Decorating Magnetic Nanoplatforms to Profile DNA Structures

Funded By NTNU Biotechnology

Beyond the conventional double helix, DNA can fold into stable non-canonical structures such as G-quadruplexes (G4s) — four-stranded arrangements formed by guanine-rich sequences. G4 structures are increasingly recognized as important regulators of gene transcription, DNA replication, telomere maintenance, and genomic stability, making them attractive targets for both diagnostics and G4-targeted therapies. However, existing detection methods such as G4-ChIP-seq are limited by antibody cross-reactivity, disruption of native chromatin during sample preparation, and a lack of single-cell resolution — creating a need for more precise, genome-wide profiling tools.

This ongoing PhD project addresses this gap by developing polymer-grafted magnetic nanoplatforms functionalized with G4-targeting ligands for selective capture, enrichment, and detection of G4 structures in genomic DNA. The approach combines pH-responsive polymer coatings, which are designed to promote endosomal escape and controlled release, with magnetic nanoparticles that allow easy manipulation and separation for downstream genomic analysis.

A key focus to date has been understanding how surface initiator density governs polymer brush growth on hydrophilic, tetraethylene glycol (TREG)-stabilized Fe₃O₄ nanoparticles (~8 nm) — a less-studied alternative to conventional hydrophobic substrates. Using a pre-synthesized APTES–BiBB initiator immobilized at systematically varied surface loadings, surface-initiated ARGET ATRP was used to grow poly(methyl methacrylate) (PMMA) brushes as a non-pH-responsive model system, isolating the effect of initiator density on chain growth from curved nanoparticle surfaces. This yielded grafting densities of approximately 0.02–0.07 chains/nm² across the initiator loading range tested, quantified using a combination of TGA, MP-AES, STEM particle sizing, and GPC molecular weight analysis.

The platform was then extended to pH-responsive poly(2-(diethylamino)ethyl methacrylate) (PDEAEMA) brushes, where grafting density proved to be a key driver of polymer conformation and stimuli-responsive behavior. Dynamic light scattering showed density-dependent swelling, with greater chain extension at lower pH due to protonation of tertiary amine groups, and higher grafting densities amplifying this size response. These findings establish grafting density, tuned via initiator loading, as a central parameter controlling the structural and functional behavior of polymer brushes on hydrophilic magnetic nanoparticle surfaces — laying the groundwork for the next stages of the project, which will investigate controlled degrafting, endosomal escape, and ultimately G4 binding and profiling using the functionalized nanoplatforms.