1. Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III) 
Thomas E Cheatham, Peter A Kollman 
Structure 
Volume 5, Issue 10, Pages (October 1997)
DOI: /S (97)

2. Figure 1
Root mean square deviation (rmsd) versus time of the simulation of A-DNA with four Co(NH3)63+ ions. The rmsd values (Å) were calculated, using the program carnal, over the entire trajectory taken at 1 ps intervals. The rmsd to canonical B-DNA is shown in black and the rmsd to canonical A-DNA is shown in gray from the A-start simulation.
Structure 1997 5, DOI: ( /S (97) )

3. Figure 2
Rmsd versus time of the simulation of B-DNA with four Co(NH3)63+ ions. The rmsd values (Å) were calculated, using the program carnal over the entire trajectory taken at 1 ps intervals. The rmsd to canonical B-DNA is shown in black and the rmsd to canonical A-DNA is shown in gray from the B-start simulation.
Structure 1997 5, DOI: ( /S (97) )

4. Figure 3
Sugar pucker pseudorotation values versus time for each individual nucleotide. Separate graphs are shown for each nucleotide in the d[ACCCGCGGGT]2 duplex representing the sugar pucker pseudorotation phase (°) as a function of time (ps) from the B-start simulation. Low values (< 30°) represent C3′-endo and values above ∼150° represent C2′-endo.
Structure 1997 5, DOI: ( /S (97) )

5. Figure 4
Stereo views of the average structures from the simulations compared to the A-DNA crystal structure. All the structures were all-atom rms fitted to the crystal structure prior to display. (a) The average structure from the control simulation from 1–2 ns. (b) An overlay of the A-start (1–2 ns) and B-start (2.5–3.3 ns) average structures. (c) The refined structure of d[ACCCGCGGGT]2 crystallized in the presence of Ba2+ [10] (crystal) obtained from the Nucleic Acid Database (pdb220d.ent) [50].
Structure 1997 5, DOI: ( /S (97) )

6. Figure 5
Distances across the major groove and from the Co(NH3)63+ ions to DNA in the A-start simulation. All distances are in angstroms and plotted versus time in picoseconds at 1 ps intervals. The data has been smoothed by performing a running average over 25 ps. To make the specification of the atoms more concise in the text which follows, the symbol ‘:’ denotes the start of the residue number and separates the atom name. The DNA is residues (5′ to 3′) 1–10 and 11–20 and the Co(NH3)63+ ions are residues 21–24. (a) Distances representing the bend or width across the major groove. These are to (black), to (blue), to (red) and to (yellow). Short distances (< 15 Å) are found in A-DNA structures compared with ∼20 Å for B-DNA structures (see Table 2, control). (b) Distances representing the approach from the first Co(NH3)63+ ion to base pairs in the center of the major groove. These are from to the center of mass of and (black), to the center of mass of and (blue), to the center of mass of and (red), and to the center of mass of and (yellow). The short distances here show that the first Co(NH3)63+ ion is close to the GpGpG pocket on the second strand (:17,18,19). (c) Same as (b) except distances are from the second Co(NH3)63+ ion, The short distances show that this ion is in the other GpGpG pocket (:7,8,9). (d) Distances representing the proximity of the third Co(NH3)63+ ion to the bend across the major groove. This is represented as the distance of the to the bisector or midpoint of the distances presented in (a), using the same color scheme. Plots equivalent to (b) and (c) are not shown for the third and fourth Co(NH3)63+ ions as these never move into the GpGpG pockets, but instead remain in proximal association with the backbone. Short distances (< ∼5 Å) in this plot suggest that the ion is bridging the opposing strands across the major groove. (e) Same as (d) except the distances are from
Structure 1997 5, DOI: ( /S (97) )

7. Figure 6
Distances across the major groove and from the Co(NH3)63+ ions to DNA in the B-start simulation. The plots are equivalent to those in Figure 5, except the data is from the B-start simulation.
Structure 1997 5, DOI: ( /S (97) )

8. Figure 7
Hydration and counterion association of A-DNA in the presence of Co(NH3)63+. Iso-contours of the water oxygen (blue), Co(NH3)63+ cobalt (yellow) and Co(NH3)63+ nitrogen (red) atomic density over the time range of 1000 to 2000 ps is displayed in stereo along with the average structure from the A-start simulation. The average structure was created, and the atomic density generated, as described in the Materials and methods section. The whole molecule is shown in (a) and a close up into the top GpGpG region is shown in (b). The atomic density is contoured at a level of 12.0 hits per 1000 frames or roughly three times the bulk water density.
Structure 1997 5, DOI: ( /S (97) )

9. Figure 8
The A-DNA and B-DNA starting structures. Stereo views of the starting DNA structures (in gray) and hand-placed Co(NH3)63+ ions (in black) are presented.
Structure 1997 5, DOI: ( /S (97) )