POLYCYTOSINE REGIONS CONTAINED IN DNA HAIRPIN LOOPS INTERACT VIA A 4-STRANDED, PARALLEL STRUCTURE SIMILAR TO THE I-MOTIF

Thermal denaturation profiles of an oligodeoxy-nucleotide that forms a hairpin structure with a cytidine-rich loop show an unexpected transi tion at 60 degrees C at pH 5.0 but not at pH 8.0. Analytical ultracent rifugation shows that this transition reflects dimer formation via the interaction of loops from two molecules to form a novel structure ter med the h-dimer. The dependence of this structure on low pH implies th e formation of cytosine - protonated cytosine base pairs. NMR spectros copy, thermal denaturation and ultraviolet absorption spectral analysi s suggest a similarity to the i-motif structure recently proposed for the interaction of deoxycytidine oligomers. The use of hairpin loops t o farm i-motif-like structures may prove useful in searches for cognat e proteins and possibly in the production of antibodies.