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M. Ilchenko and I. Dubey
bifurcated H-bonds (S 4 symmetry). The structures of G-octet with two bifurcated
bonds (C 2 symmetry) was also investigated. Analysis of binding energies demonstrated that G-quartet with two bifurcated bonds (C 2 symmetry) is the most stable
structure in gas phase. It was also shown that G-quartets with no bifurcated bonds
(C 2 , S 4 , C 4h symmetries) did not give a stable structure at the M05-2X/6-31 + G(d, p)
level in gas phase. At the M06-2X/6-31 + G(d, p) level, optimization of the three different types of quartets studied resulted in the quartet with all bifurcated H-bonds
with S 4 symmetry. We have independently come to analogous conclusions on the
stability of G-quartets n vacuum [96]. As to the effect of aqueous medium, our data
strongly differ from those obtained in [84]. We have found that full optimization
of G-quartets in water results in immediate zero barrier transformation of all types
of G-quartets into a single structure with Hoogsteen-type bonding. These data are
supported by the results presented in [97] demonstrating that the structures of S 4
symmetry are global minima in water for G-quartets with Hoogsteen-type system
of hydrogen bonds. We also suppose that Jissy et al. [84] were not correct while
mentioning that there is one quartet with two bifurcated bonds in PDB crystal structure of G-quartet 1LVS. In our opinion, quartet of this type more closely resembles
the deformed G-quartets with Hoogsteen bonding. We have found only one more
paper in the literature [98] where the analogous mixed quartet form was briefly
mentioned, although with no comparison with other possible structures. The authors
studied guanosine 5’-hydrazide self-assemblies in the gel state by the combination
of spectral data and B3LYP/6-31G** DFT calculations and concentrated mainly
on the dependence of H-bond parameters on the orientation of ribose fragments in
nucleoside.
It was recognized early that the ability to stabilize guanine gels depends on the
cation nature and that the ionic radius is important for complex stability; in the alkali series K
+
promotes the most stable complexes [80]. Cations play a critical role
in stabilizing G-quadruplex structures to the extent when changing e.g. potassium
cation for Na
+
can completely alter the whole topology of G-quadruplex [37–43,
69–74]. It is not surprising therefore that the role of metal ions in formation and
stability of G-quadruplex structures was studied thoroughly in a number of theoretical works.
In addition to the above mentioned research, the authors of [84] have also performed calculations for Li
+
, Na
+
, K
+
, Be
2+
, Mg
2+
and Ca
2+
complexes of G-tetrads.
Calculations showed that for an isolated quartet, the metal ion with the smallest
ionic radius in their respective groups (IA and IIA) form more stable complexes.
Other properties such as the HOMO-LUMO gap and polarizability have also been
analyzed. The variation in the polarizability has been studied with respect to the
movement of cations along the central cavity of the quartet to show that such movement leads to a large anisotropy of polarization and hence the refractive index (η)
thereby creating optical birefringence which have potential applications in biomolecular imaging.
The structures and interaction energies of guanine and uracil quartets have been
determined by B3LYP hybrid density functional calculations in [99]. The total interaction energy of the C 4h -symmetric guanine quartet consisting of Hoogsteen-type
M. Ilchenko and I. Dubey
bifurcated H-bonds (S 4 symmetry). The structures of G-octet with two bifurcated
bonds (C 2 symmetry) was also investigated. Analysis of binding energies demonstrated that G-quartet with two bifurcated bonds (C 2 symmetry) is the most stable
structure in gas phase. It was also shown that G-quartets with no bifurcated bonds
(C 2 , S 4 , C 4h symmetries) did not give a stable structure at the M05-2X/6-31 + G(d, p)
level in gas phase. At the M06-2X/6-31 + G(d, p) level, optimization of the three different types of quartets studied resulted in the quartet with all bifurcated H-bonds
with S 4 symmetry. We have independently come to analogous conclusions on the
stability of G-quartets n vacuum [96]. As to the effect of aqueous medium, our data
strongly differ from those obtained in [84]. We have found that full optimization
of G-quartets in water results in immediate zero barrier transformation of all types
of G-quartets into a single structure with Hoogsteen-type bonding. These data are
supported by the results presented in [97] demonstrating that the structures of S 4
symmetry are global minima in water for G-quartets with Hoogsteen-type system
of hydrogen bonds. We also suppose that Jissy et al. [84] were not correct while
mentioning that there is one quartet with two bifurcated bonds in PDB crystal structure of G-quartet 1LVS. In our opinion, quartet of this type more closely resembles
the deformed G-quartets with Hoogsteen bonding. We have found only one more
paper in the literature [98] where the analogous mixed quartet form was briefly
mentioned, although with no comparison with other possible structures. The authors
studied guanosine 5’-hydrazide self-assemblies in the gel state by the combination
of spectral data and B3LYP/6-31G** DFT calculations and concentrated mainly
on the dependence of H-bond parameters on the orientation of ribose fragments in
nucleoside.
It was recognized early that the ability to stabilize guanine gels depends on the
cation nature and that the ionic radius is important for complex stability; in the alkali series K
+
promotes the most stable complexes [80]. Cations play a critical role
in stabilizing G-quadruplex structures to the extent when changing e.g. potassium
cation for Na
+
can completely alter the whole topology of G-quadruplex [37–43,
69–74]. It is not surprising therefore that the role of metal ions in formation and
stability of G-quadruplex structures was studied thoroughly in a number of theoretical works.
In addition to the above mentioned research, the authors of [84] have also performed calculations for Li
+
, Na
+
, K
+
, Be
2+
, Mg
2+
and Ca
2+
complexes of G-tetrads.
Calculations showed that for an isolated quartet, the metal ion with the smallest
ionic radius in their respective groups (IA and IIA) form more stable complexes.
Other properties such as the HOMO-LUMO gap and polarizability have also been
analyzed. The variation in the polarizability has been studied with respect to the
movement of cations along the central cavity of the quartet to show that such movement leads to a large anisotropy of polarization and hence the refractive index (η)
thereby creating optical birefringence which have potential applications in biomolecular imaging.
The structures and interaction energies of guanine and uracil quartets have been
determined by B3LYP hybrid density functional calculations in [99]. The total interaction energy of the C 4h -symmetric guanine quartet consisting of Hoogsteen-type