Article (Scientific journals)
Structure of triplex DNA in the gas phase.
Arcella, Annalisa; Portella, Guillem; Ruiz, Maria Luz et al.
2012In Journal of the American Chemical Society, 134 (15), p. 6596-606
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Keywords :
DNA/chemistry; Gases/chemistry; Mass Spectrometry; Molecular Dynamics Simulation; Nucleic Acid Conformation
Abstract :
[en] 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.
Research center :
Giga-Systems Biology and Chemical Biology - ULiège
Disciplines :
Biochemistry, biophysics & molecular biology
Chemistry
Author, co-author :
Arcella, Annalisa
Portella, Guillem
Ruiz, Maria Luz
Eritja, Ramon
Vilaseca, Marta
Gabelica, Valérie ;  Université de Liège - ULiège > Département de chimie (sciences) > GIGA-R : Laboratoire de spectrométrie de masse (L.S.M.)
Orozco, Modesto
Language :
English
Title :
Structure of triplex DNA in the gas phase.
Publication date :
2012
Journal title :
Journal of the American Chemical Society
ISSN :
0002-7863
eISSN :
1520-5126
Publisher :
American Chemical Society, Washington, United States - District of Columbia
Volume :
134
Issue :
15
Pages :
6596-606
Peer reviewed :
Peer Reviewed verified by ORBi
Funders :
F.R.S.-FNRS - Fonds de la Recherche Scientifique [BE]
Commentary :
(c) 2012 American Chemical Society
Available on ORBi :
since 25 October 2012

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