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 (L act 2 ) versus relative length minus one (R L -1) are shown in the absence of compound (open triangles) and presence of DB75 (solid triangles) for cis A 5 (purple), cis ATATA (red), and cis A5-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. cis A5 trans A5 cis ATAT trans ATAT 20 bp M21 cis A5 trans A5 cis ATAT trans ATAT 20 bp M21 cis A5 trans A5 cis ATAT trans ATAT Bal-31 AB

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