| ŠPAČKOVÁ, Naděžda, Imre BERGER and Jiří ŠPONER. Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations. Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 2001, vol. 123, No 14, p. 3295-3307. ISSN 0002-7863. |
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@article{399752,
author = {Špačková, Naděžda and Berger, Imre and Šponer, Jiří},
article_location = {Washington, D.C.},
article_number = {14},
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},
language = {eng},
issn = {0002-7863},
journal = {Journal of the American Chemical Society},
title = {Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations},
volume = {123},
year = {2001}
}
TY - JOUR
ID - 399752
AU - Špačková, Naděžda - Berger, Imre - Šponer, Jiří
PY - 2001
TI - Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations
JF - Journal of the American Chemical Society
VL - 123
IS - 14
SP - 3295
EP - 3295
PB - American Chemical Society
SN - 00027863
KW - PARTICLE-MESH-EWALD
KW - STRANDED GUANINE TETRAPLEX
KW - OXYTRICHA TELOMERIC DNA
KW - BONDED G-TETRAD
KW - CRYSTAL-STRUCTURE
KW - NUCLEIC-ACIDS
KW - FORCE-FIELD
KW - ANGSTROM RESOLUTION
KW - MINOR-GROOVE
KW - SODIUM-IONS
N2 - 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+).
ER -
ŠPAČKOVÁ, Naděžda, Imre BERGER and Jiří ŠPONER. Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations. \textit{Journal of the American Chemical Society}. Washington, D.C.: American Chemical Society, 2001, vol.~123, No~14, p.~3295-3307. ISSN~0002-7863.
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