NDI and DAN DNA: Nucleic Acid-Directed Assembly of NDI and DAN

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• 作者：Brian A. Ikkanda ; Stevan A. Samuel ; Brent L. Iverson
• 刊名：Journal of Organic Chemistry
• 出版年：2014
• 出版时间：March 7, 2014
• 年：2014
• 卷：79
• 期：5
• 页码：2029-2037
• 全文大小：452K
• 年卷期：v.79,no.5(March 7, 2014)
• ISSN：1520-6904

文摘

Two novel DNA base surrogate phosphoramidites 1 and 2, based upon relatively electron-rich 1,5-dialkoxynaphthalene (DAN) and relatively electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (NDI), respectively, were designed, synthesized, and incorporated into DNA oligonucleotide strands. The DAN and NDI artificial DNA bases were inserted within a three-base-pair region within the interior of a 12-mer oligonucleotide duplex in various sequential arrangements and investigated with CD spectroscopy and UV melting curve analysis. The CD spectra of the modified duplexes indicated B-form DNA topology. Melting curve analyses revealed trends in DNA duplex stability that correlate with the known association of DAN and NDI moieties in aqueous solution as well as the known favorable interactions between NDI and natural DNA base pairs. This demonstrates that DNA duplex stability and specificity can be driven by the electrostatic complementarity between DAN and NDI. In the most favorable case, an NDI鈥揇AN鈥揘DI arrangement in the middle of the DNA duplex was found to be approximately as stabilizing as three A鈥揟 base pairs.