Relevant bibliographies by topics / Near-cognate tRNA

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Academic literature on the topic 'Near-cognate tRNA'

Author: Grafiati
Published: 28 June 2021
Last updated: 29 July 2025

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Journal articles on the topic "Near-cognate tRNA"

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Nguyen, Ha An, S. Sunita, and Christine M. Dunham. "Disruption of evolutionarily correlated tRNA elements impairs accurate decoding." Proceedings of the National Academy of Sciences 117, no. 28 (2020): 16333–38. http://dx.doi.org/10.1073/pnas.2004170117.

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Bacterial transfer RNAs (tRNAs) contain evolutionarily conserved sequences and modifications that ensure uniform binding to the ribosome and optimal translational accuracy despite differences in their aminoacyl attachments and anticodon nucleotide sequences. In the tRNA anticodon stem−loop, the anticodon sequence is correlated with a base pair in the anticodon loop (nucleotides 32 and 38) to tune the binding of each tRNA to the decoding center in the ribosome. Disruption of this correlation renders the ribosome unable to distinguish correct from incorrect tRNAs. The molecular basis for how the
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Blanchet, Sandra, David Cornu, Isabelle Hatin, Henri Grosjean, Pierre Bertin, and Olivier Namy. "Deciphering the reading of the genetic code by near-cognate tRNA." Proceedings of the National Academy of Sciences 115, no. 12 (2018): 3018–23. http://dx.doi.org/10.1073/pnas.1715578115.

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Some codons of the genetic code can be read not only by cognate, but also by near-cognate tRNAs. This flexibility is thought to be conferred mainly by a mismatch between the third base of the codon and the first of the anticodon (the so-called “wobble” position). However, this simplistic explanation underestimates the importance of nucleotide modifications in the decoding process. Using a system in which only near-cognate tRNAs can decode a specific codon, we investigated the role of six modifications of the anticodon, or adjacent nucleotides, of the tRNAs specific for Tyr, Gln, Lys, Trp, Cys,
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Vimaladithan, A., and P. J. Farabaugh. "Special peptidyl-tRNA molecules can promote translational frameshifting without slippage." Molecular and Cellular Biology 14, no. 12 (1994): 8107–16. http://dx.doi.org/10.1128/mcb.14.12.8107-8116.1994.

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Recently we described an unusual programmed +1 frameshift event in yeast retrotransposon Ty3. Frameshifting depends on the presence of peptidyl-tRNA(AlaCGC) on the GCG codon in the ribosomal P site and on a translational pause stimulated by the slowly decoded AGU codon. Frameshifting occurs on the sequence GCG-AGU-U by out-of-frame binding of a valyl-tRNA to GUU without slippage of peptidyl-tRNA(AlaCGC). This mechanism challenges the conventional understanding that frameshift efficiency must correlate with the ability of mRNA-bound tRNA to slip between cognate or near-cognate codons. Though fr
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Vimaladithan, A., and P. J. Farabaugh. "Special peptidyl-tRNA molecules can promote translational frameshifting without slippage." Molecular and Cellular Biology 14, no. 12 (1994): 8107–16. http://dx.doi.org/10.1128/mcb.14.12.8107.

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Recently we described an unusual programmed +1 frameshift event in yeast retrotransposon Ty3. Frameshifting depends on the presence of peptidyl-tRNA(AlaCGC) on the GCG codon in the ribosomal P site and on a translational pause stimulated by the slowly decoded AGU codon. Frameshifting occurs on the sequence GCG-AGU-U by out-of-frame binding of a valyl-tRNA to GUU without slippage of peptidyl-tRNA(AlaCGC). This mechanism challenges the conventional understanding that frameshift efficiency must correlate with the ability of mRNA-bound tRNA to slip between cognate or near-cognate codons. Though fr
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5

Ieong, Ka-Weng, Gabriele Indrisiunaite, Arjun Prabhakar, Joseph D. Puglisi, and Måns Ehrenberg. "N 6-Methyladenosines in mRNAs reduce the accuracy of codon reading by transfer RNAs and peptide release factors." Nucleic Acids Research 49, no. 5 (2021): 2684–99. http://dx.doi.org/10.1093/nar/gkab033.

