In vitro selection of novel classes of GNRA tetraloop receptors

Abstract

GNRA tetraloop receptors are prevalent self‐assembling structural motifs in natural RNAs. The most recurrent of these is the 11 nucleotide (11 nt) receptor, which has a high affinity and specificity for GAAA tetraloops. This modular receptor takes advantage of three submotifs; the A‐minor interaction, AA platform and UA handle. Currently, few natural tetraloop receptors are highly specific for tetraloops other than GAAA. An in vitro selection strategy was employed to investigate whether novel receptors for non‐GAAA tetraloops with similar binding modality could exist. Using partially randomized sequences that maintain the A‐minor interaction, a number of new receptors binding GGRA and GURA tetraloops were obtained. Based on their binding affinities and specificities, a structural network probing the sequence space of these novel classes of receptors was created. Analysis of the sequence variants demonstrated that the selected receptors, albeit different from the 11 nt receptor, still retain a similar structural organization. Funded by the National Institutes of Health (R01 GM079604‐01).