The interactions between RNA structures, such as RRE in the HIV-1 geno
me, and proteins, such as Rev of HIV-1, are essential for efficient vi
ral replication. Compounds that bind specifically to such RNAs and dis
rupt their protein complexes offer a novel mechanism for inhibition of
replication of the virus. As a step in this approach, we have designe
d and characterized a series of synthetic diphenylfuran cations that s
electively inhibit Rev binding to RRE. Fluorescence titrations and gel
band-shift results indicate that the diphenylfurans bind to RRE and i
nhibit Rev complex formation in a structure-dependent manner. The deri
vative with the greatest affinity for RRE has an association constant
of greater than 10(7) M(-1) and inhibits formation of the Rev-RRE comp
lex at concentrations below 1 mu M. It binds to RRE considerably more
strongly than it binds to simple RNA duplexes. Spectral. changes and e
nergy transfer results on complex formation suggest that the compound
has a nonclassical intercalation binding mode. CD studies with modifie
d RRE hairpins indicate that the active diphenylfurans bind at the str
uctured internal loop of RRE and cause a conformational change. The mo
st active diphenylfurans are tetracations that appear to bind to RRE b
y a threading intercalation mode and cause a conformational change in
the RNA that is essential for inhibition of Rev complex formation with
RRE.