TRF1 binds a bipartite telomeric site with extreme spatial flexibility

TRF1 is a key player in telomere length regulation. Because length control was proposed to depend on the architecture of telomeres, we studied how TRF 1 binds telomeric TTAGGG repeat DNA and alters its conformation. Although t he single Myb-type helix-turn-helix motif of a TRF1 monomer can interact wi th telomeric DNA, TRF1 predominantly binds as a homodimer, Systematic Evolu tion of Ligands by Exponential enrichment (SELEX) with dimeric TRF1 reveale d a bipartite telomeric recognition site with extreme spatial variability. Optimal sites have two copies of a 5'-YTAGGGTTR-3' half-site positioned wit hout constraint on distance or orientation. Analysis of binding affinities and DNase I footprinting showed that both half-sites are simultaneously con tacted by the TRF1 dimer, and electron microscopy revealed looping of the i ntervening DNA. We propose that a flexible segment in TRF1 allows the two M yb domains of the homodimer to interact independently with variably positio ned half-sites. This unusual DNA binding mode is directly relevant to the p roposed architectural role of TRF1.