@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} }
 @article{nobles_yarian_liu_guenther_agris_2002, title={Highly conserved modified nucleosides influence Mg2+-dependent tRNA folding}, volume={30}, ISSN={["0305-1048"]}, DOI={10.1093/nar/gkf595}, abstractNote={Transfer RNA structure involves complex folding interactions of the TPsiC domain with the D domain. However, the role of the highly conserved nucleoside modifications in the TPsiC domain, rT54, Psi55 and m5C49, in tertiary folding is not understood. To determine whether these modified nucleosides have a role in tRNA folding, the association of variously modified yeast tRNA(Phe) T-half molecules (nucleosides 40-72) with the corresponding unmodified D-half molecule (nucleosides 1-30) was detected and quantified using a native polyacrylamide gel mobility shift assay. Mg2+ was required for formation and maintenance of all complexes. The modified T-half folding interactions with the D-half resulted in K(d)s (rT54 = 6 +/- 2, m5C49 = 11 +/- 2, Psi55 = 14 +/- 5, and rT54,Psi55 = 11 +/- 3 microM) significantly lower than that of the unmodified T-half (40 +/- 10 microM). However, the global folds of the unmodified and modified complexes were comparable to each other and to that of an unmodified yeast tRNA(Phe) and native yeast tRNA(Phe), as determined by lead cleavage patterns at U17 and nucleoside substitutions disrupting the Levitt base pair. Thus, conserved modifications of tRNA's TPsiC domain enhanced the affinity between the two half-molecules without altering the global conformation indicating an enhanced stability to the complex and/or an altered folding pathway.}, number={21}, journal={NUCLEIC ACIDS RESEARCH}, author={Nobles, KN and Yarian, CS and Liu, G and Guenther, RH and Agris, PF}, year={2002}, month={Nov}, pages={4751–4760} }
 @article{sengupta_vainauskas_yarian_sochacka_malkiewicz_guenther_koshlap_agris_2000, title={Modified constructs of the tRNA T Psi C domain to probe substrate conformational requirements of m(1)A(58) and m(5)U(54) tRNA methyltransferases}, volume={28}, ISSN={["0305-1048"]}, DOI={10.1093/nar/28.6.1374}, abstractNote={The TPsiC stem and loop (TSL) of tRNA contains highly conserved nucleoside modifications, m(5)C(49), T(54), Psi(55)and m(1)A(58). U(54)is methylated to m(5)U (T) by m(5)U(54)methyltransferase (RUMT); A(58)is methylated to m(1)A by m(1)A(58)tRNA methyltransferase (RAMT). RUMT recognizes and methylates a minimal TSL heptadecamer and RAMT has previously been reported to recognize and methylate the 3'-half of the tRNA molecule. We report that RAMT can recognize and methylate a TSL heptadecamer. To better understand the sensitivity of RAMT and RUMT to TSL conformation, we have designed and synthesized variously modified TSL constructs with altered local conformations and stabilities. TSLs were synthesized with natural modifications (T(54)and Psi(55)), naturally occurring modifications at unnatural positions (m(5)C(60)), altered sugar puckers (dU(54)and/or dU(55)) or with disrupted U-turn interactions (m(1)Psi(55)or m(1)m(3)Psi(55)). The unmodified heptadecamer TSL was a substrate of both RAMT and RUMT. The presence of T(54)increased thermal stability of the TSL and dramatically reduced RAMT activity toward the substrate. Local conformation around U(54)was found to be an important determinant for the activities of both RAMT and RUMT.}, number={6}, journal={NUCLEIC ACIDS RESEARCH}, author={Sengupta, R and Vainauskas, S and Yarian, C and Sochacka, E and Malkiewicz, A and Guenther, RH and Koshlap, KM and Agris, PF}, year={2000}, month={Mar}, pages={1374–1380} }
