8QPC

18mer DNA mimic Foldamer with an Aromatic linker in complex with Sac7d V26A/M29A protein

This is a non-PDB format compatible entry.

Summary for 8QPC

• Entry DOI: 10.2210/pdb8qpc/pdb
• Descriptor: DNA-binding protein 7b, N-[2-(2-methyl-1,3-dioxolan-2-yl)phenyl]-2-{[5-(trifluoromethyl)pyridin-2-yl]amino}pyridine-4-carboxamide (3 entities in total)
• Functional Keywords: foldamer, dna mimic foldamer, dna mimicry, sac7d, dna binding protein
• Biological source: Sulfolobus acidocaldarius; More
• Total number of polymer chains: 3
• Total formula weight: 12664.30

Authors

Deepak, D.,Corvaglia, V.,Wu, J.,Huc, I. (deposition date: 2023-10-01, release date: 2023-11-08, Last modification date: 2025-02-26)

Primary citation

Deepak, D.,Wu, J.,Corvaglia, V.,Allmendinger, L.,Scheckenbach, M.,Tinnefeld, P.,Huc, I.
DNA Mimic Foldamer Recognition of a Chromosomal Protein.
Angew.Chem.Int.Ed.Engl., 64:e202422958-e202422958, 2025

PubMed Abstract: 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. The interaction is diastereoselective and takes place at the DNA binding site. Crystallography revealed that the DNA mimic foldamers have a binding mode of their own and that they can bind to Sac7d without being kinked.

PubMed: 39714421
DOI: 10.1002/anie.202422958

Experimental method

X-RAY DIFFRACTION (3.24 Å)