Protonated polypurine/polypyrimidine DNA tracts that appear to lack the single-stranded pyrimidine loop predicted by the "H" model.

Three synthetic oligomers: 5'd(AG)8.dA.d(CT)(8)3'(A), 5'd(TC)7.d(TTA).d(GA)(8)3'(B) and d(GA)17(C) were cloned into the plasmid vector p915 in order to study the effects of sequence symmetry on pH-dependent structural transitions in polypurine/polypyrimidine DNA. When present in linear molecules all three sequences undergo transitions to protonated states. These are kinked to different degrees as determined by a non-denaturing gel mobility shift assay. Chemical probe analysis shows that the protonated states adopted by the linear forms of A and C exhibit certain features which have been regarded as indicating partially triple stranded "H" transition structures. The chemical reactivities of the transition structure adopted by linear molecule B and certain features of those exhibited by the transition structures of linear molecules A and C do not conform to the predictions of the "H" model.