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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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Computationally derived model of Zn2+ complexation to the hemi-deprotonated dimeric duplex consisting of consecutive FdU–dA base pairs. Zn2+ is located in the major groove with a distorted trigonal bipyramidal geometry in which the fluorine from the deprotonated FdU is one axial ligand and O4 from the second FdU is the second axial ligand. Water molecules are the equatorial ligands. White dashed lines are used to illustrate the coordinating atoms. (A) View emphasizing the Zn2+–water interactions; (B) View emphasizing Zn2+ interactions with DNA nucleobases. The triangle connecting the three water oxygens provides a visual frame of reference.
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Figure 1: Computationally derived model of Zn2+ complexation to the hemi-deprotonated dimeric duplex consisting of consecutive FdU–dA base pairs. Zn2+ is located in the major groove with a distorted trigonal bipyramidal geometry in which the fluorine from the deprotonated FdU is one axial ligand and O4 from the second FdU is the second axial ligand. Water molecules are the equatorial ligands. White dashed lines are used to illustrate the coordinating atoms. (A) View emphasizing the Zn2+–water interactions; (B) View emphasizing Zn2+ interactions with DNA nucleobases. The triangle connecting the three water oxygens provides a visual frame of reference.

Mentions: In the present studies, semi-empirical and ab initio calculations were used to determine the energetically preferred geometry for Zn2+ binding to DNA sequences containing consecutive FdU nucleotides (Figure 1). Although crystallographic and NMR studies have indicated a propensity for monovalent cations to occupy the deep, narrow minor groove of A-tract DNA sequences (10,11), the calculations revealed a distinct minimum energy conformation for the FdU–dA dimer complexed with Zn2+ under conditions when the 5′-terminal FdU was deprotonated. In this low energy structure, Zn2+ is localized in the major groove and interacts with F5 from the 5′-terminal FdU and with O4 from the 3′-terminal FdU as axial ligands in a distorted trigonal bipyramidal geometry with three water molecules occupying the equatorial sites. This previously uncharacterized structural motif is consistent with all of the spectroscopic, as well as the computational data.Figure 1.


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)

Computationally derived model of Zn2+ complexation to the hemi-deprotonated dimeric duplex consisting of consecutive FdU–dA base pairs. Zn2+ is located in the major groove with a distorted trigonal bipyramidal geometry in which the fluorine from the deprotonated FdU is one axial ligand and O4 from the second FdU is the second axial ligand. Water molecules are the equatorial ligands. White dashed lines are used to illustrate the coordinating atoms. (A) View emphasizing the Zn2+–water interactions; (B) View emphasizing Zn2+ interactions with DNA nucleobases. The triangle connecting the three water oxygens provides a visual frame of reference.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: Computationally derived model of Zn2+ complexation to the hemi-deprotonated dimeric duplex consisting of consecutive FdU–dA base pairs. Zn2+ is located in the major groove with a distorted trigonal bipyramidal geometry in which the fluorine from the deprotonated FdU is one axial ligand and O4 from the second FdU is the second axial ligand. Water molecules are the equatorial ligands. White dashed lines are used to illustrate the coordinating atoms. (A) View emphasizing the Zn2+–water interactions; (B) View emphasizing Zn2+ interactions with DNA nucleobases. The triangle connecting the three water oxygens provides a visual frame of reference.
Mentions: In the present studies, semi-empirical and ab initio calculations were used to determine the energetically preferred geometry for Zn2+ binding to DNA sequences containing consecutive FdU nucleotides (Figure 1). Although crystallographic and NMR studies have indicated a propensity for monovalent cations to occupy the deep, narrow minor groove of A-tract DNA sequences (10,11), the calculations revealed a distinct minimum energy conformation for the FdU–dA dimer complexed with Zn2+ under conditions when the 5′-terminal FdU was deprotonated. In this low energy structure, Zn2+ is localized in the major groove and interacts with F5 from the 5′-terminal FdU and with O4 from the 3′-terminal FdU as axial ligands in a distorted trigonal bipyramidal geometry with three water molecules occupying the equatorial sites. This previously uncharacterized structural motif is consistent with all of the spectroscopic, as well as the computational data.Figure 1.

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