Specific and non-specific purine trap in the T-loop of normal and suppressor tRNAs

Journal of Molecular Biology
Felix R DoyonS V Steinberg

Abstract

To elucidate the general constraints imposed on the structure of the D and T-loops in functional tRNAs, active suppressor tRNAs were selected in vivo from a combinatorial tRNA gene library in which several nucleotide positions in these loops were randomized. Analysis of the nucleotide sequences of the selected clones demonstrates that most of them contain combination U54-A58 allowing the formation of the standard reverse-Hoogsteen base-pair 54-58 in the T-loop. With only one exception, all these clones fall into two groups, each characterized by a distinct sequence pattern. Analysis of these two groups has allowed us to suggest two different types of nucleotide arrangement in the DT region. The first type, the so-called specific purine trap, is found in 12 individual tRNA clones and represents a generalized version of the standard D-T loop interaction. It consists of purine 18 sandwiched between the reverse-Hoogsteen base-pair U54-A58 and purine 57. The identity of purine 18 is restricted by the specific base-pairing with nucleotide 55. Depending on whether nucleotide 55 is U or G, purine 18 should be, respectively, G or A. The second structural type, the so-called non-specific purine trap, corresponds to the nucleotide sequenc...Continue Reading

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Citations

Mar 15, 2006·Nature Structural & Molecular Biology·Dongli PanBarry S Cooperman
May 2, 2008·The Journal of Biological Chemistry·Dongli PanBarry S Cooperman
Sep 8, 2007·Journal of Molecular Biology·Natalia KotlovaSergey V Steinberg

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