RNase-Stable RNA: Conformational Parameters of the Nucleic Acid Backbone for Binding to RNase T1
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Thomas Greiner-Stöffele
Abstract
An RNA sequence showing high stability with respect to digestion by ribonuclease T1 (RNase T1) was isolated by in vitro selection from an RNA library. Although ribonuclease T1 cleaves singlestranded RNA specifically after guanosine residues, secondary structure calculations predict several guanosines in singlestranded areas. Two of these guanosines are part of a GGCAtetraloop, a recurring structure element in the secondary structure predictions. Molecular dynamics simulations of the conformation space of the nucleotides involved in this tetraloop show on the one hand that the nucleic acid backbone of the guanosines cannot realise the conformation required for cleavage by RNase T1. On the other hand, it could be shown that an RNA molecule not forced into a tetraloop occupies this conformation several times in the course of the simulation. The simulations confirm the GGCAtetraloop as an RNasestable secondary structure element. Our results show that, besides the known prerequisite of a singlestranded RNA, RNase T1 has additional demands on the substrate conformation.
Copyright © 2001 by Walter de Gruyter GmbH & Co. KG
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