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Chiral metallo-supramolecular complexes selectively recognize human telomeric G-quadruplex DNA.

Yu H, Wang X, Fu M, Ren J, Qu X - Nucleic Acids Res. (2008)

Bottom Line: The chiral supramolecular complex has both small molecular chemical features and the large size of a zinc-finger-like DNA-binding motif.The complex is also convenient to synthesize and separate enantiomers.These results provide new insights into the development of chiral anticancer agents for targeting G-quadruplex DNA.

View Article: PubMed Central - PubMed

Affiliation: Division of Biological Inorganic Chemistry, Key Laboratory of Rare Earth Chemistry and Physics, Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China.

ABSTRACT
Here, we report the first example that one enantiomer of a supramolecular cylinder can selectively stabilize human telomeric G-quadruplex DNA. The P-enantiomer of this cylinder has a strong preference for G-quadruplex over duplex DNA and, in the presence of sodium, can convert G-quadruplexes from an antiparallel to a hybrid structure. The compound's chiral selectivity and its ability to discriminate quadruplex DNA have been studied by DNA melting, circular dichroism, gel electrophoresis, fluorescence spectroscopy and S1 nuclease cleavage. The chiral supramolecular complex has both small molecular chemical features and the large size of a zinc-finger-like DNA-binding motif. The complex is also convenient to synthesize and separate enantiomers. These results provide new insights into the development of chiral anticancer agents for targeting G-quadruplex DNA.

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(A) CD titration of d[AG3(T2AG3)3] with [Ni2L3]4+-P in 100 mM NaCl, 10 mM Tris buffer (pH 7.2) at 20°C. The concentration of [Ni2L3]4+-P was varied from 0 µM to 3 µM. (B) The change in ellipticity at 265 nm with increased concentration of [Ni2L3]4+-P derived from the CD titration, a breakpoint was observed at 1:1 ratio. DNA concentration was 1 µM/strand. (C) CD titration of d[AG3(T2AG3)3] with [Ni2L3]4+-M in 100 mM NaCl, 10 mM Tris buffer (pH 7.2) at 20°C. The concentration of [Ni2L3]4+-M was varied from 0 to 3 µM. (D) The change in ellipticity at 265 nm with increased concentration of [Ni2L3]4+-M derived from the CD titration, a breakpoint was observed at 1.67:1 ratio. DNA concentration was 1 µM/strand.
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Figure 6: (A) CD titration of d[AG3(T2AG3)3] with [Ni2L3]4+-P in 100 mM NaCl, 10 mM Tris buffer (pH 7.2) at 20°C. The concentration of [Ni2L3]4+-P was varied from 0 µM to 3 µM. (B) The change in ellipticity at 265 nm with increased concentration of [Ni2L3]4+-P derived from the CD titration, a breakpoint was observed at 1:1 ratio. DNA concentration was 1 µM/strand. (C) CD titration of d[AG3(T2AG3)3] with [Ni2L3]4+-M in 100 mM NaCl, 10 mM Tris buffer (pH 7.2) at 20°C. The concentration of [Ni2L3]4+-M was varied from 0 to 3 µM. (D) The change in ellipticity at 265 nm with increased concentration of [Ni2L3]4+-M derived from the CD titration, a breakpoint was observed at 1.67:1 ratio. DNA concentration was 1 µM/strand.

Mentions: 2-Ap fluorescence modified in different loops (Table 2) has been widely used to verify the mode of ligand binding to G-quadruplex (33) and i-motif DNA (8). Our results show that P-enantiomer can decrease 2-Ap fluorescence (8,33) and the decrease follows the order: A7 ≈ A19 > A13 (Figure 5A). This indicates that P-enantiomer may preferentially bind to the end of G-quartet by external stacking (2,33,34) and leads to the decrease of 2-Ap fluorescence (8) labeled in the two lateral loops (A7 and A19), which is consistent with a breakpoint observed at 1:1 binding ratio (Figure 6) in CD titrations (18). The interactions of the positive charged triple helical structure with the two lateral loops, grooves and DNA backbone (6,23,26) can further stabilize P-enantiomer binding. Nonlinear least-squares analysis of the fluorescence titration data (8) of A7 or A19 by P-enantiomer yielded an association constant of 2.6 ± 0.6 × 107 M−1 (Table S1). For M-enantiomer, its binding hardly decreases the 2-Ap fluorescence modified in any of the three loops (Figure 5A), and a breakpoint was observed at 1.67:1 binding ratio in CD titrations (Figure 6). These results indicate that M-enantiomer, like terbium–amino acid complex (34), may take electrostatic nonspecific binding to G-quadruplex which binding mode has been proposed by Hurley group and ours (3,34). The different binding mode of the two enantiomers is further supported by S1 nuclease digestion (8). Figure 5B shows the enzyme cleavage patterns of 5′-fluorescein-labeled quadruplex DNA after S1 nuclease digestion (8). Digestion by S1 nuclease resulted in three major cleavages (lane 2, DNA alone) occurred at three loops (8), consistent with previous studies on i-motif DNA (8) and c-myc promoter cleavage (35). In the presence of P-enantiomer, the amount of the cleavage at 5′-end (band 4) and at 3′-end (band 2) decreased dramatically while the cleavage at the diagonal loop (band 3) was hardly influenced. In the presence of M-enantiomer, the cleavage pattern was almost the same as that of DNA alone. This is in accordance with the 2-Ap fluorescence results and further supports that P-enantiomer may bind to the end of G-quartet by external stacking and contact with the two lateral loops.Figure 5.


