Enhancing G-quadruplex-based DNA nanotechnology: new lipophilic DNA G-quadruplexes with TBDPS modifications

Abstract

This study introduces a novel class of highly lipophilic DNA G-quadruplexes (G4s) obtained by installing the lipophilic tert-butyldiphenylsilyl group (TBDPS) at both ends of 5′-CG_n-3′-3′-G_nC-5′ oligonucleotides (ONs), where n = 1 or 2, featuring a 3′-3′ inversion of polarity, thus obtaining symmetric (TBDPS-5′-CG_n-3′-3′-G_nC-5′-TBDPS)₄ lipophilic G4s after annealing in K⁺-containing buffer. The new 5′-bis-conjugated TBDPS-ONs were synthesized using a tailored solid-phase approach, where the first nucleoside (dC) was linked to the polymeric support via the exocyclic amino group of the nucleobase. The effect of the presence of the TBDPS groups on G4 formation, stability, and propensity to form supramolecular G4 aggregates was assessed using ¹H NMR, circular dichroism (CD), polyacrylamide gel electrophoresis (PAGE), scanning electron microscopy (SEM), dynamic light scattering (DLS), and atomic force microscopy (AFM) analyses. The results demonstrate that the presence of four TBDPS groups at the 5′-ends of the G4 strands enhances the stability of the G4s, enabling their formation even at low K⁺ concentration (20 mmol L⁻¹). We report the formation of the smallest tetramolecular G4 observed to date, [(TBDPS-5′-CG-3′-3′-GC-5′-TBDPS)₄], which contains only two G-tetrads. Notably, this structure did not form when using the corresponding oligonucleotide sequence lacking the TBDPS groups, even at high K⁺ concentrations (up to 1 mol L⁻¹). Furthermore, the lipophilic shells located at the 5′-faces of the G4 structures promote the formation of submicrometric coffee bean-like aggregates composed of G4 units. These novel lipophilic G4s exhibit two key features: high structural symmetry and a tunable balance between their lipophilic (TBDPS groups) and hydrophilic (oligonucleotide strands) moieties. This tunability allows for precise modulation of both the extent and the properties of the resulting supramolecular assemblies. These findings provide valuable insights into developing G4-based systems in DNA nanotechnology.