Structure RMSd(A) RMSd(B) RMSd(A) RMSd(B)

Transcription

1 Structure RMSd(A) RMSd(B) RMSd(A) RMSd(B) 116d d d d d d d d d d d dc dn dnz g m d d d d d d d d d d d d d d d d ana d d dna 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

2 LEGENDS TO SUPPLEMENTARY FIGURES Figure S1.Bidimensional error profiles (LMP2 as reference) in the α/γ map for the N- puckering. 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

3 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)

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