Chemistry Commons^™

Effects Of Unpaired Bases On The Conformation And Stability Of 3-Arm Dna Junctions, Min Zhong, Michael S. Rashes, Neocles B. Leontis, Neville R. Kallenbach

Chemistry Faculty Publications

Three-arm DNA junctions, in which three double helices intersect at a branch, have unique structure and reactivity of bases at and near the branch. Their solution conformation is asymmetric in the presence of Mg2+, while bases at the branch are sensitive to single-strand-specific agents. Following the surprising report that unpaired bases at the branch stabilize three-arm junctions, we have investigated the geometry and thermodynamics of three-arm junctions containing pendant T and A bases. The results are consistent with additional structure formation in junctions containing up to four pendant bases at the branch: relative to the tight junction, the thermal stability …