Fig. 2.

Gel evidence for the operation of the device. (a) Formation and interconversion of Frame structure and PX, JX₂, and BX motifs demonstrated by nondenaturing gel electrophoresis. This is a 10% nondenaturing polyacrylamide gel, run at 22°C and stained with stains-all dye (Sigma E-7762). The lanes are described from the right: lane M, 10-bp ladder marker; lane F, the unstructured intermediate, Frame; lane P, the device assembled with PX set strands; lane J, the device assembled with JX₂ set strands; lane B, the device assembled with BX set strands. Lanes J and B (left of P) contain the products of removing the PX set strands from the material in lane P and replacing them with set strands corresponding to BX and JX₂, respectively. Lanes B and P (left of J) contain the products of removing the JX₂ set strands from the material in lane J and replacing them with those corresponding to BX and PX. Lanes J and P (left of B) contain the products of removing the BX set strands from the material in lane B and replacing them with those corresponding to JX₂ and PX. (b) Cycling the device. The gel shows the cycling of the device through six possible transitions starting from any of the three states (here, we have started with BX). Lane M shows the 10-bp ladder marker. Continuing right, lane B is the initial BX conformation, lane P is PX transformed from BX in lane B, lane J is JX₂ from PX in lane P, and lane B is BX from the JX₂. Proceeding right, lane J is JX₂ again from BX in lane B, lane P is PX from JX₂ in lane J, and finally lane B is BX from PX in lane P. Thus, BX can be formed after six steps of operation through all possible transitions. (c) Ferguson analysis of the motifs used here. The plots of the PX, JX₂, BX, and Frame molecules are compared with a double-helical molecule of similar length.