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Abstract We used quench flow to study how N6-methylated adenosines (m6A) affect the accuracy ratio between kcat/Km (i.e. association rate constant (ka) times probability (Pp) of product formation after enzyme-substrate complex formation) for cognate and near-cognate substrate for mRNA reading by tRNAs and peptide release factors 1 and 2 (RFs) during translation with purified Escherichia coli components. We estimated kcat/Km for Glu-tRNAGlu, EF-Tu and GTP forming ternary complex (T3) reading cognate (GAA and Gm6AA) or near-cognate (GAU and Gm6AU) codons. ka decreased 10-fold by m6A introduction
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O’Connor, Michael. "tRNA imbalance promotes −1 frameshifting via near-cognate decoding." Journal of Molecular Biology 279, no. 4 (1998): 727–36. http://dx.doi.org/10.1006/jmbi.1998.1832.

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Wohlgemuth, Ingo, Corinna Pohl, Joerg Mittelstaet, Andrey L. Konevega, and Marina V. Rodnina. "Evolutionary optimization of speed and accuracy of decoding on the ribosome." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1580 (2011): 2979–86. http://dx.doi.org/10.1098/rstb.2011.0138.

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Speed and accuracy of protein synthesis are fundamental parameters for the fitness of living cells, the quality control of translation, and the evolution of ribosomes. The ribosome developed complex mechanisms that allow for a uniform recognition and selection of any cognate aminoacyl-tRNA (aa-tRNA) and discrimination against any near-cognate aa-tRNA, regardless of the nature or position of the mismatch. This review describes the principles of the selection—kinetic partitioning and induced fit—and discusses the relationship between speed and accuracy of decoding, with a focus on bacterial tran
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Pernod, Ketty, Laure Schaeffer, Johana Chicher, et al. "The nature of the purine at position 34 in tRNAs of 4-codon boxes is correlated with nucleotides at positions 32 and 38 to maintain decoding fidelity." Nucleic Acids Research 48, no. 11 (2020): 6170–83. http://dx.doi.org/10.1093/nar/gkaa221.

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Abstract Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/tra
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Zhang, Jingji, Ka-Weng Ieong, Magnus Johansson, and Måns Ehrenberg. "Accuracy of initial codon selection by aminoacyl-tRNAs on the mRNA-programmed bacterial ribosome." Proceedings of the National Academy of Sciences 112, no. 31 (2015): 9602–7. http://dx.doi.org/10.1073/pnas.1506823112.

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We used a cell-free system with pureEscherichia colicomponents to study initial codon selection of aminoacyl-tRNAs in ternary complex with elongation factor Tu and GTP on messenger RNA-programmed ribosomes. We took advantage of the universal rate-accuracy trade-off for all enzymatic selections to determine how the efficiency of initial codon readings decreased linearly toward zero as the accuracy of discrimination against near-cognate and wobble codon readings increased toward the maximal asymptote, thedvalue. We report data on the rate-accuracy variation for 7 cognate, 7 wobble, and 56 near-c
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Roy, Bijoyita, Westley J. Friesen, Yuki Tomizawa, et al. "Ataluren stimulates ribosomal selection of near-cognate tRNAs to promote nonsense suppression." Proceedings of the National Academy of Sciences 113, no. 44 (2016): 12508–13. http://dx.doi.org/10.1073/pnas.1605336113.

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A premature termination codon (PTC) in the ORF of an mRNA generally leads to production of a truncated polypeptide, accelerated degradation of the mRNA, and depression of overall mRNA expression. Accordingly, nonsense mutations cause some of the most severe forms of inherited disorders. The small-molecule drug ataluren promotes therapeutic nonsense suppression and has been thought to mediate the insertion of near-cognate tRNAs at PTCs. However, direct evidence for this activity has been lacking. Here, we expressed multiple nonsense mutation reporters in human cells and yeast and identified the
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Dissertations / Theses on the topic "Near-cognate tRNA"

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Kučerová, Michaela. "Cysteinová tRNA reguluje proteosyntézu v lidských buněčných liniích." Master's thesis, 2021. http://www.nusl.cz/ntk/nusl-445948.

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A significant number of known human genetic diseases is associated with nonsense mutations leading to the introduction of a premature termination codon into the coding sequence. A termination codon can be read through by its near-cognate tRNA (tRNA with two anticodon nucleotides base-pairing with a stop codon); potentially generating C-terminally extended protein variants. In yeast, UGA stop codon was described to be read through by tRNA-Trp and tRNA-Cys. Similar was observed for tRNA-Trp in human HEK293T cell line. The aim of this thesis was to investigate if human tRNA-Cys can act as a near-
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