The GAGA factor of Drosophila binds triple-stranded DNA

The Drosophila GAGA factor binds specifically to simple repeating d(GA.TC)(n) DNA sequences. These sequences are known to be capable of forming 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 tripler with similar specificity and affinity as to a regular double-stranded B form d[AG(GA.TC)](22) sequence. The interaction of GAGA with tripler DNA cannot, however, stimulate transcription in vitro. The affinity of GAGA for triplexes of the purine motif, such as a d[AG(GA.TC)](22) intermolecular tripler, is significantly lower. The DNA binding domain 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 tripler DNA is proposed in which most of the protein-DNA contacts observed 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 affinity of the interaction.