Recognition of Ten Base Pairs of DNA by Head-to-Head Hairpin Dimers

2002-05-22T00:00:00Z (GMT) by Philipp Weyermann Peter B. Dervan
Hairpin polyamides coupled head-to head with alkyl linkers of varying lengths were synthesized, and their DNA binding properties were determined. The DNA binding affinities of six-ring hairpin dimers Im-Im-Py-(<i>R</i>)[Im-Im-Py-(<i>R</i>)<sup>HNCO(CH)</sup><sub><sup><i>n</i></sup></sub><sup>CO</sup>γ-Py-Py-Py-β-Dp]<sup>NH</sup>γ-Im-Py-Py-β-Dp (<b>1</b>−<b>4</b>) (where <i>n</i> = 1−4) for their 10-bp, 11-bp, and 12-bp match sites 5‘-<u>TGGCATACCA</u>-3‘, 5‘-<u>TGGCA</u>T<u>TACCA</u>-3‘, and 5‘-<u>TGGCA</u>TA<u>TACCA</u>-3‘ were determined by quantitative DNase I footprint titrations. The most selective dimer Im-Im-Py-(<i>R</i>)[Im-Im-Py-(<i>R</i>)<sup>HNCO(CH</sup><sub><sup>2</sup></sub><sup>)</sup><sub><sup>2</sup></sub><sup>CO</sup>γ-Py-Py-Py-β-Dp]<sup>NH</sup>γ-Im-Py-Py-β-Dp (<b>2</b>) binds the 10-bp site match site with an equilibrium association constant of <i>K</i><sub>a</sub> = 7.5 × 10<sup>10</sup> M<sup>-1</sup> and displays 25- and 140-fold selectivity over the 11-bp and 12-bp match sites, respectively. The affinity toward single base pair mismatched sequences is 4- to 8-fold lower if one hairpin module of the dimer is affected, but close to 200-fold lower if both hairpin modules face a single mismatch base pair. The head-to-head hairpin dimer motif expands the binding site size of DNA sequences targetable with polyamides.