Fig. 5. Use of transition amplitudes from experiments with negatively supercoiled DNA and positively supercoiled DNA (D l_obs,neg and D l_obs,pos) to deconvolute the extent of DNA unwinding (D l_u) and the extent of DNA unwinding (Dl_c). (A) Experiments with negatively supercoiled DNA. (B) Experiments with positively supercoiled DNA. (Upper) Idealized single-molecule traces. (Lower) Schematic illustrations of changes in structure, and changes in l, for an interaction of RNA polymerase (RNAP)-promoter interaction resulting in both DNA unwinding and DNA compaction. Dashed lines in Upper show the notional values of l in the absence of DNA compaction; dashed lines in Lower show the notional bead positions in the absence of DNA compaction. DNA unwinding has opposite effects on l in experiments with negatively and positively supercoiled DNA (increases l with positively supercoiled DNA; decreases l with negatively supercoiled DNA), whereas DNA compaction has equivalent effects on l in experiments with negatively and positively supercoiled DNA (decreases l with both negatively and positively supercoiled DNA). Therefore, effects of unwinding and compaction can be deconvoluted from data with negatively and positively supercoiled DNA by use of simple algebra: D l_u = (D l_obs,neg + D l_obs,pos)/2; and D l_c = (D l_obs,pos - D l_obs,neg)/2.