 @article{yarian_marszalek_sochacka_malkiewicz_guenther_miskiewicz_agris_2000, title={Modified nucleoside dependent Watson-Crick and wobble codon binding by tRNA(UUU)(Lys) species}, volume={39}, ISSN={["0006-2960"]}, DOI={10.1021/bi001302g}, abstractNote={Nucleoside modifications are important to the structure of all tRNAs and are critical to the function of some tRNA species. The transcript of human tRNA(Lys3)(UUU) with a UUU anticodon, and the corresponding anticodon stem and loop domain (ASL(Lys3)(UUU)), are unable to bind to poly-A programmed ribosomes. To determine if specific anticodon domain modified nucleosides of tRNA(Lys) species would restore ribosomal binding and also affect thermal stability, we chemically synthesized ASL(Lys) heptadecamers and site-specifically incorporated the anticodon domain modified nucleosides pseudouridine (Psi(39)), 5-methylaminomethyluridine (mnm(5)U(34)) and N6-threonylcarbamoyl-adenosine (t(6)A(37)). Incorporation of t(6)A(37) and mnm(5)U(34) contributed structure to the anticodon loop, apparent by increases in DeltaS, and significantly enhanced the ability of ASL(Lys3)(UUU) to bind poly-A programmed ribosomes. Neither ASL(Lys3)(UUU)-t(6)A(37) nor ASL(Lys3)(UUU)-mnm(5)U(34) bound AAG programmed ribosomes. Only the presence of both t(6)A(37) and mnm(5)U(34) enabled ASL(Lys3)(UUU) to bind AAG programmed ribosomes, as well as increased its affinity for poly-A programmed ribosomes to the level of native Escherichia coli tRNA(Lys). The completely unmodified anticodon stem and loop of human tRNA(Lys1,2)(CUU) with a wobble position-34 C bound AAG, but did not wobble to AAA, even when the ASL was modified with t(6)A(37). The data suggest that tRNA(Lys)(UUU) species require anticodon domain modifications in the loop to impart an ordered structure to the anticodon for ribosomal binding to AAA and require a combination of modified nucleosides to bind AAG.}, number={44}, journal={BIOCHEMISTRY}, author={Yarian, C and Marszalek, M and Sochacka, E and Malkiewicz, A and Guenther, R and Miskiewicz, A and Agris, PF}, year={2000}, month={Nov}, pages={13390–13395} }
 @article{yarian_basti_cain_ansari_guenther_sochacka_czerwinska_malkiewicz_agris_1999, title={Structural and functional roles of the N1-and N3-protons of Psi at tRNA's position 39}, volume={27}, ISSN={["1362-4962"]}, DOI={10.1093/nar/27.17.3543}, abstractNote={Pseudouridine at position 39 (Psi(39)) of tRNA's anticodon stem and loop domain (ASL) is highly conserved. To determine the physicochemical contributions of Psi(39)to the ASL and to relate these properties to tRNA function in translation, we synthesized the unmodified yeast tRNA(Phe)ASL and ASLs with various derivatives of U(39)and Psi(39). Psi(39)increased the thermal stability of the ASL (Delta T (m)= 1.3 +/- 0.5 degrees C), but did not significantly affect ribosomal binding ( K (d)= 229 +/- 29 nM) compared to that of the unmodified ASL (K (d)= 197 +/- 58 nM). The ASL-Psi(39)P-site fingerprint on the 30S ribosomal subunit was similar to that of the unmodified ASL. The stability, ribosome binding and fingerprint of the ASL with m(1)Psi(39)were comparable to that of the ASL with Psi(39). Thus, the contribution of Psi(39)to ASL stability is not related to N1-H hydrogen bonding, but probably is due to the nucleoside's ability to improve base stacking compared to U. In contrast, substitutions of m(3)Psi(39), the isosteric m(3)U(39)and m(1)m(3)Psi(39)destabilized the ASL by disrupting the A(31)-U(39)base pair in the stem, as confirmed by NMR. N3-methylations of both U and Psi dramatically decreased ribosomal binding ( K (d)= 1060 +/- 189 to 1283 +/- 258 nM). Thus, canonical base pairing of Psi(39)to A(31)through N3-H is important to structure, stability and ribosome binding, whereas the increased stability and the N1-proton afforded by modification of U(39)to Psi(39)may have biological roles other than tRNA's binding to the ribosomal P-site.}, number={17}, journal={NUCLEIC ACIDS RESEARCH}, author={Yarian, CS and Basti, MM and Cain, RJ and Ansari, G and Guenther, RH and Sochacka, E and Czerwinska, G and Malkiewicz, A and Agris, PF}, year={1999}, month={Sep}, pages={3543–3549} }