Effect of Microenvironment on the Geometrical Structure of d(A)5 d(T)5 and d(G)5 d(C)5 DNA Mini-Helixes and the Dickerson Dodecamer: A Density Functional Theory Study.

We report a comprehensive quantum-chemical study on d(A)5·d(T)5 and d(G)5·d(C)5 DNA mini-helixes and the Dickerson dodecamer d[CGCGAATTCGCG]. The research was performed to model the evolution of the spatial structure of d(A)5·d(T)5 and d(G)5 d(C)5 DNA mini-helixes all the way from vacuum to water bulk. The influence of external factors such as the presence of counterions and the extent of hydration was included. Also, for comparison, limited calculations have been carried out on the Dickerson dodecamer. The study has been performed at the density functional theory level using B97D3 and ωB97XD exchange-correlation functionals augmented by the Def2SVP basis set. We found that the (dA)5·(dT)5 anion when placed in vacuum forms a DNA duplex, which possesses an intermediate form between a helix and a ladder. The presence of compensating Na+ counterions or explicit microhydration of minor and major grooves stabilizes a DNA mini-helix of B-shape. Factors such as water bulk play a minor role. Somewhat different behavior has been found in the case of the (dG)5·(dC)5 duplex. In this case, we observe the formation of B-type mini-helixes even for the (dG)5·(dC)5 anion placed in vacuum. This is due to an additional stabilization originated from the appearance of an extra hydrogen bond, compared to an AT base pair. To assess whether the obtained results are transferable to different sizes of mini-helixes, similar calculations have been performed for the duplex formed by the Dickerson dodecamer which contains a total of 12 dG·dC and dA·dT base pairs. It has been found that in vacuum, analogous to the d(A)5·d(T)5 duplex, this system possesses a shape which is also quite close to a ladder. However, the presence of factors such as hydration restores the B-type geometry. Also, our results completely in line with the results of electrospray-ionization experiments suggest that uncompensated by counterions the DNA backbone preserves the duplex geometry in vacuum. We present arguments that this state is kinetically unstable.