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Structural differences between native (modified) and in vitro transcribed (unmodified) Escherichia coli tRNA(Val) were explored by comparing their temperature-absorbance profiles as a function of magnesium ion concentration and by probing their solution conformation with single- and double-strand-specific endonucleases. In vitro transcribed tRNA(Val) has a less ordered structure as monitored by thermal melting profiles; its Tm is appreciably lower than that of native tRNA(Val) at all Mg2+ concentrations. Structure probing experiments with nuclease S1 and ribonuclease V1 show that the unmodified tRNA(Val) transcript is more susceptible to nuclease attack at low Mg2+ concentrations, particularly in the D- and T-loops, indicative of at least a partial disruption of D-loop/T-loop interactions. These experiments also provide evidence for temperature-dependent alternative conformations of the anticodon loop of native tRNA(Val). Modified nucleosides are essential for the stability of these conformers; they cannot be detected in the unmodified in vitro transcript. The observations suggest that post-transcriptional modifications in tRNA allow the adoption of unique conformations and act to stabilize those that are biologically active.

nucleic acids research

Probing structural differences between native and<i>in vitro</i>transcribed<i>Escherichia coli</i>valine transfer RNA: evidence for stable base modification-dependent conformers

Probing structural differences between native andin vitrotranscribedEscherichia colivaline transfer RNA: evidence for stable base modification-dependent conformers