Cooperativity in A-tract structure and bending properties of composite TnAn blocks

The existence of intrinsically curved DNA molecules incorporating short runs of adenines is undisputed, but none of the current models can explain the entire experimental data set. Recently, Burkhoff and Tullius Burkhoff, A. M., & Tullius, T. D. (1988) Nature 331, 455-457] offered an explanation for Hagerman's observations on A4T4N2 vs T4A4N2 polymers Hagerman, P. J. (1986) Nature 321, 449-450], which showed that A4T4N2 multimers migrate anomalously slowly on polyacrylamide gels and T4A4N2 multimers migrate normally. In A4T4N2 multimers Burkhoff and Tullius observe a hydroxy-radical cutting pattern associated with bent DNA and a B-like cutting pattern in T4A4N2. They attribute this difference in cutting pattern to a clash in the TA step of T4A4N2 and suggest that TA4N5 might already adopt an unbent B-DNA conformation Tullius T. D., & Burkhoff, A. M. (1988) in Structure and Expression. Vol. 3: DNA Bending and Curvature (Olson, W. K., Sarma, M. H., Sarma, R. H., & Sundaralingam, M., Eds.) pp 77-85, Adenine Press, Guilderland, NY]. We show that the conformation adopted by TnAn blocks is similar to that of AnTn blocks. Two A-tract structures of opposite polarity coexist in both blocks. Moreover, we demonstrate a cooperative buildup of a T-tract structure adjacent to an A-tract structure that cannot be predicted by any of the current models. We conclude that AA steps do not assume the same conformation in long tracts of A's as in isolated AA steps. Therefore, the assumption of nearest-neighbor models, that global curvature is an additive phenomenon of local effects, is invalid.