Next generation hairpin polyamides with (R)-3,4-diaminobutyric acid turn unit

Abstract

The characterization of a new class of pyrrole-imidazole hairpin polyamides with beta-amino-gamma-turn units for recognition of the DNA minor groove is reported. A library of eight hairpins containing ( R)- and ( S)-3,4-diaminobutyric acid (beta-amino-gamma-turn) has been synthesized, and the impact of the molecules on DNA-duplex stabilization was studied for comparison with the parent gamma-aminobutyric acid (gamma-turn) and standard ( R)-2,4-diaminobutyric acid (alpha-amino-gamma-turn)-linked eight-ring polyamides. For some, but not all, sequence compositions, melting temperature analyses have revealed that both enantiomeric forms of the beta-amino-gamma-turn increase the DNA-binding affinity of polyamides relative to the ( R)-alpha-amino-gamma-turn. The ( R)-beta-amine residue may be an attractive alternative for constructing hairpin polyamide conjugates. Biological assays have shown that ( R)-beta-amino-gamma-turn hairpins are able to inhibit androgen receptor-mediated gene expression in cell culture similar to hairpins bearing the standard ( R)-alpha-amino-gamma-turn, from which we infer they are cell-permeable.

Figure 1

Schematic representation of hairpin polyamides with increased DNA-binding affinity caused by different γ-turn units. Hairpin polyamides targeted to DNA sequence 5′-TGGTCA-3′ are shown as ball-and-stick models. Ball-and-stick representation legend: black and white circles represent N-methylimidazole and N-methylpyrrole units, respectively, half-circles represent γ-aminobutyric acid, white diamonds represent β-alanine units, and half-circles containing a cross represent 3-(dimethylamino)-1-propylamine (Dp) as tail.

Figure 2

Chemical structures for hairpins 1–16 targeted to DNA sequences: (A) 5′-TGTTCA-3′, (B) 5′-TGGTCA-3′, (C) 5′-TGGGCA-3′, and (D) 5′-TGGGGA-3′.

Figure 3

Normalized UV denaturation profiles of 12mer DNA duplex 5′-CGATGGTCAAGC-3′/5′-GCTTGACCATCG-3′ in the absence and presence of hairpin polyamides 5–8.

Figure 4

Illustrative models of different turn conformations for hairpin polyamides containing the (R)-α-amino-γ-turn (A and B), (S)-β-amino-γ-turn (C and D), and the (R)-β-amino-γ-turn (E and F) bound to the minor groove of DNA (dark gray = carbons, white = hydrogen, blue = nitrogen, red = oxygen).

Figure 5

Chemical structures and ball-and-stick models of acetylated hairpin polyamides 17–19 targeted to DNA sequence 5′-TGGTCA-3′.

Figure 6

Schematic representation of the androgen receptor (AR)-mediated transcription complex with the androgen response element (ARE).

Figure 7

(A) Chemical structures and ball-and-stick models of matched and mismatched polyamides 20–23, targeted to DNA sequence 5′-AGAACA-3′. (B) Inhibition of DHT-induced PSA and KLK2 expression by 20–23 measured by quantitative real-time RT-PCR.