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. 2021 Mar 21;49(7):3651–3660. doi: 10.1093/nar/gkab153

Figure 1.

Figure 1.

Nano-scale conformation change associated with the B–Z transition (B-DNA (red) and Z-DNA (blue)) is monitored by smFRET. (A) Negative supercoiling (by magnetic tweezers) induces the B–Z transition in a DNA construct immobilized on surface by digoxigenin (Dig)/anti-Dig binding and attached to a magnetic bead by biotin (Bio)/NeutrAvidin binding. The negatively supercoiled molecule also displays schematically a denaturation bubble as well as plectonemes. The conformational state of the Core region is determined from the FRET state of the two dyes embedded therein (B-DNA: middle EFRET; Z-DNA: low EFRET). (B) Reversible B–Z transition in (TG)11 controlled by negative supercoiling (σ: upper panel). Negative σ (< -0.01) triggers the B–Z transition revealed by smFRET (lower panel: EFRET(B-DNA) ∼ 0.5 and EFRET(Z-DNA) ∼ 0.2). (C) Design of the DNA tether molecule, which contains a Core fragment (blue, hatched) with a donor (Cy3, green) and an acceptor (Cy5, red) dye separated by 14 base pairs.