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Chem Sci. 2014 Oct 1;5(10):4076-4081.

Trifluoromethylated Nucleic Acid Analogues Capable of Self-Assembly through Hydrophobic Interactions.

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Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China.
Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Science, 345 Lingling Lu, Shanghai, 200032, China.


An artificial nucleic acid analogue capable of self-assembly into duplex merely through hydrophobic interactions is presented. The replacement of Watson-Crick hydrogen bonding with strictly hydrophobic interactions has the potential to confer new properties and facilitate the construction of complex DNA nanodevices. To study how the hydrophobic effect works during the self-assembly of nucleic acid bases, we have designed and synthesized a series of fluorinated nucleic acids (FNA) containing 3,5-bis(trifluoromethyl) benzene (F) and nucleic acids incorporating 3,5-dimethylbenzene (M) as hydrophobic base surrogates. Our experiments illustrate that two single-stranded nucleic acid oligomers could spontaneously organize into a duplex entirely by hydrophobic base pairing if the bases were size-complementary and the intermolecular forces were sufficiently strong.

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