@article{guenther_sit_gracz_dolan_townsend_liu_newman_agris_lommel_2004, title={Structural characterization of an intermolecular RNA-RNA interaction involved in the transcription regulation element of a bipartite plant virus}, volume={32}, ISSN={["1362-4962"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-3042761419&partnerID=MN8TOARS}, DOI={10.1093/nar/gkh585}, abstractNote={The 34-nucleotide trans-activator (TA) located within the RNA-2 of Red clover necrotic mosaic virus folds into a simple hairpin. The eight-nucleotide TA loop base pairs with eight complementary nucleotides in the TA binding sequence (TABS) of the capsid protein subgenomic promoter on RNA-1 and trans-activates subgenomic RNA synthesis. Short synthetic oligoribonucleotide mimics of the RNA-1 TABS and the RNA-2 TA form a weak 1:1 bimolecular complex in vitro with a K(a) of 5.3 x 10(4) M(-1). K(a) determination for a series of RNA-1 and RNA-2 mimic variants indicated optimum stability is obtained with seven-base complementarity. Thermal denaturation and NMR show that the RNA-1 TABS 8mers are weakly ordered in solution while RNA-2 TA oligomers form the predicted hairpin. NMR diffusion studies confirmed RNA-1 and RNA-2 oligomer complex formation in vitro. MC-Sym generated structural models suggest that the bimolecular complex is composed of two stacked helices, one being the stem of the RNA-2 TA hairpin and the other formed by the intermolecular base pairing between RNA-1 and RNA-2. The RCNMV TA structural model is similar to those for the Simian retrovirus frameshifting element and the Human immunodeficiency virus-1 dimerization kissing hairpins, suggesting a conservation of form and function.}, number={9}, journal={NUCLEIC ACIDS RESEARCH}, publisher={Oxford University Press (OUP)}, author={Guenther, RH and Sit, TL and Gracz, HS and Dolan, MA and Townsend, HL and Liu, GH and Newman, WH and Agris, PF and Lommel, SA}, year={2004}, month={May}, pages={2819–2828} }
 @article{yarian_townsend_czestkowski_sochacka_malkiewicz_guenther_miskiewicz_agris_2002, title={Accurate translation of the genetic code depends on tRNA modified nucleosides}, volume={277}, ISSN={["0021-9258"]}, DOI={10.1074/jbc.M200253200}, abstractNote={Transfer RNA molecules translate the genetic code by recognizing cognate mRNA codons during protein synthesis. The anticodon wobble at position 34 and the nucleotide immediately 3′ to the anticodon triplet at position 37 display a large diversity of modified nucleosides in the tRNAs of all organisms. We show that tRNA species translating 2-fold degenerate codons require a modified U34 to enable recognition of their cognate codons ending in A or G but restrict reading of noncognate or near-cognate codons ending in U and C that specify a different amino acid. In particular, the nucleoside modifications 2-thiouridine at position 34 (s2U34), 5-methylaminomethyluridine at position 34 (mnm5U34), and 6-threonylcarbamoyladenosine at position 37 (t6A37) were essential for Watson-Crick (AAA) and wobble (AAG) cognate codon recognition by tRNA UUU Lys at the ribosomal aminoacyl and peptidyl sites but did not enable the recognition of the asparagine codons (AAU and AAC). We conclude that modified nucleosides evolved to modulate an anticodon domain structure necessary for many tRNA species to accurately translate the genetic code.}, number={19}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Yarian, C and Townsend, H and Czestkowski, W and Sochacka, E and Malkiewicz, AJ and Guenther, R and Miskiewicz, A and Agris, PF}, year={2002}, month={May}, pages={16391–16395} }