Antiparallel G-Quadruplex Formation Hinders Conversion to a Parallel Topology

Abstract

G-quadruplexes (G4s) are four-stranded structures formed by guanine-rich sequences. While their structures, properties, and applications have been extensively studied, an understanding of their folding processes remains limited. In this study, we investigated the folding of the sequence d[(G₃T₂)₃G₃] in potassium solutions, focusing on the impact of a folding intermediate on the overall folding process. Our results indicate that this sequence eventually folds into a parallel G4 structure, either directly or through an antiparallel conformation intermediate, suggesting the existence of a specific competitive folding process. Detailed kinetic analysis using stopped-flow techniques reveals that the antiparallel conformation forms much faster than the parallel one. This antiparallel G4 slowly converts to the thermodynamically favored parallel topology, thus slowing the overall folding rate. As a result, the formation of the parallel quadruplex via an antiparallel G4 intermediate is slower than the direct process, indicating that this antiparallel conformation negatively impacts the overall folding process in a temperature-dependent manner. Interestingly, sodium was shown to facilitate the conversion from antiparallel to parallel. These analyses highlight the complexity of the G4 folding process, which is crucial for most biological applications.