P-stilbazole moieties as artificial base pairs for photo-cross-linking of DNA duplex

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[1] Kashida, Hiromu
[2] Doi, Tetsuya
[3] Sakakibara, Takumi
[4] Hayashi, Takamitsu
[5] Asanuma, Hiroyuki
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Kashida, H. (kashida@nubio.nagoya-u.ac.jp) | 1600年 / American Chemical Society卷 / 135期
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In this study; we report a photo-cross-linking reaction between p-stilbazole moieties. p-Stilbazoles were introduced into base-paring positions of complementary DNA strands. The [2 + 2] photocycloaddition reaction occurred rapidly upon light irradiation at 340 nm. Consequently; duplex was cross-linked and highly stabilized after 3 min irradiation. The CD spectrum of the cross-linked duplex indicated that the B-form double-helical structure was not severely distorted. NMR analysis revealed only one conformation of the duplex prior to UV irradiation; whereas two diastereomers were detected after the photo-cross-linking reaction. Before UV irradiation; p-stilbazole can adopt two different stacking modes because of rotation around the single bond between the phenyl and vinyl groups; these conformations cannot be discriminated on the NMR time scale due to rapid interconversion. However; photo-cross-linking fixed the conformation and enabled discrimination both by NMR and HPLC. The artificial base pair of p-methylstilbazolium showed almost the same reactivity as p-stilbazole; indicating that positive charge does not affect the reactivity. When a natural nucleobase was present in the complementary strand opposite p-stilbazole; the duplex was significantly destabilized relative to the duplex with paired p-stilbazole moieties and no photoreaction occurred between p-stilbazole and the nucleobase. The p-stilbazole pair has potential as a third base pair for nanomaterials due to its high stability and superb orthogonality. © 2013 American Chemical Society;
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