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Zn2+ selectively stabilizes FdU-substituted DNA through a unique major groove binding motif.

Ghosh S, Salsbury FR, Horita DA, Gmeiner WH - Nucleic Acids Res. (2011)

Bottom Line: Mg(2+) neither inhibited EtBr complexation nor had as strong of a stabilizing effect.DNA sequences that did not contain consecutive FdU were not stabilized by Zn(2+).A lipofectamine preparation of the Zn(2+)-DNA complex displayed enhanced cytotoxicity toward prostate cancer cells relative to the individual components prepared as lipofectamine complexes indicating the potential utility of Zn(2+)-DNA complexes for cancer treatment.

View Article: PubMed Central - PubMed

Affiliation: Department of Cancer Biology, Program in Molecular Genetics, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA.

ABSTRACT
We report, based on semi-empirical calculations, that Zn(2+) binds duplex DNA containing consecutive FdU-dA base pairs in the major groove with distorted trigonal bipyramidal geometry. In this previously uncharacterized binding motif, O4 and F5 on consecutive FdU are axial ligands while three water molecules complete the coordination sphere. NMR spectroscopy confirmed Zn(2+) complexation occurred with maintenance of base pairing while a slight hypsochromic shift in circular dichroism (CD) spectra indicated moderate structural distortion relative to B-form DNA. Zn(2+) complexation inhibited ethidium bromide (EtBr) intercalation and stabilized FdU-substituted duplex DNA (ΔT(m) > 15 °C). Mg(2+) neither inhibited EtBr complexation nor had as strong of a stabilizing effect. DNA sequences that did not contain consecutive FdU were not stabilized by Zn(2+). A lipofectamine preparation of the Zn(2+)-DNA complex displayed enhanced cytotoxicity toward prostate cancer cells relative to the individual components prepared as lipofectamine complexes indicating the potential utility of Zn(2+)-DNA complexes for cancer treatment.

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CD spectra demonstrate Zn2+ selectively induces a hypsochromic shift upon addition to DNA hairpins containing consecutive FdU–dA base pairs. Spectra for each hairpin were acquired in the presence and absence of Zn2+ and Mg2+ at the indicated concentrations. The CD spectra indicate that complexation with Zn2+ alters the structure of DNA hairpins that contain consecutive FdU–dA base pairs. Computational studies indicate base slide and tilt accompany Zn2+ complexation (Figure 1B). (A) 3′FdU hairpin; (B) 5′ FdU hairpin; (C) Alt-FdU hairpin; (D) No-FdU sequence.
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Figure 4: CD spectra demonstrate Zn2+ selectively induces a hypsochromic shift upon addition to DNA hairpins containing consecutive FdU–dA base pairs. Spectra for each hairpin were acquired in the presence and absence of Zn2+ and Mg2+ at the indicated concentrations. The CD spectra indicate that complexation with Zn2+ alters the structure of DNA hairpins that contain consecutive FdU–dA base pairs. Computational studies indicate base slide and tilt accompany Zn2+ complexation (Figure 1B). (A) 3′FdU hairpin; (B) 5′ FdU hairpin; (C) Alt-FdU hairpin; (D) No-FdU sequence.

Mentions: CD was used to evaluate alterations to DNA structure caused by Mg2+ or Zn2+ binding. All four DNA hairpins displayed CD spectral features characteristic of B-form DNA (Figure 4). The addition of Zn2+, but not Mg2+, resulted in a concentration-dependent blue-shift of ∼20 nm for the maximal positive ellipticity near 280 nm selectively for the DNA sequences containing consecutive FdU nucleotides. The CD spectra for the control sequence consisting of only native nucleotides displayed no significant variability upon addition of either Mg2+ or Zn2+ (Figure 4). The maximal ellipticity at 280 nm depends on base pairing, base stacking and base tilting, and shifts in this maximum for the FdU-containing sequences are consistent with alterations in local base pair geometry upon Zn2+ complex formation.Figure 4.


