240
V. Poltev et al.
3.1 Flexibility of the Sugar-Phosphate Backbone
Torsion angles of single polynucleotide chains continuously vary in relatively wide
regions. Out of those bands, only selected sets of torsion ranges are compatible with
double stranded structure of Watson-Crick A:T and G:C nucleoside pairs. Rather
small consistent variations of the torsions can result in large changes of macroscopic
parameters of the helices belonging to the same conformation family. Because of that
each family can contain infinite number of conformers. We will consider here some
B-like conformation families of DNA. Majority of cdDMPs of such DNA fragments
deposited in NDB consist of both strands belonging to the “classical” BI family.
Nevertheless many fragments contain cdDMP with one or two strands being different
from BI. Here, we consider cdDMPs with SPB of BI, BII conformation families and
with those classified in paper [12] as 32, 86, 110, 116, and 117 conformational classes.
These classes (families) distinguish one from another due to significantly different
values of two or three torsions. For instance, two of the most studied families, BI
and BII, differ mainly in ε (C4
–C3
–O3
–P) and ζ (C3
–O3
–P–O5
) torsions. Mean
values of ζ torsion changes from 259° for BI family to 170° for BII family, while mean
ε torsion changes from 183° to 245° [12]. The conformations of SPB presented in
Fig. 3 demonstrate the differences in mutual position of atoms in these two families.
Other B-like conformation families differ from the canonical one by the change
in two or three torsion angles while retaining the major characteristic features of
B-structure. The crank of α and γ torsions to g
+ and g
− regions respectively produce conformations of family 116, while conformation family 117 emerges as a
consequence of changes in torsion angles α, β, and γ to mean values 249°, 73°, and
172° respectively. Figure 4 illustrates molecular models of two conformations of
dGpdT:dApdC with SPB belonging to different families.
Figure 5 provides graphic illustration of differences in mean torsion angles for
selected cdDMPs. Table 1 presents numerical values of their torsions. The BI and
BII conformation families carry the SPB fragment in the conformation that matches
the energy minimum of the free SPB unit. Both DFT and MM computations of SPB
predict the torsion angles to be in the same region as that observed in the variety
of conformations of cdDMPs in these families. The conformation family 117 is the
only one among the selected systems that has all the torsions differ by less than 30°
from the energy minimum conformation of the free SPB. Three other families have
at least two torsions exceeding that threshold.
3.2 Multiplicity of Feasible Base-Base Complexes
Intermolecular interactions between the DNA bases have been studied since 1961
using various computational methods. Molecular structure of the bases enables the
formation of variety of their pairwise complexes as well as complexes of three and
four bases corresponding to energy minima. Experimentally observed or theoretically
V. Poltev et al.
3.1 Flexibility of the Sugar-Phosphate Backbone
Torsion angles of single polynucleotide chains continuously vary in relatively wide
regions. Out of those bands, only selected sets of torsion ranges are compatible with
double stranded structure of Watson-Crick A:T and G:C nucleoside pairs. Rather
small consistent variations of the torsions can result in large changes of macroscopic
parameters of the helices belonging to the same conformation family. Because of that
each family can contain infinite number of conformers. We will consider here some
B-like conformation families of DNA. Majority of cdDMPs of such DNA fragments
deposited in NDB consist of both strands belonging to the “classical” BI family.
Nevertheless many fragments contain cdDMP with one or two strands being different
from BI. Here, we consider cdDMPs with SPB of BI, BII conformation families and
with those classified in paper [12] as 32, 86, 110, 116, and 117 conformational classes.
These classes (families) distinguish one from another due to significantly different
values of two or three torsions. For instance, two of the most studied families, BI
and BII, differ mainly in ε (C4
–C3
–O3
–P) and ζ (C3
–O3
–P–O5
) torsions. Mean
values of ζ torsion changes from 259° for BI family to 170° for BII family, while mean
ε torsion changes from 183° to 245° [12]. The conformations of SPB presented in
Fig. 3 demonstrate the differences in mutual position of atoms in these two families.
Other B-like conformation families differ from the canonical one by the change
in two or three torsion angles while retaining the major characteristic features of
B-structure. The crank of α and γ torsions to g
+ and g
− regions respectively produce conformations of family 116, while conformation family 117 emerges as a
consequence of changes in torsion angles α, β, and γ to mean values 249°, 73°, and
172° respectively. Figure 4 illustrates molecular models of two conformations of
dGpdT:dApdC with SPB belonging to different families.
Figure 5 provides graphic illustration of differences in mean torsion angles for
selected cdDMPs. Table 1 presents numerical values of their torsions. The BI and
BII conformation families carry the SPB fragment in the conformation that matches
the energy minimum of the free SPB unit. Both DFT and MM computations of SPB
predict the torsion angles to be in the same region as that observed in the variety
of conformations of cdDMPs in these families. The conformation family 117 is the
only one among the selected systems that has all the torsions differ by less than 30°
from the energy minimum conformation of the free SPB. Three other families have
at least two torsions exceeding that threshold.
3.2 Multiplicity of Feasible Base-Base Complexes
Intermolecular interactions between the DNA bases have been studied since 1961
using various computational methods. Molecular structure of the bases enables the
formation of variety of their pairwise complexes as well as complexes of three and
four bases corresponding to energy minima. Experimentally observed or theoretically