Heteromeric oligoamide foldamers composed of 8-amino-2-quinolinecarboxylic acid and 7-amino-8-fluoro-2-quinolinecarboxylic acid bearing cationic water-solubilizing side chains were prepared using solid-phase synthesis (SPS). The sequences were designed to adopt a single- or a double-helical motif depending on the nature of the solvent, DMSO or water, respectively. Self-association was demonstrated by NMR and mass spectrometry. Dimerization in water was found to be much stronger than observed previously in organic solvents for analogous oligoamide sequences.
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Angew Chem Int Ed Engl
December 2024
Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany.
Helical aromatic oligoamide foldamers bearing anionic side chains that mimic the overall shape and charge surface distribution of DNA were synthesized. Their interactions with chromosomal protein Sac7d, a non-sequence-selective DNA-binder that kinks DNA, were investigated by Surface Plasmon Resonance (SPR), Isothermal Titration Calorimetry (ITC), Circular Dichroism spectroscopy (CD), melting curve analysis, Atomic Force Microscopy (AFM), and Nuclear Magnetic Resonance (NMR), as well as by single crystal X-ray crystallography. The foldamers were shown to bind to Sac7d better than a DNA duplex of comparable length.
View Article and Find Full Text PDFOrg Biomol Chem
December 2024
Department of Pharmacy, Ludwig-Maximilians-Universität, Butenandtstraße 5-13, D-81377 München, Germany.
A biotinylated helical aromatic oligoamide foldamer equivalent in size to a 24mer peptide was designed without any prejudice other than to display various polar and hydrophobic side chains at its surface. It was synthesized on solid phase, its - and -helical conformers were separated by HPLC on a chiral stationary phase, and the solid state structure of a non-biotinylated analogue was elucidated by X-ray crystallography. Pull-down experiments from a yeast cell lysate using the foldamer as a bait followed by proteomic analysis revealed potential protein binding partners.
View Article and Find Full Text PDFChem Commun (Camb)
August 2024
Univ. Bordeaux, CNRS, Bordeaux INP, CBMN (UMR 5248), 2 rue Escarpit, 33600 Pessac, France.
J Am Chem Soc
May 2024
Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Luoyu Road No. 1037, 430074, Wuhan, China.
In this study, we demonstrate that an aromatic oligoamide sequence assembles into a trimeric helix-turn-helix architecture with a disulfide linkage, and upon cleavage of this linkage, it reconstructs into an antiparallel double helix. The antiparallel double helix is accessible to encapsulate a diacid guest within its cavity, forming a 2:1 host-guest complex. In contrast, hydrogen-bonding interactions between the trimeric-assembled structure and guests induce a conformational shift in the trimeric helix, resulting in a cross-shaped double-helix complex at a 2:2 host-guest ratio.
View Article and Find Full Text PDFChemistry
March 2024
Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany.
DNA mimic foldamers based on aromatic oligoamide helices bearing anionic phosphonate side chains have been shown to bind to DNA-binding proteins sometimes orders of magnitude better than DNA itself. Here, we introduce new features in the DNA mimic foldamers to facilitate structural investigations of their interactions with proteins. Thirteen new foldamer sequences have been synthesized and characterized using NMR, circular dichroism, molecular modeling, and X-ray crystallography.
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