Each of the 39 oligomers was constructed with a canonical B-DNA conformation. Simulations were carried out with periodic boundary conditions within a truncated octahedral cell, using the AMBER suite of programs  (1) with the parmbsc0 modifications  (2) to the parm99 force field  (3,4).

Simulations were run with 150 mM KCl using the parameters from Dang  (5). The number of ions was adjusted to ensure a zero net charge for the solute-counterion complex. Counterions were initially placed at random within the simulation cell, but at least 5 Å from DNA and at least 3.5 Å from one another. The complex was then solvated with a layer of water at least 10 Å thick. Water was modeled using the SPC/E parameters  (6), but eight oligomers were also run with the TIP4PEW parameters  (7) for comparison purposes.

A typical simulation thus involved around 11,500 water molecules and between 37,000 and 47,000 atoms in total (the large variation being due to the use of two water models). Electrostatic interactions were treated using the particle mesh Ewald method  (8) with a real-space cutoff of 9 Å and cubic B-spline interpolation onto the charge grid with a spacing of ∼ 1 Å. Lennard-Jones interactions were truncated at 9 Å and the pairlist was built with a buffer region and a triggered list update whenever a particle moved more than 0.5 Å from the previous update. Initial equilibration, involving energy minimization of the solvent, then of the solute-solvent system, followed by a slow thermalization, followed the protocol described earlier   (see ABC publication list).

Production simulations were carried out using an NPT ensemble and the Berendsen algorithm  (9) to control temperature and pressure, with a coupling constant of 5 ps for both parameters. All chemical bonds involving hydrogen atoms were restrained using SHAKE  (10), allowing for stable simulations with a 2 fs time step. Center of mass motion was removed every 5000 steps to avoid kinetic energy building up in translational motion  (11) and to keep the solute centered in the simulation cell.

Each of the 39 oligomers was simulated for 1000 ns, saving conformational snapshots every 1 ps. Only the final 900 ns were then used for the following analyses. This led to a database of 35.1 μs of trajectories, containing more than 35 million conformational snapshots. This  dataset (in a compressed format) requires roughly 90 terabyte of storage. A version without solvent, requires just over 300 gigabytes.

The first stage of conformational analysis was performed using Curves+, which provides a full set of helical, backbone and groove geometry parameters (12). Curves+ uses the commonly agreed "Tsukuba" reference frame to describe each base  (13) and respects the Cambridge convention for the names and signs of all helical parameters  (14).

Parameters are grouped into five sets: intra-base pair, or intra-BP for short, (shear, stretch, stagger, buckle, propeller, opening); BP-axis (Xdisp, Ydisp, inclination and tip); inter-BP (shift, slide, rise, tilt, roll, twist); backbone (in the 5'→3' direction for each nucleotide, α P-O5', β O5'-C5', γ C5'-C4', δ C4'-C3', ε C3'-O3', ζ O3'-P, the glycosidic angle χ and the sugar pucker phase and amplitude); groove (minor and major groove widths and depths).

All Curves+ parameters are output in an unformatted file which can be analyzed with the program, Canal (12). Canal can analyze individual base pairs or base pair steps within the data from a single oligomer trajectory or make a cumulative analysis over many trajectories.

References

1.   Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham III, T.E., DeBolt, S., Ferguson, D., Seibel, G.L. and Kollman, P.A. (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comp. Phys. Commun., 91, 1-41.

2.   Perez, A., Marchan, I., Svozil, D., Sponer, J., Cheatham, T.E.3., Laughton, C.A. and Orozco, M. (2007) Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys J, 92, 3817-3829.

3.   Cheatham, T.E.3., Cieplak, P. and Kollman, P.A. (1999) A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J Biomol Struct Dyn, 16, 845-862.

4.   Case, D.A., Cheatham, T.E., Darden, T., Gohlke, H., Luo, R., Merz, K.M., Onufriev, A., Simmerling, C., Wang, B. and Woods, R.J. (2005) The Amber biomolecular simulation programs. J Comput Chem, 26, 1668-1688.

5.   Dang, L.X. (1995) Mechanism and thermodynamics of ion selectivity in aqueous-solutions of 18-crown-6 ether - A molecular dynamics study. J Am Chem Soc, 117, 6954-6960.

6.   Berendsen, H.J.C., Grigera, J.R. and Straatsma, T.P. (1987) The missing term in effective pair potentials. J. Phys. Chem., 91, 6269-6271.

7.   Horn, H.W., Swope, W.C., Pitera, J.W., Madura, J.D., Dick, T.J., Hura, G.L. and Head-Gordon, T. (2004) Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. J Chem Phys, 120, 9665-9678.

8.   Essmann, U., Perera, L., Berkowitz, M.L., Darden, T., Lee, H. and Pedersen, L.G. (1995) A smooth particle mesh Ewald method. J Chem Phys, 103, 8577-8593.

9.   Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A. and Haak, J.R. (1984) Molecular dynamics with coupling to an external bath. J. Chem. Phys., 81, 3684-3690..

10.   Ryckaert, J.P., Ciccotti, G. and Berendsen, H.J.C. (1977) Numerical Integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comp. Phys., 23, 327-341..

11.   Harvey, S.C., Tan, R.K.Z. and Cheatham, T.E. (1998) The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition. J Comput Chem, 19, 726-740.

12.   Lavery, R., Moakher, M., Maddocks, J.H., Petkeviciute, D. and Zakrzewska, K. (2009) Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Res, 37, 5917-5929.

13.   Olson, W.K., Bansal, M., Burley, S.K., Dickerson, R.E., Gerstein, M., Harvey, S.C., Heinemann, U., Lu, X.J., Neidle, S., et al. (2001) A standard reference frame for the description of nucleic acid base-pair geometry. J Mol Biol, 313, 229-237.

14.   Dickerson, R.E. (1989) Definitions and nomenclature of nucleic acid structure components. Nucleic Acids Res, 17, 1797-1803.