DNA Machines: Bipedal Walker and Stepper

Abstract

The assembly of a "bipedal walker" and of a "bipedal stepper" using DNA constructs is described. These DNA machines are activated by H(+)/OH(-) and Hg(2+)/cysteine triggers. The bipedal walker is activated on a DNA template consisting of four nucleic acid footholds. The forward "walking" of the DNA on the template track is activated by Hg(2+) ions and H(+) ions, respectively, using the thymine-Hg(2+)-thymine complex or the i-motif structure as the DNA translocation driving forces. The backward "walking" is activated by OH(-) ions and cysteine, triggers that destroy the i-motif or thymine-Hg(2+)-thymine complexes. Similarly, the "bipedal stepper" is activated on a circular DNA template consisting of four tethered footholds. With the Hg(2+)/cysteine and H(+)/OH(-) triggers, clockwise or anticlockwise stepping is demonstrated. The operation of the DNA machines is followed optically by the appropriate labeling of the walker-foothold components with the respective fluorophores/quenchers units.