognition system.
Chem Biodivers
June 2004
Department of Structural Biology, Instituto de Biología Molecular de Barcelona, C.S.I.C., Jordi Girona 18-26, E-08034 Barcelona.
Oligonucleotide-peptide conjugates 1-3 were prepared by sequential addition of the appropriate Boc-protected amino acids, followed by nucleoside phosphoramidites in the same support. These molecules are designed to be used for triplex formation and for the directed assembly of nanomaterials. The structures of the desired oligonucleotide-peptide conjugates were confirmed by mass spectrometry on small oligonucleotide-peptide conjugates, by gel electrophoresis, and by hybridization with complementary oligonucleotides.
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