Figure 1.
Scheme of two hTel G-quadruplex structures involved in this work.
Syn and anti glycosidic bond orientations are drawn in white and gray. From layer 1 to layer 3 are three G-quartets named from the orient of the first strand of G-quadruplexes.
Table 1.
List of simulations involved in this work.
Figure 2.
Structural dynamics of anti-parallel and hybrid type hTel G-quadruplex on different time scales assessed by pairwise RMSD matrices.
Figure 3.
Structural dynamics of anti_bsc0 loops.
(a), distance and angle between two thymine bases T and T
of the upper diagonal loop. The small fluctuation reflects that these two thymine bases stacked with each other in the trajectory. (b), distance and angle between A
and upper G-quartet, in the first 250 ns, A
stacked with the G-quartet, but then this stacking structure was destroyed. (c), angle between T
and T
and angle between T
and A
.
Figure 4.
TTA loops conformations discussed in this work.
Thymine in blue, adenine in green and guanine in yellow. Hydrogen bonds are drawn in gray dash lines, and all bonds connected with hydrogen are hidden.
Table 2.
Distance and angle between loop bases and their reference base groupsa.
Table 3.
Details of hydrogen bonds between loop bases and between loop base and quartet base.
Table 4.
Comparison of the absolute free energiesa of the different conformations of the loops.
Figure 5.
Structural dynamics of hybrid_bsc0 loops.
(a), distance and angle between two thymine bases T and T
of double chain reversal loop. (b), The RMSD of T
T
A
loop in [3+1] hybrid structure, and the NMR experimental structure was chosen as reference. (c), angle between T
and T
and angle between T
and A
.
Figure 6.
The probability distribution of the RMSD of G-quartets in anti_bsc0 and hybrid_bsc0 models (solid lines), and in anti_stem and hybrid_stem (dash lines).
Figure 7.
Illustration of the G-quartet base-triads.
(a), G-quartet base-triads. All four bases have similar Z-axis but distinct X-axis and Y-axis. (b), Calculating for Z by rotating the Z
by
/2 about the rt axis, and
is the angle between two Z-axes Z
and Z
.