Table 1.
Summary of main MD results for the different DNA helices considered. All WC base pairs are in Z-DNA form. Considering the TRs, these sequences describe homoduplexes, except for the terminal bases (when present) that are bonded to their WC counterpart. For example, the sequence 5′-C(GGC)4G-3′ has as complementary strand, 5′-C(GGC)4G-3′. The ‘ZZ’ or ‘BZ’ subindices in the structural labels indicate that that GG mismatches are in Z-DNA form, i.e., forming ZZ junctions; or in B-DNA form, i.e, forming BZ junctions with the adjacent WC pairs. ‘Ribbon’-DNA indicates a DNA that is unwinding such that its strands become nearly parallel, as it would occur in a B-to-Z DNA transition. All simulations results presented here were obtained in a 5M NaCl salt environment. Additional low salt (0M and 150mM) simulations were all unstable, and are not explicitly noted here. Interaction notation: base-stacking ‘::’, Hbonds between Gs in the same mismatch ‘·’, and Hbonds between mismatched Gs in different pairs ‘:’
| Label | Sequence | Force fields | Stability | Long-lived stackings |
|---|---|---|---|---|
| GGC4BZ, in, GGC4ZZ, in | C(GGC)4G | BSC0, BSC1 | Unstable. Ribbon-DNA forms very fast | |
| GGC4BZ, out | C(GGC)4G | BSC0 | Stable | |
| GGC4ZZ, out | C(GGC)4G | BSC0, BSC1, OL15 | BSC0 and OL15 stable, BSC1 unstable | |
| GGC8BZ, out | (GGC)8 | BSC0, BSC1, OL15 | Stable. Mismatches remain out for all three FFs. All (BSC0) or many (BSC1, OL15) mismatches align towards their 5′-end, sometimes forming H-bonds with the backbone | BSC1: G35:G8, G35::G38; OL15: G14::G17, G14::G41, G14::G38::G41, G11::G35 |
| GGC8ZZ, out | (GGC)8 | BSC0, BSC1, OL15 | Stable. Many mismatches align towards their 5′-end, sometimes forming H-bonds with the backbone. G11·G38 flipped inside the core in BSC1 | BSC1: G20::G32; G17::G26; G38::G41 |
| GGC8BZ, in | (GGC)8 | BSC0, BSC1, OL15 | Unstable. Bent structures lose helical shape and deform | |
| GGC8ZZ, in | (GGC)8 | BSC0, BSC1, OL15 | Semi-stable. All the mismatched GG residues stay inside the helical core, helices tend to bend. Ribbon-DNA forms: Bases show half a turn (180°) after 24 base pairs, i.e. ∼7.5° twist per base pair | |
| CGG4ZZ, in | G(CGG)4C | BSC0, BSC1, OL15 | Stable. All the mismatched GG residues stay inside the helical core, G9·G20 flip out in BSC1 | |
| CGG4ZZ, out | G(CGG)4C | BSC0, BSC1, OL15 | Unstable, various bases flip back in, a trend that increases with simulation time | |
| GGC4ZZ, alt | (GGC)4G | BSC0, BSC1, OL15 | Stable. All the single Gs remain extruded far enough so that the whole become symmetric and stable | BSC1: G8::G24; OL15: G8::G24 |