(a)(b)
(c)(d)
(e)(f)
(g)(h)
(i)(j)
Figure S1.Root-mean-square displacements (Å) of G-tetrad guanines compared to minimized reference structures over 50 nanosecond simulation:(a) G3-antiparallel, (b) G4-antiparallel, (c) G4-parallel, (d) G5-antiparallel, (e) G5-parallel, (f) G6-antiparallel, (g) G6-parallel, (h) G7-antiparallel, (i) G7-parallel, and (j) G7-antiparallel, assuming the formation of “T-tetrads”.
(a) (b)
(c) (d)
(e)
Figure S2. The final snapshots of50 nanosecond simulations for G-tetrads G4-G7. Only those strand orientations that are energetically less favorable are presented:(a) G4-parallel, (b) G5-parallel, (c) G6-antiparallel, (d) G7-parallel,and (e) G7-antiparallel, assuming the formation of “-tetrads”.
Figure S3. Energy-variable dissociation curves for [G5]5-, [G6]5-, and [G7]5-.
Figure S4. Energy-variable dissociation curves for [(G3)2]5- and [(G4)2]5-.
Table S1. Summary of the number of stacking pairs and hydrogen bonding (HB) pairs in the last 100 picoseconds restrained and 50 nanoseconds non-restrained MD simulations.
Quadruplex / No. Stacking / No. HB among the quartet atoms / No. HB between quartet and non-quartet atomsMinimization / MD / Minimization / MD / Minimization / MD
G1-ammonium / 9 / 12 / 30.0 / 38.6 / 10.6 / 10.9
G1 / 9 / 6 / 46.0 / 42.4 / 8 / 12.7
G3-antiparallel / 9 / 7 / 45.0 / 44.5 / 6 / 14.0
G4-antiparallel / 8 / 6 / 36.0 / 28.6 / 0 / 13.9
G4-parallel / 7 / 5 / 33.0 / 23.9 / 2 / 15.3
G5-antiparallel / 8 / 6 / 38.0 / 24.9 / 1 / 16.7
G5-parallel / 6 / 5 / 33.0 / 24.9 / 1 / 16.8
G6-antiparallel / 7 / 2 / 34.0 / 28.7 / 2 / 11.2
G6-parallel / 6 / 3 / 33.0 / 26.4 / 5 / 15.3
G7-antiparallel / 4 / 2 / 24.0 / 2.4 / 2 / 15.6
G7-parallel / 2 / 2 / 23.0 / 8.4 / 3 / 27.2
G7-T-tetrad / 4 / 2 / 9.0 / 20.8 / 6 / 23.2