Chiral metallo-supramolecular complexes selectively recognize human telomeric G-quadruplex DNA.

Yu H, Wang X, Fu M, Ren J, Qu X - Nucleic Acids Res. (2008)

(A) CD titration of d[AG3(T2AG3)3] with [Ni2L3]4+-P in 100 mM NaCl, 10 mM Tris buffer (pH 7.2) at 20°C. The concentration of [Ni2L3]4+-P was varied from 0 µM to 3 µM. (B) The change in ellipticity at 265 nm with increased concentration of [Ni2L3]4+-P derived from the CD titration, a breakpoint was observed at 1:1 ratio. DNA concentration was 1 µM/strand. (C) CD titration of d[AG3(T2AG3)3] with [Ni2L3]4+-M in 100 mM NaCl, 10 mM Tris buffer (pH 7.2) at 20°C. The concentration of [Ni2L3]4+-M was varied from 0 to 3 µM. (D) The change in ellipticity at 265 nm with increased concentration of [Ni2L3]4+-M derived from the CD titration, a breakpoint was observed at 1.67:1 ratio. DNA concentration was 1 µM/strand.
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Figure 6: (A) CD titration of d[AG3(T2AG3)3] with [Ni2L3]4+-P in 100 mM NaCl, 10 mM Tris buffer (pH 7.2) at 20°C. The concentration of [Ni2L3]4+-P was varied from 0 µM to 3 µM. (B) The change in ellipticity at 265 nm with increased concentration of [Ni2L3]4+-P derived from the CD titration, a breakpoint was observed at 1:1 ratio. DNA concentration was 1 µM/strand. (C) CD titration of d[AG3(T2AG3)3] with [Ni2L3]4+-M in 100 mM NaCl, 10 mM Tris buffer (pH 7.2) at 20°C. The concentration of [Ni2L3]4+-M was varied from 0 to 3 µM. (D) The change in ellipticity at 265 nm with increased concentration of [Ni2L3]4+-M derived from the CD titration, a breakpoint was observed at 1.67:1 ratio. DNA concentration was 1 µM/strand.
Mentions: 2-Ap fluorescence modified in different loops (Table 2) has been widely used to verify the mode of ligand binding to G-quadruplex (33) and i-motif DNA (8). Our results show that P-enantiomer can decrease 2-Ap fluorescence (8,33) and the decrease follows the order: A7 ≈ A19 > A13 (Figure 5A). This indicates that P-enantiomer may preferentially bind to the end of G-quartet by external stacking (2,33,34) and leads to the decrease of 2-Ap fluorescence (8) labeled in the two lateral loops (A7 and A19), which is consistent with a breakpoint observed at 1:1 binding ratio (Figure 6) in CD titrations (18). The interactions of the positive charged triple helical structure with the two lateral loops, grooves and DNA backbone (6,23,26) can further stabilize P-enantiomer binding. Nonlinear least-squares analysis of the fluorescence titration data (8) of A7 or A19 by P-enantiomer yielded an association constant of 2.6 ± 0.6 × 107 M−1 (Table S1). For M-enantiomer, its binding hardly decreases the 2-Ap fluorescence modified in any of the three loops (Figure 5A), and a breakpoint was observed at 1.67:1 binding ratio in CD titrations (Figure 6). These results indicate that M-enantiomer, like terbium–amino acid complex (34), may take electrostatic nonspecific binding to G-quadruplex which binding mode has been proposed by Hurley group and ours (3,34). The different binding mode of the two enantiomers is further supported by S1 nuclease digestion (8). Figure 5B shows the enzyme cleavage patterns of 5′-fluorescein-labeled quadruplex DNA after S1 nuclease digestion (8). Digestion by S1 nuclease resulted in three major cleavages (lane 2, DNA alone) occurred at three loops (8), consistent with previous studies on i-motif DNA (8) and c-myc promoter cleavage (35). In the presence of P-enantiomer, the amount of the cleavage at 5′-end (band 4) and at 3′-end (band 2) decreased dramatically while the cleavage at the diagonal loop (band 3) was hardly influenced. In the presence of M-enantiomer, the cleavage pattern was almost the same as that of DNA alone. This is in accordance with the 2-Ap fluorescence results and further supports that P-enantiomer may bind to the end of G-quartet by external stacking and contact with the two lateral loops.Figure 5.

Bottom Line: The chiral supramolecular complex has both small molecular chemical features and the large size of a zinc-finger-like DNA-binding motif.The complex is also convenient to synthesize and separate enantiomers.These results provide new insights into the development of chiral anticancer agents for targeting G-quadruplex DNA.

View Article: PubMed Central - PubMed

Affiliation: Division of Biological Inorganic Chemistry, Key Laboratory of Rare Earth Chemistry and Physics, Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China.

ABSTRACT
Here, we report the first example that one enantiomer of a supramolecular cylinder can selectively stabilize human telomeric G-quadruplex DNA. The P-enantiomer of this cylinder has a strong preference for G-quadruplex over duplex DNA and, in the presence of sodium, can convert G-quadruplexes from an antiparallel to a hybrid structure. The compound's chiral selectivity and its ability to discriminate quadruplex DNA have been studied by DNA melting, circular dichroism, gel electrophoresis, fluorescence spectroscopy and S1 nuclease cleavage. The chiral supramolecular complex has both small molecular chemical features and the large size of a zinc-finger-like DNA-binding motif. The complex is also convenient to synthesize and separate enantiomers. These results provide new insights into the development of chiral anticancer agents for targeting G-quadruplex DNA.

Show MeSH