A naturally occurring , noncanonical GTP aptamer made

GTP plays a central role in diverse cellular processes, and at least three percent of the proteins in the human proteome bind GTP. The fundamental role played by GTP in cells, as well as the emerging realization that the functions of biological proteins and RNAs may not be as distinct as once thought, led us to hypothesize that RNA molecules that bind GTP might also be widespread in nature. To test this hypothesis, we used in vitro selection to search a pool of phylogenetically diverse genome-derived RNA fragments for new examples of naturally occurring GTP aptamers. This study revealed that such aptamers are abundant, especially in the genomes of eukaryotes. The majority of the aptamers identified had the potential to form G-quadruplex structures, and further analysis confirmed that most G-quadruplexes exhibit an intrinsic GTP-binding activity. Here, we report the discovery of a second class of naturally occurring GTP-binding RNA aptamer, which we have designated the “CA motif.” Members of this aptamer class contain multiple copies of CA-rich sequence motifs such as CAACA arranged in tandem repeats. Although recent studies indicate that RNA tandem repeats can play biological roles, including roles in human disease, the functional properties of such repeats are still not well understood. A second intriguing feature of the CA motif aptamer is that its sequence requirements are not consistent with those of a canonical nucleic acid structure. For example, CA motif variants with limited potential for Watson-Crick base pairing, including those made of repeats containing only cytidine and adenosine nucleotides, can still bind GTP. Circular dichroism (CD) analysis of the CA motif aptamer also supports the idea of an unusual structure: the characteristic CD spectrum of the CA motif aptamer is distinct from that of several common types of nucleic acid structures, including A-form RNA. Although much less widespread in nature than the previously described G motif, the CA motif was detected in 70 percent of the approximately 400 eukaryotic genomes analyzed, and several examples were identified whose ability to bind GTP has been conserved in evolution. Taken together, these results reveal the existence of a second type of naturally occurring GTP aptamer with a noncanonical structure, and reveal a new potential biochemical activity of naturally occurring RNA tandem repeats.