Zn2+ selectively stabilizes FdU-substituted DNA through a unique major groove binding motif.

Ghosh S, Salsbury FR, Horita DA, Gmeiner WH - Nucleic Acids Res. (2011)

CD spectra demonstrate Zn2+ selectively induces a hypsochromic shift upon addition to DNA hairpins containing consecutive FdU–dA base pairs. Spectra for each hairpin were acquired in the presence and absence of Zn2+ and Mg2+ at the indicated concentrations. The CD spectra indicate that complexation with Zn2+ alters the structure of DNA hairpins that contain consecutive FdU–dA base pairs. Computational studies indicate base slide and tilt accompany Zn2+ complexation (Figure 1B). (A) 3′FdU hairpin; (B) 5′ FdU hairpin; (C) Alt-FdU hairpin; (D) No-FdU sequence.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105383&req=5

Figure 4: CD spectra demonstrate Zn2+ selectively induces a hypsochromic shift upon addition to DNA hairpins containing consecutive FdU–dA base pairs. Spectra for each hairpin were acquired in the presence and absence of Zn2+ and Mg2+ at the indicated concentrations. The CD spectra indicate that complexation with Zn2+ alters the structure of DNA hairpins that contain consecutive FdU–dA base pairs. Computational studies indicate base slide and tilt accompany Zn2+ complexation (Figure 1B). (A) 3′FdU hairpin; (B) 5′ FdU hairpin; (C) Alt-FdU hairpin; (D) No-FdU sequence.
Mentions: CD was used to evaluate alterations to DNA structure caused by Mg2+ or Zn2+ binding. All four DNA hairpins displayed CD spectral features characteristic of B-form DNA (Figure 4). The addition of Zn2+, but not Mg2+, resulted in a concentration-dependent blue-shift of ∼20 nm for the maximal positive ellipticity near 280 nm selectively for the DNA sequences containing consecutive FdU nucleotides. The CD spectra for the control sequence consisting of only native nucleotides displayed no significant variability upon addition of either Mg2+ or Zn2+ (Figure 4). The maximal ellipticity at 280 nm depends on base pairing, base stacking and base tilting, and shifts in this maximum for the FdU-containing sequences are consistent with alterations in local base pair geometry upon Zn2+ complex formation.Figure 4.

Bottom Line: Mg(2+) neither inhibited EtBr complexation nor had as strong of a stabilizing effect.DNA sequences that did not contain consecutive FdU were not stabilized by Zn(2+).A lipofectamine preparation of the Zn(2+)-DNA complex displayed enhanced cytotoxicity toward prostate cancer cells relative to the individual components prepared as lipofectamine complexes indicating the potential utility of Zn(2+)-DNA complexes for cancer treatment.

View Article: PubMed Central - PubMed

Affiliation: Department of Cancer Biology, Program in Molecular Genetics, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA.

ABSTRACT
We report, based on semi-empirical calculations, that Zn(2+) binds duplex DNA containing consecutive FdU-dA base pairs in the major groove with distorted trigonal bipyramidal geometry. In this previously uncharacterized binding motif, O4 and F5 on consecutive FdU are axial ligands while three water molecules complete the coordination sphere. NMR spectroscopy confirmed Zn(2+) complexation occurred with maintenance of base pairing while a slight hypsochromic shift in circular dichroism (CD) spectra indicated moderate structural distortion relative to B-form DNA. Zn(2+) complexation inhibited ethidium bromide (EtBr) intercalation and stabilized FdU-substituted duplex DNA (ΔT(m) > 15 °C). Mg(2+) neither inhibited EtBr complexation nor had as strong of a stabilizing effect. DNA sequences that did not contain consecutive FdU were not stabilized by Zn(2+). A lipofectamine preparation of the Zn(2+)-DNA complex displayed enhanced cytotoxicity toward prostate cancer cells relative to the individual components prepared as lipofectamine complexes indicating the potential utility of Zn(2+)-DNA complexes for cancer treatment.

Show MeSH
Related in: MedlinePlus