Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

Stabilization effects induced by modified nucleotides in tRNA T-loop motifs

tRNAs are known to contain more than 100 chemically modified nucleotides. Although frequent, their biological role and significance are still largely unknown. Among them, pseudouridine (Ψ; the C-glycoside isomer of uridine), is the most recurrent modification and is, therefore, sometimes designated as the 5th nucleotide. Ψ is highly phylogenetically conserved in tRNA at position 55 of T-loops, a structural motif essential for the tRNA 3D cloverleaf arrangement. The interdigitation of the T- and D- loops forms a C=G platform that is solvent exposed and essential for the recognition of tRNAs by T-box riboswitches and ribosomes. Besides Ψ residues, T-loops include two additional modified bases: thymine (T) and 1-methyladenine (1MA), which are also highly conserved.

To investigate the role of T-loop modified nucleotides, we performed explicit solvent molecular dynamics (MD) simulations on several variants of tRNAPhe. Besides well-described hydrogen bond networks that are involved in the stabilization of the loop, we discuss the occurrence and dynamical characteristics of an overlooked phosphate-π contact characteristic of U-turn motifs i.e. the stacking of OP2(R57) atom over the aromatic surface of Ψ55 (Figure). Surprisingly stable water molecules (several ns residency times) were identified at different locations of this motif.

To assess the involvement of the modified nucleotides in the stabilization of this long-resident water molecules and consequently in the stabilization of the D- and T-loop interdigitation motif leading to the formation of a stable C=G platform, we performed MD simulations on tRNA structures selectively deprived of the Ψ, T and 1MA modified residues. Presented data provide insights on stabilization effects associated with modified nucleotides and on the roles this highly conserved cluster of modified nucleotides plays in recognition process involving these interdigidated loops.


Dominique Sydow
Filip Leonarski
Luigi D’Ascenzo
Pascal Auffinger

Architecture et Reactivite de l'ARN
Universite de Strasbourg
Institut de Biologie Moleculaire et Cellulaire du CNRS
Strasbourg, 67084, France