The Drosophila GAGA factor binds specifically to simple repeating d(GA
.TC)(n) DNA sequences. These sequences are known to be capable of form
ing triple-stranded DNA as well as other non-B-DNA conformations. Here
, it is shown that GAGA binds to a d[CT(GA.TC)](22) intermolecular tri
pler with similar specificity and affinity as to a regular double-stra
nded B form d[AG(GA.TC)](22) sequence. The interaction of GAGA with tr
ipler DNA cannot, however, stimulate transcription in vitro. The affin
ity of GAGA for triplexes of the purine motif, such as a d[AG(GA.TC)](
22) intermolecular tripler, is significantly lower. The DNA binding do
main of GAGA is sufficient for efficient binding to tripler DNA. Eased
on the reported solution structure of the complex of GAGA-DNA binding
domain with double-stranded DNA, a model for its interaction with tri
pler DNA is proposed in which most of the protein-DNA contacts observe
d in duplex DNA are maintained, especially those occurring through the
minor groove. The higher negative charge of the tripler is likely to
have also an important contribution to both the specificity and affini
ty of the interaction.