TIT for TAT: The properties of inosine and adenosine in TATA box DNA

The sequence dependent conformation. flexibility and hydration properties o f DNA molecules constitute selectivity determinants in the formation of pro tein-DNA complexes. TATA boxes in which AT basepairs (bp) have been substit uted by IC bp (TITI box) allow for probing these selectivity determinants f or the complexation with the TATA box-binding protein (TBP) with different sequences but identical chemical surfaces. The reference promoter Adenoviru s 2 Major Late Promoter (mlp) is formed by the apposition of two sequences with very different dynamic properties: an alternating TATA sequence and an A-tract. For a comparative study, we carried out molecular dynamics simula tions of two DNA oligomers, one containing the mlp sequence (2 ns), and the other an analog where AT basepairs were substituted by IC basepairs (1 ns) . The simulations, carried out with explicit solvent and counterions, yield straight purine tracts, the A-tract being stiffer than the I-tract, an alt ernating structure for the YRYR tracts, and hydration patterns that differ between the purine tracts and the alternating sequence tracts. A detailed a nalysis of the proposed interactions responsible for the stiffness of the p urine tracts indicates that the stacking between the bases bears the strong est correlation to stiffness. The hydration properties of the minor groove in the two oligomers are distinctly different. Such differences are likely to be responsible for the stronger binding of TBP to mlp over the inosine-s ubstituted variant. The calculations were made possible by the development, described here, of a new set of forcefield parameters for inosine that com plement the published CHARMM all-hydrogen nucleic acid parametrization.