The Structure and Dynamics of DNA-cation Systems

A study of long-term effects of the polycationic spermidine molecules on the conformational stability of the oligonucleotides d(A)20 and d(A-T)20 using molecular dynamics simulations has been carried out, with an investigation into the effects of multivalent cations, particularly magnesium, on the structural preferences of the sequences. The preference of B-form DNA over A-form induced by the univalent sodium is shown to be largely disrupted by magnesium, and it is also demonstrated that magnesium ions could potentially be a source of conformational instability. The introduction of spermidine has been proven to be a source of stabilisation to the DNA structures by restricting their motions and hence greatly reducing the fluctuations in multiple parameters. However it is also shown that the overall stabilising power is not directly proportional to the number of spermidine molecules present around the DNA macromolecule. The effect of caesium ions on the conformational preference of specific DNA sequences of d(ACCGGCGCCACA) and d(ACCGGCGCCGGT) has been studied using sodium as a reference. It is found that although caesium is monovalent like sodium, it does not induce a strong preference of B-form over A-form, but rather provides extra stability for the initial state. Furthermore, it has also been demonstrated that being palindromic does not seem to provide structural stability for short DNA sequences.