Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine
| Authors | |
|---|---|
| Year of publication | 2001 |
| Type | Article in Periodical |
| Magazine / Source | Biophysical Journal |
| MU Faculty or unit | |
| Citation | |
| Field | Biophysics |
| Keywords | STRANDED GUANINE TETRAPLEX; OXYTRICHA TELOMERIC DNA; MESH EWALD METHOD; G-C REPEATS; CRYSTAL-STRUCTURE; FORCE-FIELD; BASE-PAIRS; AB-INITIO; G-QUARTET; STABLE TRAJECTORIES |
| Description | The ability of the four-stranded guanine (G)-DNA motif to incorporate nonstandard guanine analogue bases 6-oxopurine (inosine, I), 6-thioguanine (tG), and 8-thiopurine (tl) has been investigated using large-scale molecular dynamics simulations. The simulations suggest that a G-DNA stem can incorporate inosines without any marked effect on its structure and dynamics. In the simulations, the incorporation of 6-thioguanine and 6-thiopurine sharply destabilizes four-stranded G-DNA structures, in close agreement with experimental data. The main reason is the size of the thiogroup leading to considerable steric conflicts and expelling the cations out of the channel of the quadruplex stem. The G-DNA stem can accommodate a single thioguanine base with minor perturbations. Incorporation of a thioguanine quartet layer is associated with a large destabilization of the G-DNA stem whereas the all-thioguanine quadruplex immediately collapses. |
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