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An RNA sequence showing high stability with respectto digestion by ribonuclease T1 (RNase T1) was isolated by in vitro selectionfrom an RNA library. Although ribonuclease T1 cleaves singlestranded RNAspecifically after guanosine residues, secondary structure calculations predictseveral guanosines in singlestranded areas. Two of these guanosines are part ofa GGCAtetraloop, a recurring structure element in the secondary structurepredictions. Molecular dynamics simulations of the conformation space of thenucleotides involved in this tetraloop show on the one hand that the nucleicacid backbone of the guanosines cannot realise the conformation required forcleavage by RNase T1. On the other hand, it could be shown that an RNA moleculenot forced into a tetraloop occupies this conformation several times in thecourse of the simulation. The simulations confirm the GGCAtetraloop as anRNasestable secondary structure element. Our results show that, besides theknown prerequisite of a singlestranded RNA, RNase T1 has additional demands onthe substrate conformation.

RNase-Stable RNA: Conformational Parameters of the Nucleic Acid Backbone for Binding to RNase T1