Structural insights into DNA mimic foldamer recognition of DNA binding proteins

Deepak (2024): Structural insights into DNA mimic foldamer recognition of DNA binding proteins. Dissertation, LMU München: Fakultät für Chemie und Pharmazie

Abstract

The remarkable folding capabilities of biopolymers such as proteins and DNA underpin their exceptional performances in various biological processes, including molecular recognition, catalysis, and information storage. These natural biopolymers have the unique ability to precisely position functional groups in three-dimensional space, orchestrating their dynamic functions. Inspired by biopolymers, foldamers have been developed, molecules that fold into three-dimensional shapes and provide access to functions beyond the capabilities of biopolymers. Taking inspiration from DNA mimic proteins, abiotic DNA mimics based on aromatic oligoamide foldamers were designed to mimic the shape and surface features of double-stranded DNA. These foldamers previously have been shown to interfere with protein-nucleic acid interactions (PNIs) and bind better than DNA itself. In this thesis, we present the design features of DNA mimic foldamers with features including C2-symmetry (to mimic palindromic DNA sequences), chirality control (to mimic the B-DNA by introducing stereogenic center in the foldamer) suitable for biophysical and structural characterization with DNA binding proteins. Initial efforts made towards the recognition of Sac7d protein were performed by first characterizing the binding of the racemic DNA mimic foldamers using surface plasmon resonance and circular dichroism. Later, we characterized the binding of chiral C2-symmetrical DNA mimic foldamers with Sac7d using X-ray crystallography and nuclear magnetic resonance. As evidenced by solid-state structure elucidation, DNA mimic foldamer finds a novel binding orientation on Sac7d despite maintaining the key interactions involved with Sac7d-DNA complex, which was also confirmed in solution by NMR spectroscopy. Next, we investigated the binding of Dpo4 and hcGAS with DNA mimic foldamers. In this regard, we crystallized and solved the structure of the apo hcGAS protein. Initial crystals of the hcGAS-foldamer diffracted only to a lower resolution. For Dpo4, it was first crystallized, and structure was solved with its DNA sequence, and 4 Å data for Dpo4-foldamer was collected. However, efforts are ongoing to collect higher-resolution datasets and screen different lengths of foldamers with both proteins. Put together, our results present DNA mimic foldamer as a potential molecular tool to interfere with and investigate protein-DNA interactions. The findings of this research may unlock new possibilities in understanding and manipulating protein-nucleic acid interactions, with broad implications for biology and pharmacology.

• Dokumententyp: Dissertationen (Dissertation, LMU München)
• Keywords: Foldamer, DNA Mimic Foldamer, Sac7d, hcGAS
• Themengebiete: 500 Naturwissenschaften und Mathematik ; 500 Naturwissenschaften und Mathematik > 540 Chemie
• Fakultäten: Fakultät für Chemie und Pharmazie
• Sprache der Hochschulschrift: Englisch
• Datum der mündlichen Prüfung: 16. Januar 2024
• 1. Bericht­erstatter:in: Huc, Ivan