Selective Enrichment of Hypermethylated DNA by a Multivalent Binding Platform

Abstract The preselection of hypermethylated DNA (hmDNA) from liquid biopsy samples is key to enable early‐stage cancer diagnostics. Due to limited selectivity of the existing preselection approaches, however, wide integration in the clinic is currently prohibited. Here, it is argued that an affinity method on a surface, such as used in affinity chromatography, can be significantly improved by employing the principles of multivalency and superselectivity. In the here proposed method, a methyl binding domain (MBD) protein immobilized at a surface is used as a receptor for (hyper)methylated DNA. By the organization of multiple MBDs on a surface, a multivalent binding platform is achieved. The MBD surface receptor density on that platform is key to increase the enrichment selectivity of hmDNA as a single MBD protein binds both methylated and non‐methylated DNA with a small difference in affinity. When the receptor density is varied, multivalent analyte binding typically responds in a non‐linear fashion, which phenomenon is called superselectivity. By careful tuning of the MBD density, it is envisaged that the selectivity for methylated over non‐methylated DNA can be optimized. Strong applicability is foreseen in a medical setting by implementing such an enrichment step in an analytical process or a lab‐on‐a‐chip device.