Structure
116d
117d
118d
137d
160d
172d
189d
197d
1d78
1d82
1d93
1dc0
1dn6
1dnz
1g00
1m77
220d
232d
243d
257d
260d
281d
295d
2d47
2d94
317d
321d
348d
382d
395d
396d
399d
3ana
414d
440d
9dna
RMSd(A)
RMSd(B)
RMSd(A)
RMSd(B)
1.1
1.2
1.6
1.5
1.4
1.5
1.5
1.2
1.3
1.6
1.5
2.5
1.8
1.4
1.0
1.4
1.3
2.6
1.6
1.1
1.2
1.2
1.5
1.5
1.9
1.5
1.6
1.4
1.1
1.2
1.3
2.7
1.3
1.5
1.4
1.7
5.7
5.6
2.6
4.7
4.9
3.2
2.7
3.7
3.0
2.6
2.7
4.0
3.7
4.5
2.3
5.1
4.6
4.1
2.5
2.5
4.7
3.1
2.7
6.2
2.7
2.7
5.1
4.7
4.6
4.8
4.6
6.8
3.3
4.4
4.9
2.7
3.8
4.3
3.0
3.4
3.6
3.4
2.6
2.6
3.0
3.1
2.9
4.4
3.6
4.0
2.4
3.5
3.3
4.2
3.0
2.4
3.7
2.6
3.1
4.1
2.8
2.8
4.3
3.8
3.6
3.5
3.9
3.5
3.6
3.6
3.5
3.0
3.5
2.7
1.9
2.8
2.6
1.6
2.4
2.2
1.9
2.1
2.5
3.1
2.7
2.4
1.3
2.5
2.9
2.3
2.0
1.3
2.3
2.3
2.0
2.7
1.8
2.5
2.5
2.1
2.6
2.3
2.3
4.1
2.7
2.97
2.93
2.00
Table S1. RMSd (in Å) from canonical A and B forms obtained from (LEFT columns, in
roman) canonical A/B conformations and the last 100 ps of parmbsc0 MD simulations
(RIGHT columns in italics) for 36 A-DNAs in the Nottingham database.
-1-
LEGENDS TO SUPPLEMENTARY FIGURES
Figure S1.Bidimensional error profiles (LMP2 as reference) in the α/γ map for the Npuckering. Relative energies are in kcal/mol and degrees.
Figure S2. Selected monodimensional profiles in relevant regions of the α/γ map for both
North and South puckerings. Yellow: parmbsc0, blue: LMP2, pink: DFT.
Figure S3. Variation in the widhts of the grooves (TOP) and BI/BII transitions (BOTTOM) in
parm94 (orange) and parm99 (magenta) MD simulations. Experimental values are marked in
solid with their associated standard deviation as dashed lines (black: X-ray; red: NMR).
Figure S4. Variation in the total number of hydrogen bonds in two independent 200 ns MD
simulations of DD (green and blue) using parmbsc0. The maximum number of canonical
hydrogen bonds for this structure is 26 (see Table 4).
Figure S5. Variation of twist with the sequence as determined in parm94 (orange) and
parm99 (magenta) simulations. The average values obtained by taking all NMR (red) or X-ray
(black) structures for this sequence are shown as reference.
Figure S6. Distribution of the backbone torsions during MD simulations of DD (parmbsc0 in
green and parm99 in red) compared with the distribution of values in experimental databases
of B-DNA (in blue).
Figure S7. Distribution of helical parameters during MD simulations of DD (parmbsc0 in
green and parm99 in red) compared with the distribution of values in experimental databases
of B-DNA (in blue).
Figure S8. Evolution of α/γ pairs for the 8 central basepairs of DD during one 200 ns
parmbsc0 simulation. Alfa is magenta (strand I) and yellow (strand II), gamma is blue (strand
I) and green (strand II).
Figure S9. Distribution of different average helical basepair step parameters in parmbsc0
simulations of Nottingham’s database of B-DNAs. Displacements are in Å and angles in
degrees.
Figure S10. Evolution along time of different structural parameters in parmbsc0 simulations
of DD-RNA (panel A) and a RNA duplex rich in mismatches (URL064; panel B).
Figure S11. Evolution along time of different structural parameters in parmbsc0 simulations
of a RNA-pseudoknot (UR0004).
Figure S12. Evolution along time of rmsd to experimental structure (TOP), average twist
(MIDDLE) and average groove width (BOTTOM) in parmbsc0 simulations of parallel
stranded G-DNA.
Figure S13. Evolution along time of rmsd to experimental structure (TOP) and average
groove width (BOTTOM) in parmbsc0 simulations of antiparallel G-DNA..
-2-
Figure S14. Parmbsc0 simulations of antiparallel triplex based on the d(A-A·T) motif. TOP:
Evolution along time of rmsd: to X-ray structure using common backbone atoms (green) and
to average structure using all atoms (black). MIDDLE: Evolution of average twist along time.
BOTTOM: Evolution of groove width along time (brown: major-major groove; blue: minormajor groove; magenta: minor groove).
Figure S15. Parmbsc0 simulations of antiparallel triplex based on the d(G-G·C) motif. TOP:
Evolution along time of rmsd: to X-ray structure using common backbone atoms (green) and
to average structure using all atoms (black). MIDDLE: Evolution of average twist along time.
BOTTOM: Evolution of groove width along time (brown: major-major groove; blue: minormajor groove; magenta: minor groove).
Figure S16. Parmbsc0 simulations of parallel triplex based on the d(T·A-T) motif. TOP:
Evolution along time of rmsd: to X-ray structure using common backbone atoms (green) and
to average structure using all atoms (black). MIDDLE: Evolution of average twist along time.
BOTTOM: Evolution of groove width along time (brown: major-major groove; blue: minormajor groove; magenta: minor groove).
Figure S17. Evolution along time of rmsd to experimental (green) and average (black) (TOP),
average twist (MIDDLE) and average groove width (BOTTOM) in parmbsc0 simulations of
ZDNA.
Figure S18. Evolution along time of different helical parameters in parmbsc0 simulations of
antiparallel Hoogsteen duplex DNA.
Figure S19. Evolution along time of different helical parameters in parmbs0 simulations of
DNA·RNA hybrid. RMSd: yellow: VS NMR, blue: VS Aform, pink: VS Bform.
Figure S20. Distribution of the time needed to achieve RMSd(B)<RMSd(A) in 36
simulations of duplex DNA starting from the A-type experimental conformation
(Nottingham’s database of A-DNAs).
-3-
Figure S1
-4-
Figure 2
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Figure S3
-6-
Figure S4
-7-
Figure S5
-8-
Figure S6
-9-
Figure S7
- 10 -
Figure S8
- 11 -
Figure S9
- 12 -
Figure 10.
- 13 -
Figure S11
- 14 -
Figure S12
- 15 -
Figure S13
- 16 -
Figure S14
- 17 -
Figure S15
- 18 -
Figure S16
- 19 -
Figure S17
- 20 -
Figure S18
- 21 -
Figure S19
- 22 -
Figure S20
- 23 -