Simulated Single-Molecule FRET Trajectories: A Comparative Analysis Between Three Telomeric G-quadruplexes

Abstract

The human telomeric DNA sequence d[AGGG(TTAGGG)3] is known to have multiple conformations in vitro. The primary objective of this study is to understand folding and unfolding mechanisms of three human telomeric quadruplexes. Relative stabilities of two quadruplex structures, an anti-parallel and parallel form, were studied using molecular simulations and molecular modeling techniques. A third mixed form which contains the sequence d[TTGGG(TTAGGG)3A], along with the parallel and anti-parallel form was pushed away from its original conformation via a bias command on the sugar-phosphate backbone. It was found that the anti-parallel conformation was the most stable, in that it remained closest to its original conformation. Common characteristics are seen throughout the simulations, particularly stacking near the 3′ end that outlasts the rest of the structure. In an effort to understand the unfolding mechanism or transition state between observed structures, theoretical FRET signals were calculated by analyzing the movement of backbones during simulation. The movement of the backbone in simulations supports published results, namely that similar structures are seen in other studies, and the theoretical FRET signals show similarities to single molecule studies. Clustering by rmsd values shows 7 distinct possible unfolding mechanisms with similarities to published results. A more complete understanding of the stabilizing and destabilizing factors involved in quadruplexes will allow further research into the possible manipulation of the cell cycle and has been cited as an important and promising aspect in the field of cancer research.