How the structure of an adenine tract depends on sequence context: a new model for the structure of TnAn DNA sequences

Abstract

We present a new model to explain the bending and local structural properties of TnAn sequences in DNA. Current models suggest that an adenine tract has the same unusual structure when found in a TnAn sequence as it has when surrounded by mixed-sequence B-DNA. On the basis of hydroxyl radical cleavage patterns of several TnAn sequences, we instead propose that the T2A2 or T3A3 core of such sequences is B-DNA-like but that adenines and thymines outside of this core, if sufficient in number, can form the unusual structure adopted by adenine tracts surrounded by mixed sequence DNA. We pursued further the structure of T7A7N7, a molecule which exhibits reduced electrophoretic mobility on native polyacrylamide gels and is therefore presumed to be bent. We attempted to mimic the structure of T7A7N7 that was predicted by our model by designing two new sequences, one in which the T3A3 core of T7A7N7 is substituted by six nucleotides of mixed sequence (N6) and the other in which the T2A2 core is replaced by N4. Hydroxyl radical cleavage patterns of all three molecules are nearly indistinguishable. All three molecules run anomalously slowly on a native polyacrylamide gel, with the mobility of T4N6A4N7 > T7A7N7 approximately T5N4A5N7. Analysis of the hydroxyl radical cutting pattern of T7A7N7 by Fourier transformation reveals the occurrence of an unusual structure at intervals of approximately 10 bp, a periodicity which is not evident in the sequence of the DNA.