Engineered domain swapping indicates context dependent functional role of RNA G-quadruplexes

Abstract

RNA domain swapping typically demonstrates conservation of the native function of the domain in a non-native context. In contrast, we employed RNA engineering to demonstrate deviation of G-quadruplex (GQ) function that is contingent upon its context dependent location, which is opposite to their native functional role. Known translation repressing RNA GQs were engineered into human VEGF IRES A replacing the endogenous GQ domain essential for translation. Alternatively, the translation inhibitory GQ motif within the 5′-UTR of MT3-MMP mRNA was replaced with two known GQ motifs that are essential for translation. The results indicate that the engineered GQ domains can adopt GQ structures in a foreign environment with a functional role reversal to accommodate the need of the endogenous swapped motifs. The observations establish the functionality and context dependent modularity of RNA GQ structures.