Supplementary Material for Large, Sequence-Dependent Effects on DNA Conformation by

1. Supplementary Material for Large, Sequence-Dependent Effects on DNA Conformation by Minor Groove Binding Compounds Denise S. Tevis, Arvind Kumar, Chad E. Stephens, David W. Boykin, and W. David Wilson* Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA *To whom correspondence should be addressed. Tel: +1.404.413.5503; Fax: +1.404.413.5505; Email: wdw@gsu.edu Supplementary Materials Figure 1. PAGE experiment with DB351 (A) and DB1213 (B) cast in the gel. Duplexes were incubated with compound prior to electrophoresis. Samples were digested with Bal-31 exonuclease prior to electrophoresis as indicated. Supplementary Materials Figure 2. PAGE experiment with no compound present (A). Plot of actual length squared (Lact2) versus relative length minus one (RL-1) are shown in the absence of compound (open triangles) and presence of DB75 (solid triangles) for cisA5 (purple), cis ATATA (red), and cisA5-ATATA (green) duplexes (B). The sequence for the mixed duplex is shown in the bottom of the figure. Sequences not discussed in this paper were removed from this gel.

2. trans A5 20 bp trans ATAT M21 cis ATAT cis A5 cis A5 trans A5 cis ATAT trans ATAT trans A5 trans ATAT M21 cis A5 cis ATAT Bal-31 20 bp A B

3. mixed 20 bp M21 cis A5 M21 cis ATAT A B mixed 5’-GAAAAACGCCGCATATACGCC GGCTTTTTGCGGCGTATATGC-5’