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

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Authors

ŠPAČKOVÁ Naděžda BERGER Imre ŠPONER Jiří

Year of publication 2001
Type Article in Periodical
Magazine / Source Journal of the American Chemical Society
MU Faculty or unit

Faculty of Science

Citation
Field Biophysics
Keywords PARTICLE-MESH-EWALD; STRANDED GUANINE TETRAPLEX; OXYTRICHA TELOMERIC DNA; BONDED G-TETRAD; CRYSTAL-STRUCTURE; NUCLEIC-ACIDS; FORCE-FIELD; ANGSTROM RESOLUTION; MINOR-GROOVE; SODIUM-IONS
Description Large-scale molecular dynamics (MD) simulations have been utilized to study G-DNA quadruplex molecules containing mixed GCGC and all-guanine GGGG quartet layers. Incorporation of mixed GCGC quartets into G-DNA stems substantially enhances their sequence variability. The mixed quadruplexes form rigid assemblies that require integral monovalent cations for their stabilization. The interaction of cations with the all-guanine quartets is the leading contribution for the stability of the four-stranded assemblies, while the mixed quartets are rather tolerated within the structure. The simulations predict that two cations are preferred to stabilize a four-layer quadruplex stem 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 connecting the guanine/cytosine stretches forming the stems, and the cation type present (Na+ or K+).
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