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Abstract
In view of the current paucity of experimental structural data, the molecular modelling of DNA triple helices plays a particularly important role in helping to understand more clearly their structure and the factors contributing to their stabiiity. At the same time, it makes it difficult to assess the “realism” of the simulations. We have used molecular modelling, and particularly molecular dynamics, to study both (poly-purine)-(polypyrimidine)(polypyrimidine) and (polypyrimidine)·(polypurine)·(polypurine) triplexes. The importance of treating solvation and electrostatic interactions in as accurate a manner as possible is clear, resulting in the need for large scale molecular simulations.
Recently, there has been discussion as to whether the (polypurine)·(polypyrimidine)·(polypyrimidine)-type triplexes have conformational features (particularly sugar puckers) resembling A-DNA, as in the original fibre-diffraction-derived model, or more like B-DNA. Reported here are the results of two 160ps molecular dynamics simulations of the triplex d(A)10.d(T)10.d(T)10, performed with explicit solvent under periodic boundary conditions, starting from both A-and B-type structures. Both simulations show similar behaviour, with partial unwinding of the helices (reduction in twist and increase in rise), and a preponderance of O1′-endo sugar puckers.