Figure 3: Design and construction of a ds DNA–RNA hybrid knot. | Nature Communications

Figure 3: Design and construction of a ds DNA–RNA hybrid knot.

From: Synthesizing topological structures containing RNA

Figure 3

(a–c) Three views of 3D helical model of the ds DNA–RNA hybrid knot: along the threefold rotation axis (a), the axis of the outer (b) and inner (c) helices. The template DNA strand is shown in red and the complementary RNA strand in blue. Also see Supplementary Fig. 3 for stereo views. (d,e) AFM images for the ds hybrid circle (d) and knot (e). Scale bar, 50 nm. (f) Nuclease digestion confirming the formation of the hybrid knot. Lanes 1–3, purified ds hybrid knot undigested (lane 1), digested by DNase I (lane 2) or by RNase H (lane 3). Lanes 4–6, purified ds hybrid circle undigested (lane 4), digested by DNase I (lane 5) or by RNase H (lane 6). Lanes 7 and 8, ssDNA references of the ssDNA template knot and circle. Lanes 9 and 10, ssRNA references (TKj(+) and Cj), which are of the same size with the RNA strand in the ds hybrid structures but a different sequence.

Back to article page