High-Affinity DNA Targeting Using Readily Accessible Mimics of N2鈥?Functionalized 2鈥?Amino-伪-L-LNA

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• 作者：Saswata Karmakar ; Brooke A. Anderson ; Rie L. Rathje ; Sanne Andersen ; Troels B. Jensen ; Poul Nielsen ; Patrick J. Hrdlicka
• 刊名：Journal of Organic Chemistry
• 出版年：2011
• 出版时间：September 2, 2011
• 年：2011
• 卷：76
• 期：17
• 页码：7119-7131
• 全文大小：1070K
• 年卷期：v.76,no.17(September 2, 2011)
• ISSN：1520-6904

文摘

N2鈥?Pyrene-functionalized 2鈥?amino-伪-L-LNAs (locked nucleic acids) display extraordinary affinity toward complementary DNA targets due to favorable preorganization of the pyrene moieties for hybridization-induced intercalation. Unfortunately, the synthesis of these monomers is challenging (20 steps, <3% overall yield), which has precluded full characterization of DNA-targeting applications based on these materials. Access to more readily accessible functional mimics would be highly desirable. Here we describe short synthetic routes to a series of O2鈥?intercalator-functionalized uridine and N2鈥?intercalator-functionalized 2鈥?N-methyl-2鈥?aminouridine monomers and demonstrate, via thermal denaturation, UV鈥搗is absorption and fluorescence spectroscopy experiments, that several of them mimic the DNA-hybridization properties of N2鈥?pyrene-functionalized 2鈥?amino-伪-L-LNAs. For example, oligodeoxyribonucleotides (ONs) modified with 2鈥?O-(coronen-1-yl)methyluridine monomer Z, 2鈥?O-(pyren-1-yl)methyluridine monomer Y, or 2鈥?N-(pyren-1-ylmethyl)-2鈥?N-methylaminouridine monomer Q display prominent increases in thermal affinity toward complementary DNA relative to reference strands (average 螖T_m/mod up to +12 掳C), pronounced DNA-selectivity, and higher target specificity than 2鈥?amino-伪-L-LNA benchmark probes. In contrast, ONs modified with 2鈥?O-(2-napthyl)uridine monomer W, 2鈥?O-(pyren-1-yl)uridine monomer X or 2鈥?N-(pyren-1-ylcarbonyl)-2鈥?N-methylaminouridine monomer S display very low affinity toward DNA targets. This demonstrates that even conservative alterations in linker chemistry, linker length, and surface area of the appended intercalators have marked impact on DNA-hybridization characteristics. Straightforward access to high-affinity building blocks such as Q, Y, and Z is likely to accelerate their use in DNA-targeting applications within nucleic acid based diagnostics, therapeutics, and material science.