Single-molecule FRET reveals a cooperative effect of two methyl group modifications in the folding of human mitochondrial tRNA(Lys).

Using a combination of advanced RNA synthesis techniques and single molecule spectroscopy, the deconvolution of individual contributions of posttranscriptional modifications to the overall folding and stabilization of human mitochondrial tRNA(Lys) is described. An unexpected destabilizing effect of two pseudouridines on the native tRNA folding was evidenced. Furthermore, the presence of m(2)G10 alone does not facilitate the folding of tRNA(Lys), but a stabilization of the biologically functional cloverleaf shape in conjunction with the principal stabilizing component m(1)A9 exceeds the contribution of m(1)A alone. This constitutes an unprecedented cooperative effect of two nucleotide modifications in the context of a naturally occurring RNA, which may be of general importance for tRNA structure and help understanding several recently described decay pathways for hypomodified tRNAs.