Figure 1.

Molecular vises were used to apply compressive forces to short strands of duplex DNA. (A) Possible conformations of a molecular vise. The base-pairing force in the hairpin stem (composed of all A-T base pairs) imparted a roughly constant compressive force on the ends of the target strand (top duplex). When the target strand was shorter than the buckling length (left and center images), it withstood the compressive force and remained rigid. The dye separation increased as the target strand grew longer, resulting in a decrease of FRET efficiency. Past the buckling transition (right image), the target strand bent under the compressive force and the FRET efficiency recovered. Molecular cartoons were generated using Nucleic Acid Builder (18) and PyMOL (19). (B and C) Combined measurements of electrophoretic mobility and FRET. Molecular vises of five loop sizes (30, 36, 40, 46 and 50 nt) were each bound with varying-length target strands, analyzed by native PAGE, and imaged on a commercial scanner (B). FRET efficiency was quantified from gel images and plotted for each loop size as a function of the target strand length (C). The local minimum in FRET efficiency at a target strand length of 40 bp signified the buckling transition and was consistent with the predictions of a statistical mechanical model (shaded areas; see Supplementary Methods for details). The buckling transition also manifested as a change in the dependence of electrophoretic mobility on target length (B; quantified in Supplementary Figure S2). Error bars in (C) are SEM from four independent replicates.