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Detection Of Mg2+-Dependent, Coaxial Stacking Rearrangements In A Bulged Three-Way Dna Junction By Single-Molecule Fret, Michael P. Leveille, Thao Tran, Gianna Dingillo, Brian Cannon

Physics: Faculty Publications and Other Works

Three-way helical junctions (3WJs) arise in genetic processing, and they have architectural and functional roles in structured nucleic acids. An internal bulge at the junction core allows the helical domains to become oriented into two possible, coaxially stacked conformers. Here, the helical stacking arrangements for a series of bulged, DNA 3WJs were examined using ensemble fluorescence resonance energy transfer (FRET) and single-molecule FRET (smFRET) approaches. The 3WJs varied according to the GC content and sequence of the junction core as well as the pyrimidine content of the internal bulge. Mg2+ titration experiments by ensemble FRET show that both …