RNA LEGO : Construction of functional RNA nanostructures

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We have previously shown that RNA substrates consisting of two stem-loops connected by a short linker can be used to construct specific circular or linear self-assemblies through loop-loop interactions. We also showed that by adjusting the strength of the loop-loop interaction, the assembly and disassembly of the RNA structures could be controlled in a magnesium-dependent manner (Horiya et al., Chem.＆ Biol., 2003).During this project term, we obtained the following results:1) We showed that RNA substrates consisting of three stem-loops could be used to construct dendrimeric assemblies (Fujiya and Harada, Nucleic Acids Symp.Ser., 2004).2) We demonstrated that the interconversion between circular and linear RNA assemblies could be regulated by an external substrate such as magnesium ion (Ohmori et al., Nucleic Acids Symp.Ser., 2005).3) We showed that circular RNA assemblies can be efficiently isomerized to a thermodynamically stable structure. Using this structural isomerization as a functional switch, RNA substrates that assemble into circular dimers through loop-loop interactions, and isomerizes to form peptide binding sites and catalytic domains were designed (Li et al., J.Am.Chem.Soc., 2006).4) We showed that thermal isomerization can be used as a switch to construct complex nanostructures. This was accomplished by designing RNA loop-loop complexes that upon thermal isomerization form 5'- and 3'-single stranded regions complementary to each other. Such substrates can be used to form linear and two-dimensional assemblies (Kunimoto et al., in preparation).