Figure 1. A) When a DNA fiber is wrapped around itself, with its ends restrained (in this case, the ends are fixed to each other forming a circle), supercoils are formed and trap torsional stress (top). The only way to remove the stress is to break the DNA and let the ends counter-rotate (middle). We wondered what happens dynamically if stress is applied to an open DNA fiber. If the DNA is rigid enough, the whole molecule would rotate as a unit and no supercoils would form, or if the DNA is flexible enough, the whole fiber would writhe around itself in response to applied torque (bottom). B) Linear, open molecules with divergent promoters were transcribed in vitro; concurrent recombination between loxP sites bracketing the interposed DNA, which was excised as closed circles, trapped any supercoils residing in or transiting through the interposed segment at the instant of recombination. Transcription generates torque as the double helical template is threaded through the RNA polymerase active site. Without transcription (Trx), no stress would be captured; the number of transient supercoils captured was expected to reveal how rigid or flexible the DNA was. C) A sample result: ongoing transcription (+) traps a large number of supercoils. Without transcription (–) very few supercoils are trapped. D) Factors recognizing dynamic changes in DNA structure resulting from transcriptional torque provide the necessary effector components to construct a molecular “cruise control.” FUSE, far upstream element; FBP, FUSE binding protein; FIR, FBP interacting repressor; loxP, target sequences for the site-specific Cre recombinase. T3 and T7 indicate bacteriophage T3 and T7 promoters.