Telomeric G-quadruplex Intermediates unveiled by Complex Markov Network Analysis

G-quadruplexes are secondary, non-canonical RNA/DNA structures formed by guanine-rich sequences assembled into four-stranded helical structures by the progressive stacking of G-Tetrads, planar arrangements of guanines stabilised by monovalent ions such as K ⁺ or Na ⁺ . Their stability plays a very important role in the prevention of DNA degradation, leading to the promotion or inhibition of specific biological pathways upon formation. In this work we study the different conformations of these structures through their Free Energy Landscape at different temperatures. All-atom simulations are adopted according to a mesoscopic G-quadruplex model previously developed by our group. We use a small number of significant reaction coordinates to analyze the evolution of the system by applying two dimensionality reduction techniques: Principal Component Analysis (PCA) and time-Independent Component Analysis (tICA). The data of the trajectories of the system in this reduced space are encoded into a Complex Markov Network which, in conjunction with an Stochastic Steepest Descent, provides an hierarchical organization of the different nodes into basins of attraction, so revealing the main intermediate states and the most relevant transitions the system undergoes in its denaturation path.