Figure 1.

Molecular construction and square cell. (A) Schematic of the DNA binding to the inner glass capillary and the magnetic bead such that pulling the bead away from the surface will cause the dsDNA shown on the right side of the diagram to be separated into two single DNA strands. Note that the figure is not to scale, considering that λ DNA contains 48,502 bp. (B) Schematic of the side view of the square capillary containing the round glass capillary to which the DNA molecules are bound. The magnetic tweezer apparatus exerts the controlled force on the magnetic beads, a microscope is used for observation, and two thermoelectric coolers are used to control the temperature of the sample during the initial incubation. The magnetic beads are pulled to the right in a direction parallel to the bottom and top surfaces of the square capillary, and perpendicular to the surface of the round capillary at a height equal to the radius of the round capillary, where we focus the microscope. This design allows us to view DNA molecules that are offset from the surfaces of the square capillary, and to infer the number of separated base pairs by measuring the separation between the magnetic bead and the surface of the round capillary.