Design, biological activity and NMR-solution structure of a DNA analogue of yeast tRNA^Phe anticodon domain

Design of biologically active DNA analogues of the yeast tRNA^Phe anticodon domain, tDNA^Phe _AC, required the introduction of a d(m⁵C)-dependent, Mg²⁺-induced structural transition and the d(m¹G) disruption of an intra-loop dCdG base pair. The modifications were introduced at residues corresponding to m⁵C-40 and wybutosine-37 in tRNA^Phe. Modified tDNA^Phe _AC inhibited translation by 50% at a tDNA^Phe _AC:ribosome ratio of 8:1. The molecule's structure has been determined by NMR spectroscopy and restrained molecular dynamics with an overall r.m.s.d. of 2.8 Å and 1.7 Å in the stem, and is similar to the tRNA^Phe anticodon domain in conformation and dimensions. The tDNA^Phe _AC structure may provide a guide for the design of translation inhibitors as potential therapeutic agents.

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