Structures of the B-form (A) and cisplatin-induced bent (B) DNA duplexes.

<p>The duplexes with the PDB codes of 2K0V and 1A84 are shown. The distances between the C2’ atoms of the modified nucleosides were calculated using the PyMOL 1.7.1 software.</p

HPLC analysis of disulfide bond formation in duplexes containing the cisplatin adduct.

<p>(<b>A</b>–<b>F</b>) Chromatograms of the duplexes, in which × represents cisplatin, after the reactions for the indicated length of time. The y-axis of each chromatogram was normalized. The cross-linked products and the sulfinic acid-containing oligonucleotides are indicated by an arrow and an asterisk, respectively, and the results of the DTT treatment of the products are shown in red. (<b>G</b>) Comparison of the product formation between GG-6 and Pt-6. The product peak areas in panels <b>B</b> and <b>E</b> were quantified.</p

Effect of the linker length on the rate of the disulfide bond formation.

<p>(<b>A</b>) Pt-6 (C4) (open circles) and Pt-6 (C3) (filled circles); (<b>B</b>) AP-6 (C4) (open squares) and AP-6 (C3) (filled squares); (<b>C</b>) 64–6 (C4) (open triangles) and 64–6 (C3) (filled triangles). The dashed and continuous lines represent the decrease of the starting materials and the increase of the cross-linked products, respectively, and the standard errors are shown. The curve fitting was performed with the Origin 9.1 software, and the kinetic constants for the product formation are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117798#pone.0117798.t001" target="_blank">Table 1</a>.</p

HPLC analysis of disulfide bond formation in duplexes containing the (6–4) photoproduct.

<p>C4 and C3 represent the 4-mercaptobutyl and 3-mercaptopropyl groups, respectively. The y-axis of each chromatogram was normalized. The cross-linked products are indicated by an arrow, and the results of the DTT treatment of the products are shown in red.</p

Disulfide bond formation dependent on the helix bending of DNA.

<p>(<b>A</b>) Schematic presentation of this study. Two mercaptoalkyl groups were attached to positions across the major groove of a duplex (left), and a disulfide bond was formed when helix bending occurred into the major groove (right). (<b>B</b>) The chemical structure of the thiol-tethered nucleoside. Another modified nucleoside bearing the 3-mercaptopropyl group was also used. (<b>C</b>–<b>E</b>) The chemical structures of the cisplatin adduct (<b>C</b>), the abasic site analog (<b>D</b>), and the (6–4) photoproduct (<b>E</b>).</p

Structures of the B-form (A) and cisplatin-induced bent (B) DNA duplexes.

<p>The duplexes with the PDB codes of 2K0V and 1A84 are shown. The distances between the C2’ atoms of the modified nucleosides were calculated using the PyMOL 1.7.1 software.</p

HPLC analysis of disulfide bond formation in duplexes containing the abasic site analog.

<p>(<b>A</b>, <b>B</b>, <b>C</b>, <b>E</b>, and <b>F</b>) Chromatograms of the duplexes, in which X represents the abasic site analog, after the reactions for the indicated length of time. C4 and C3 represent the 4-mercaptobutyl and 3-mercaptopropyl groups, respectively. The y-axis of each chromatogram was normalized. The cross-linked products and the sulfinic acid-containing oligonucleotides are indicated by an arrow and an asterisk, respectively, and the results of the DTT treatment of the products are shown in red. (<b>D</b>) Comparison of the product formation between AP-6 (C4) and AP·A-6 (C4). The product peak areas in panels <b>A</b> and <b>B</b> were quantified.</p