title: Structure of triplex DNA in the gas phase.
abstract: Extensive (more than 90 microseconds) molecular dynamics simulations complemented with ion-mobility mass spectrometry experiments have been used to characterize the conformational ensemble of DNA triplexes in the gas phase. Our results suggest that the ensemble of DNA triplex structures in the gas phase is well-defined over the experimental time scale, with the three strands tightly bound, and for the most abundant charge states it samples conformations only slightly more compact than the solution structure. The degree of structural alteration is however very significant, mimicking that found in duplex and much larger than that suggested for G-quadruplexes. Our data strongly supports that the gas phase triplex maintains an excellent memory of the solution structure, well-preserved helicity, and a significant number of native contacts. Once again, a linear, flexible, and charged polymer as DNA surprises us for its ability to retain three-dimensional structure in the absence of solvent. Results argue against the generally assumed roles of the different physical interactions (solvent screening of phosphate repulsion, hydrophobic effect, and solvation of accessible polar groups) in modulating the stability of DNA structures.
authors.affiliation: Joint IRB BSC Research Program in Computational Biology, Institute for Research in Biomedicine, Baldiri Reixach 10, Barcelona 08028, Spain.
authors.forename: Annalisa
authors.initials: A
authors.lastname: Arcella
authors.forename: Guillem
authors.initials: G
authors.lastname: Portella
authors.forename: Maria Luz
authors.initials: ML
authors.lastname: Ruiz
authors.forename: Ramon
authors.initials: R
authors.lastname: Eritja
authors.forename: Marta
authors.initials: M
authors.lastname: Vilaseca
authors.forename: Valérie
authors.initials: V
authors.lastname: Gabelica
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
mesh_terms: D004247:DNA / Q000737:chemistry*; D005740:Gases / Q000737:chemistry*; D013058:Mass Spectrometry; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation
chemical_list: D005740:Gases; C051802:triplex DNA; D004247:DNA