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Nucleic Acids Research, 1993, Vol. 21, No. 21 4948-4953
© 1993

STRUCTURAL BIOLOGY

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

Wesley B. Derrick+ and Jack Horowitz*

Department of Biochemistry and Biophysics, Iowa State University Ames, IA 50011, USA

*To whom correspondence should be addressed

Received July 9, 1993. Revised September 10, 1993. Accepted September 10, 1993.

Structural differences between native (modified) and in transcribed (unmodified) Escherichia coli tRNAVal 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 tRNAVal has a less ordered structure as monitored by thermal melting profiles; its Tm is appreciably lower than that of native tRNAVal at all Mg2+ concentrations. Structure probing experiments with nuclease S1 and ribonuclease V1 show that the unmodified tRNAVal 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 tRNAVal. Modified nucleosides are essential for the stability of these conformers; they cannot be detected in the unmodified in vitro transcript. The observations suggest that posttranscriptional modifications in tRNA allow the adoption of unique conformations and act to stabilize those that are biologically active.

+Present address: Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309-0215, USA


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