Conformational Dynamics of DNA G‐Quadruplex in Solution Studied by Kinetic Capillary Electrophoresis Coupled On‐line with Mass Spectrometry

Abstract

Abstract G‐quadruplex‐forming DNA/RNA sequences play an important role in the regulation of biological functions and development of new anticancer and anti‐aging drugs. In this work, we couple on‐line kinetic capillary electrophoresis with mass spectrometry (KCE‐MS) to study conformational dynamics of DNA G‐quadruplexes in solution. We show that peaks shift and its widening in KCE can be used for measuring rate and equilibrium constants for DNA–metal affinity interactions and G‐quadruplex formation; and ion mobility mass spectrometry (IM‐MS) provides information about relative sizes, absolute molecular masses and stoichiometry of DNA complexes. KCE‐MS separates a thrombin‐binding aptamer d[GGTTGGTGTGGTTGG] from mutated sequences based on affinity to potassium, and reveals the apparent equilibrium folding constant ( K F ≈150 μ m ), folding rate constant ( k on ≈1.70×10 3 s −1 m −1 ), unfolding rate constant ( k off ≈0.25 s −1 ), half‐life time of the G‐quadruplex ( t 1/2 ≈2.8 s), and relaxation time ( τ ≈3.9 ms at physiological 150 m m [K + ]). In addition, KCE‐MS screens for a GQ‐stabilizing/‐destabilizing effect of DNA binding dyes and an anticancer drug, cisplatin.