Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations

Large-scale molecular dynamics (MD) simulations have been utilized to study G-DNA quadruplex molecules containing mixed GCGC and all-guanine GGGG quar tet layers. Incorporation of mixed GCGC quartets into G-DNA stems substanti ally enhances their sequence variability. The mixed quadruplexes form rigid assemblies that require integral monovalent cations for their stabilizatio n. The interaction of cations with the all-guanine quartets is the leading contribution for the stability of the four-stranded assemblies, while the m ixed quartets are rather tolerated within the structure. The simulations pr edict that two cations are preferred to stabilize a four-layer quadruplex s tem composed of two GCGC and two all-guanine quartets. The distribution of cations in the structure is influenced by the position of the GCGC quartets within the quadruplex, the presence and arrangement of thymidine loops con necting the guanine/cytosine stretches forming the stems, and the cation ty pe present (Na+ or K+). The simulations identify multiple nanosecond-scale stable arrangements of the thymidine loops present in the molecules investi gated. In these thymidine loops, several structured pockets are identified capable of temporarily coordinating cations. However, no stable association of cations to a loop has been observed. The simulations reveal several pat hs through the thymidine loop regions that can be followed by the cations w hen exchanging between the central ion channel in the quadruplex stem and t he surrounding solvent. We have carried out 20 independent simulations whil e the length of simulations reaches a total of 90 ns,rendering this study o ne of the most extensive MD investigations carried out on nucleic acids so far. The trajectories provide a largely converged characterization of the s tructural dynamics of these four-stranded G-DNA molecules.