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

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-(R)[Im-Im-Py-(R)^HNCO(CH)_nCOγ-Py-Py-Py-β-Dp]^NHγ-Im-Py-Py-β-Dp (1−4) (where n = 1−4) for their 10-bp, 11-bp, and 12-bp match sites 5‘-TGGCATACCA-3‘, 5‘-TGGCATTACCA-3‘, and 5‘-TGGCATATACCA-3‘ were determined by quantitative DNase I footprint titrations. The most selective dimer Im-Im-Py-(R)[Im-Im-Py-(R)^{HNCO(CH₂)₂CO}γ-Py-Py-Py-β-Dp]^NHγ-Im-Py-Py-β-Dp (2) binds the 10-bp site match site with an equilibrium association constant of K_a = 7.5 × 10¹⁰ M^-1 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.