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Nucleic acid quadruplexes based on 8‑halo-9-deazaxanthines : energetics and noncovalent interactions in quadruplex stems
pl
dc.type
JournalArticle
pl
dc.description.physical
5353-5365
pl
dc.abstract.en
Structural and energetic features of arti
fi
cial DNA quadruplexes consisting of base tetrads and their stacks with
Na
+
/K
+
ion(s) inside the central pore and incorporating halogenated derivatives of xanthine, 8-
fl
uoro-9-deazaxanthine (FdaX), 8-
chloro-9-deazaxanthine (CldaX), 8-bromo-9-deazaxanthine (BrdaX), or 8-iodo-9-deazaxanthine (IdaX), have been investigated
by modern state-of-the-art computational tools. The DNA (or RNA) quadruplex models based on 8-halo-9-deazaxanthines are
predicted to be more stable relative to those with unmodi
fi
ed xanthine due to the increased stabilizing contributions coming from
all three main types of weak interactions (H-bonding, stacking, and ion coordination). Methods for analyzing the electron density
are used to understand the nature of forces determining the stability of the system and to gain a predictive potential. Quadruplex
systems incorporating polarizable halogen atoms (chlorine, bromine, or iodine) bene
fi
t signi
fi
cantly from the stabilizing stacking
between the individual tetrads due to an increased dispersion contribution as compared to xanthine and guanine, natural
references used. Ion coordination induces a signi
fi
cant rearrangement of electron density in the quadruplex stem as visualized by
electron deformation density (EDD) and analyzed by ETS-NOCV and Voronoi charges. Na
+
induces larger electron polarization
from the quadruplex toward the ion, whereas K
+
has a higher propensity to electron sharing (identi
fi
ed by QTAIM delocalization
index). We expect that our results will contribute to the development of novel strategies to further modify and analyze the natural
G-quadruplex core.
pl
dc.description.volume
10
pl
dc.description.number
12
pl
dc.identifier.doi
10.1021/ct5007554
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dc.identifier.eissn
1549-9626
pl
dc.title.journal
Journal of Chemical Theory and Computation
pl
dc.language.container
eng
pl
dc.affiliation
Wydział Chemii : Zakład Chemii Teoretycznej im. K. Gumińskiego
pl
dc.affiliation
Wydział Chemii : Zakład Metod Obliczeniowych Chemii
pl
dc.subtype
Article
pl
dc.rights.original
bez licencji
pl
.pointsMNiSW
[2014 A]: 40
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