Design, synthesis and structural analysis of novel bent DNAs containing cyclic uridylate dimer analogues

We developed novel bent DNAs containing cyclic uridylate dimmer analogues (Figure 1, 1a-c), which possess an alkylene linkage with various length. These structural properties were revealed by fluorescence energy transfer (FRET) experiments, and their bending angles were found to be quite deep. This result suggests that our strategy can be applicable to highly refined studies to analyze various structure-specific DNA recognitions.