Solution structure of a DNA three-way junction containing two unpaired thymidine bases. Identification of sequence features that decide conformer selection

The solution structure of a DNA three-way junction (3H) containing two unpa ired thymidine bases at the branch site (3HT2), was determined by NMR. Arms A and B of the 3HT2 form a quasi-continuous stacked helix, which is underw ound at the junction and has an increased helical rise. The unstacked arm C forms an acute angle of approximately 55 degrees with the unique arm A. Th e stacking of the unpaired thymidine bases on arm C resembles the folding o f hairpin loops. From this data, combined with the reported stacking behavi or of 23 other 3HS2 s, two rules are derived that together correctly reprod uce their stacking preference. These rules predict, from the sequence of an y 3HS2, its stacking preference. The structure also suggests a. plausible m echanism for structure-specific recognition of branched nucleic acids by pr oteins. (C) 2000 Academic Press.