Binding of hairpin pyrrole and imidazole polyamides to DNA: relationship between torsion angle and association rate constants

Abstract

N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides are small organic molecules that bind to DNA with sequence specificity and can be used as synthetic DNA-binding ligands. In this study, five hairpin eight-ring Py-Im polyamides 1-5 with different number of Im rings were synthesized, and their binding behaviour was investigated with surface plasmon resonance assay. It was found that association rate (k(a)) of the Py-Im polyamides with their target DNA decreased with the number of Im in the Py-Im polyamides. The structures of four-ring Py-Im polyamides derived from density functional theory revealed that the dihedral angle of the Py amide carbonyl is 14∼18°, whereas that of the Im is significantly smaller. As the minor groove of DNA has a helical structure, planar Py-Im polyamides need to change their conformation to fit it upon binding to the minor groove. The data explain that an increase in planarity of Py-Im polyamide induced by the incorporation of Im reduces the association rate of Py-Im polyamides. This fundamental knowledge of the binding of Py-Im polyamides to DNA will facilitate the design of hairpin Py-Im polyamides as synthetic DNA-binding modules.

Figure 1.

Structures of Py–Im polyamides 1–5.

Figure 2.

Sequences of 5′-biotinylated hairpin DNAs (ODN1–5). X represents biotin. The binding sequences of the Py–Im polyamides are shown in bold.

Figure 3.

SPR sensorgrams for the interaction of Py–Im polyamides with hairpin DNAs immobilized on a sensor chip SA. (A) Py–Im polyamide 1 with ODN1 at a concentration range from 1.25 × 10⁻⁸ (lowest curve) to 2.0 × 10⁻⁷ M (highest curve). (B) Py–Im polyamide 2 with ODN2 at a concentration range from 1.25 × 10⁻⁸ (lowest curve) to 2.0 × 10⁻⁷ M (highest curve). (C) Py–Im polyamide 3 with ODN3 at a concentration range from 2.5 × 10⁻⁸ (lowest curve) to 4.0 × 10⁻⁷ M (highest curve). (D) Py–Im polyamide 4 with ODN4 at a concentration range from 2.5 × 10⁻⁸ (lowest curve) to 8.0 × 10⁻⁷ M (highest curve). (E) Py–Im polyamide 5 with ODN5 at a concentration range from 2.5 × 10⁻⁸ (lowest curve) to 8.0 × 10⁻⁷ M (highest curve).

Figure 4.

Models of four-ring polyamide subunits calculated by density functional theory. Angles indicate the dihedral angles between each Py or Im and the contiguous amide (N1-C2-CO-O). (A) Py-Py-Py-Py. Dotted line indicates the N-to-N distance at both ends of the four-ring polyamide. (B) Im-Py-Py-Py, (C) Py-Py-Im-Py, (D) Im-Py-Im-Py and (E) Im-Im-Im-Im.