Contrasting enantioselective DNA preference: chiral helical macrocyclic lanthanide complex binding to DNA

Abstract

There is great interest in design and synthesis of small molecules which selectively target specific genes to inhibit biological functions in which particular DNA structures participate. Among these studies, chiral recognition has been received much attention because more evidences have shown that conversions of the chirality and diverse conformations of DNA are involved in a series of important life events. Here, we report that a pair of chiral helical macrocyclic lanthanide (III) complexes, (M)-Yb[L(SSSSSS)](3+) and (P)-Yb[L(RRRRRR)](3+), can enantioselectively bind to B-form DNA and show remarkably contrasting effects on GC-rich and AT-rich DNA. Neither of them can influence non-B-form DNA, nor quadruplex DNA stability. Our results clearly show that P-enantiomer stabilizes both poly(dG-dC)(2) and poly(dA-dT)(2) while M-enantiomer stabilizes poly(dA-dT)(2), however, destabilizes poly(dG-dC)(2). To our knowledge, this is the best example of chiral metal compounds with such contrasting preference on GC- and AT-DNA. Ligand selectively stabilizing or destabilizing DNA can interfere with protein-DNA interactions and potentially affect many crucial biological processes, such as DNA replication, transcription and repair. As such, bearing these unique capabilities, the chiral compounds reported here may shed light on the design of novel enantiomers targeting specific DNA with both sequence and conformation preference.

Figure 1.

Variations of the melting temperature ΔT_m (ΔT_m = T_m − T_m⁰, T_m and T_m⁰ represent the melting temperature of DNA in the presence or absence of complex) for complexes binding to ct-DNA (A), AT-DNA (B) and GC-DNA (C), respectively, as a function of concentration of (P)-Yb (solid square) and (M)-Yb (open square). DNA concentration was 20 µM in bp. T_m values were obtained from first-derivative plots of the thermal denaturation curves.

Scheme 1.

(A) Chiral helical macrocyclic lanthanide (III) complexes (M- and P-enantiomer) can stabilize AT-DNA. P-enantiomer shows much stronger effect than M-enantiomer under the same conditions; (B) Contrasting enantioselectivity of M- and P-enantiomer on GC-DNA. M-enantiomer destabilize GC-DNA while P-enantiomer stabilize DNA under the same conditions. The structures of (M)-Yb[L_SSSSSS]³⁺ and (P)-Yb[L_RRRRRR]³⁺ complexes are based on crystallographic data reported previously (41,42).

Figure 2.

CD titrations of DNA with (P)-Yb or (M)-Yb in 5 mM Tris–HCl buffer (pH = 7.2) at 25°C. (A) AT-DNA was titrated with (P)-Yb; (B) AT-DNA was titrated with (M)-Yb; (C) GC-DNA was titrated with (P)-Yb; (D) GC-DNA was titrated with (M)-Yb. DNA concentration was 30 µM in bp and the complex concentrations were varied from 0 to 42 µM. The CD backgrounds of the two enantiomers were subtracted, respectively.

Figure 3.

Up: SPR sensorgrams for the interactions of (P)-Yb (A) and (M)-Yb (B) with AT-DNA. Middle: SPR sensorgrams for the interactions of (P)-Yb (C) and (M)-Yb (D) with GC-DNA. DNA sequences are given in ‘Materials and Methods’ section. The concentrations of complexes are listed in the figure. Bottom: The binding curves of AT-DNA (E) and GC-DNA (F) binding with (P)-Yb (solid circles) and (M)-Yb (open circles). The data were fitted in a two-site model.

Figure 4.

(A) Fluorescence emission spectra of EB alone (black); ct-DNA-EB (red); ct-DNA-EB after addition of (P)-Yb (green) and (M)-Yb (blue). (B) Fluorescence emission spectra of Hoechst 33258 alone (black); ct-DNA-Hoechst 33258 (red); ct-DNA-Hoechst 33258 after addition of (P)-Yb (green) and (M)-Yb (blue). Insert: Degree of fluorophore (EB, Hoechst 33 258) displacement with increased molar ratios of (P)-Yb to DNA (solid circles) and (M)-Yb to DNA (open circles). DNA was 20 µM in bp. EB and Hoechst 33 258 was 6.6 µM. The experiments were carried out in 5 mM Tris–HCl buffer (pH = 7.2) at 25°C.

Figure 5.

CD spectra of methylene green (black); ct-DNA (red); ct-DNA-methylene green (blue); ct-DNA-methylene green after addition of (P)-Yb (green) and (M)-Yb (pink). Insert: The change in ellipticity at 650 and 620 nm with increased molar ratios of (P)-Yb to DNA (solid circles) and (M)-Yb to DNA (open circles). DNA was 30 µM in bp. The experiments were carried out in 5 mM Tris–HCl buffer (pH = 7.2) at 25°C.