TectoRNA: modular assembly units for the construction of RNA nano-objects

Structural information on complex biological RNA molecules can be exploited to design tectoRNAs or artificial modular RNA units that can self-assemble through tertiary interactions thereby forming nanoscale RNA objects. The s elective interactions of hairpin tetraloops with their receptors can be use d to mediate tectoRNA assembly. Here we report on the modulation of the spe cificity and the strength of tectoRNA assembly tin the nanomolar to micromo lar range) by variation of the length of the RNA subunits, the nature of th eir interacting motifs and the degree of flexibility of linker regions inco rporated into the molecules. The association is also dependent on the conce ntration of magnesium, Monitoring of tectoRNA assembly by lead(ll) cleavage protection indicates that some degree of structural flexibility is require d for optimal binding. With tectoRNAs one can compare the binding affinitie s of different tertiary motifs and quantify the strength of individual inte ractions. Furthermore, in analogy to the synthons used in organic chemistry to synthesize more complex organic compounds, tectoRNAs form the basic ass embly units for constructing complex RNA structures on the nanometer scale. Thus, tectoRNA provides a means for constructing molecular scaffoldings th at organize functional modules in three-dimensional space for a wide range of applications.