Search for the optimal linker in tandem hairpin polyamides

In order to target specific DNA sequences ≥10 base pairs in size by minor groove binding ligands, a search for the optimal linker in dimers of hairpin polyamides was initiated. Two series of tandem polyamides ImPyIm-(R)[ImPyIm-(R)^(H2N)γ-PyPyPy-L]^(HN)γ-PyPyPy-β-Dp (1a–e), where L represents a series of 4–8 carbon long aliphatic amino acid linkers, and ImPyIm-(R)[ImPyIm-(R)^(H2N)γ-PyPyPyIm-L]^(HN)γ-PyPyPy-β-Dp (2a–e), where L represents a series of 2–6 carbon long aliphatic amino acid linkers, were synthesized and characterized by quantitative DNase I footprinting. β, γ and Dp represents β-alanine, γ-aminobutyric acid, and 3-(dimethylamino)propylamine, respectively. It was found that the five-carbon 5-aminovaleric acid (δ), is suitable to span one base-pair (bp) of DNA when incorporated into a tandem polyamide. ImPyIm-(R)[ImPyIm-(R)^(H2N)γ-PyPyPy-δ]^(HN)γ-PyPyPy-β-Dp (1b) binds the 10 bp binding-site 5′-AGTGAAGTGA-3′ with equilibrium association constant K_a=3.2×10^(10) M^(−1) and ImPyIm-(R)[ImPyIm-(R)^(H2N)γ-PyPyPyIm-δ]^(HN)γ-PyPyPy-β-Dp (2d) binds the 11 bp binding-site 5′-AGTGATAGTGA-3′ with K_a=9.7×10^9 M^(−1). Tandem 1b also bind the 11 bp site but with lower affinity affording a 15-fold specificity for the shorter binding site. Replacing a methylene group in the amino acid linker with an oxygen atom to form tandem polyamide ImPyIm-(R)[ImPyIm-(R)^(H2N)γ-PyPyPy-E]^(HN)γ-PyPyPy-β-Dp (4) where E represents the ether linker, resulted in that an 80-fold specificity for the 10 bp binding site over the 11 bp site