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. Author manuscript; available in PMC: 2015 May 21.
Published in final edited form as: Biophys Chem. 2011 May 13;159(1):73–81. doi: 10.1016/j.bpc.2011.05.008

Figure 1.

Figure 1

Schematic representation of DNA constructs used in this work. Sequences of the constructs are provided in Materials and Methods. C1 and C2 are fork junction DNA constructs with the last base-pair of ds portion at −11 and −12 position, respectively. C3 is analogous to C2 but contains a 1 bp gap in the nontemplate strand of the spacer region. C4 corresponds to a construct where short duplex containing −35 region is connected to a short hairpin contain −10 region via a long flexible linker. C5 and C6 are short hairpin and duplex constructs containing −10 and −35 sequences, respectively. R1 and R2 are Cy5-labeled constructs analogous to C2 and C5, respectively. C7 and C8 are 75 bp long promoter DNA constructs with fluorescence probes to monitor using FRET spacer DNA deformations (C7) and promoter melting (C8).