Supplementary Material for

Large, Sequence-Dependent Effects on DNA Conformation byMinor 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 (Lact

2) versus relative length minus one (RL-1) are shown in the absence of compound (open triangles) and presence of DB75 (solid triangles) for cis A5 (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.

cis

A5

tran

s A5

cis

ATAT

tran

s AT

AT

20 b

p

M21

cis

A5

tran

s A5

cis

ATAT

tran

s AT

AT

20 b

p

M21

cis

A5

tran

s A5

cis

ATAT

tran

s AT

AT

Bal-31A B

mixed 5’-GAAAAACGCCGCATATACGCC GGCTTTTTGCGGCGTATATGC-5’

cis

A5

cis

ATAT

20 b

p

M21

M21

mix

ed

A

0

0.5

1

1.5

2

1 104 1.5 104 2 104 2.5 104 3 104 3.5 104 4 104

cis A5cis ATATAcis A5-ATATA

RL-1

Lact

2

B