Influence of the polyamines spermine and spermidine on yeast tRNAphe as revealed from its imino proton NMR spectrum

Abstract

A comparison of imino proton NMR spectra of yeast tRNAPhe recorded at various solution conditions indicates, that polyamines have a limited effect on the structure of this tRNA molecule. Polyamines are found to catalyse the solvent exchange of several imino protons in yeast tRNAPhe not only of non hydrogen bonded imino protons, but also of imino protons of the GU and of some AU and tertiary base pairs. It is concluded that at low levels of catalysing components the exchange rates of the latter protons are not determined by the base pair lifetime. In the presence of high levels of spermidine the solvent exchange rates of imino protons of several base pairs in the molecule were assessed as a function of the temperature. Apparent activation energies derived from these rates were found to be less than 80 kJ/mol, which is indicative for (transient) independent opening of the corresponding base pairs. In the acceptor helix the GU base pair acts as a dynamic dislocation. The AU base pairs at one side of the GU base pair exhibit faster transient opening than the GC base pairs on the other side of this wobble pair. The base pairs m2GC10 and GC11 from the D stem and GC28 from the anticodon stem show relatively slow opening up to high temperatures. Model studies suggest that 1-methyladenosine, an element of tRNA itself, catalyses imino proton solvent exchange in a way similar to polyamines.

Properties of pseudouridine N1 imino protons located in the major groove of an A-form RNA duplex

“…The increased exchange of O&N1 protons in the presence of spermidine has been noted previously (27,28) for the {55 NI proton in yeast tRNAPhe. 155 is in the T-loop of tRNA, where it is hydrogen-bonded through the C4 carbonyl to the G18 NI proton, and through the N3 proton to phosphate 58.…”

“…In the NMR experiments of Tropp and Redfield (27), the addition of spermidine to yeast tRNAPhe decreased the exchange rate of the 055 N3 proton, while that of the V55 NI proton was increased. This selective protection of 155 N3 H could be due to a specific interaction which stabilized the tertiary folding; the destabilization of NI H could be due to catalysis by the spermidine (28). Similarly, the non-hydrogen-bonded 639 NI proton disappears from the NMR spectrum when spermidine is present (28), while the hydrogen-bonded &39 N3 proton is stable.…”

Novel Design Architecture for Genetic Stability of Recombinant Poliovirus: the Manipulation of G/C Contents and Their Distribution Patterns Increases the Genetic Stability of Inserts in a Poliovirus-Based RPS-Vax Vector System

“…Considering the stringency of picornavirus packaging, if the recombinant RNA, in three-dimensional structure, is too voluminous to be encased in the rigid capsid, packaging pressure may cause a deletion of the nonessential foreign insert. The three-dimensional conformation of the insert RNA is associated, at least in part, with the number of hydrogen bonds in canonically base-paired regions and sequence-dependent free energy (4,6,15,31). Based on this rationale, we have studied the correlation between genetic stability and the G/C contents of each insert and found that most of the stable inserts showed a high G/C content of over 40% (Table 1 and Fig.…”

Probing the conformation of human tRNA3Lys in solution by NMR

“…Nuclear magnetic resonance (NMR) has long been a powerful tool to monitor tRNA folding and conformation. The earliest studies of RNAs using NMR focused on the exchangeable imino proton spectrum of natural tRNAs that could be obtained in high yield [20,[34][35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50][51][52]. The imino proton spectra of various tRNAs were assigned, and used to probe the folding and dynamics of tRNAs under different solution conditions.…”