Novel Insight into Proximal DNA Domain Interactions from Temperature‐Controlled Electrospray Ionization Mass Spectrometry

Abstract

Abstract Quadruplexes are non‐canonical nucleic acid structures essential for many cellular processes. Hybrid quadruplex–duplex oligonucleotide assemblies comprised of multiple domains are challenging to study with conventional biophysical methods due to their structural complexity. Here, we introduce a novel method based on native mass spectrometry (MS) coupled with a custom‐built temperature‐controlled nanoelectrospray ionization (TCnESI) source designed to investigate interactions between proximal DNA domains. Thermal denaturation experiments were aimed to study unfolding of multi‐stranded oligonucleotide constructs derived from biologically relevant structures and to identify unfolding intermediates. Using the TCnESI MS, we observed changes in T m and thermodynamic characteristics of proximal DNA domains depending on the number of domains, their position, and order in a single experiment.