Predictive modelling of topology and loop variations in dimeric DNA quadruplex structures

Abstract

We have used a combination of simulated annealing (SA), molecular dynamics (MD) and locally enhanced sampling (LES) methods in order to predict the favourable topologies and loop conformations of dimeric DNA quadruplexes with T2 or T3 loops. This follows on from our previous MD simulation studies on the influence of loop lengths on the topology of intramolecular quadruplex structures [P. Hazel et al. (2004) J. Am. Chem. Soc., 126, 16 405-16 415], which provided results consistent with biophysical data. The recent crystal structures of d(G4T3G4)2 and d(G4BrUT2G4) (P. Hazel et al. (2006) J. Am. Chem. Soc., in press) and the NMR-determined topology of d(TG4T2G4T)2 [A.T. Phan et al. (2004) J. Mol. Biol., 338, 93-102] have been used in the present study for comparison with simulation results. These together with MM-PBSA free-energy calculations indicate that lateral T3 loops are favoured over diagonal loops, in accordance with the experimental structures; however, distinct loop conformations have been predicted to be favoured compared to those found experimentally. Several lateral and diagonal loop conformations have been found to be similar in energy. The simulations suggest an explanation for the distinct patterns of observed dimer topology for sequences with T3 and T2 loops, which depend on the loop lengths, rather than only on G-quartet stability.

Figure 1

Schematic diagrams of the (a) parallel, (b) lateral and (c) diagonal loop dimeric G-quadruplexes which were simulated in this work.

Figure 2

Structures with lateral T3 loops over the wide quadruplex groove, generated during SA runs. (a) T3-Lw-1, (b) T3-Lw-2, (c) T3-Lw-3, (d) T3-Lw-4, (e) T3-Lw-5 and (f) T3-Lw-6. The loop bases are shown in green and a G-quartet in black. Lw indicates a lateral loop over the wide quadruplex groove, as opposed to the narrow groove (Ln).

Figure 3

Structures with lateral T3 loops over the narrow quadruplex groove, generated using SA. (a) T3-Ln-1, (b) T3-Ln-2 and (c) T3-Ln-3.

Figure 4

T₃ lateral loop final structures after LES simulations. (a) T₃-L_w-1 loop 1 and (c) 2 after 4 ns LES simulation, (b) T₃-L_w-2 loop 1 and (d) loop 2 after 2.7 ns LES simulation and (e) T₃-L_n-1 loop 1 after 4 ns LES simulation. The five LES copies are shown overlapped in each case. A G-quartet is also shown in black.

Figure 5

T₃ diagonal loop MD simulation. (a) Stable loop conformation averaged over the final 2 to 4 ns of MD and (b) final structure of the unstable loop, which formed within the last 200 ps of the simulation.

Figure 6

T₂ final loop conformations after 4 ns MD simulation (400 ps only for the diagonal loop). (a) Diagonal T₂ loop, (b) lateral T₂ loop over the narrow groove, (c) lateral T₂ loop over the wide groove and (d) parallel T₂ loops. The loops are shown in purple, and G-quartets in black, channel K⁺ ions are shown as red spheres.

Figure 7

MD simulations of (a) d(G₄T₃G₄)₂. X-ray structure T₃ loop conformation averaged over 2 to 4 ns (b) NMR structure T₃ loop conformation averaged over 2 to 4 ns and (c) most favourable predicted T₃-L_w-5 loop averaged over 1 to 2 ns MD.

Figure 8

(a) Head-to-tail and (b) head-to-head quadruplex structures with two T₂ loops shown in purple. The complete quadruplexes are shown, with K⁺ channel ions in red. These structures have been averaged over the final 2 ns of the 4 ns simulations.