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1. Full Text Desulfuration of 2-thiouridine with hydrogen peroxide in the physiological pH range 6.6a7.6 is pH-dependent and results in two distinct products
by Sochacka, Elzbieta and Bartos, Paulina and Kraszewska, Karina and Nawrot, Barbara
Bioorganic and Medicinal Chemistry Letters, ISSN 0960-894X, 11/2013, Volume 23, Issue 21, pp. 5803 - 5805
The 2-thiomodified nucleosides, located at first position of tRNAs anticodon, may constitute a primary target for oxidative attack under conditions of... 
Anticodons
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2. Full Text Anticodon Loop Modifications Modulate Structural Flexibility in E. coli tRNA super(Arg1, 2) that Lacks a U-turn Conformation in Solution
by Cantara, WA and Bilbille, Y and Kim, J and Malkiewicz, A and Agris, PF
Journal of Biomolecular Structure and Dynamics, ISSN 0739-1102, 06/2011, Volume 28, Issue 6, pp. 1072 - 1072
Three of the six codons that are decoded by tRNA super(Arg) in E. coli are read by the isoacceptors tRNA super(Arg1, 2). The anticodon stem and loop domain... 
Anticodons
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3. Full Text TRNA deamination by ADAT requires substrate-specific recognition mechanisms and can be inhibited by tRFs
by Frigolé, Helena Roura and Camacho, Noelia and Coma, Maria Castellví and Fernández-Lozano, Carla and García-Lema, Jorge and Rafels-Ybern, Àlbert and Canals, Albert and Coll, Miquel and de Pouplana, Lluís Ribas
RNA, ISSN 1355-8382, 05/2019, Volume 25, Issue 5, pp. 607 - 619
Adenosine deaminase acting on transfer RNA (ADAT) is an essential eukaryotic enzyme that catalyzes the deamination of adenosine to inosine at the first... 
ADAT | Inosine | TRF | Adenosine | Deaminase | TRNA | inosine | METHYLATION | ADENOSINE-DEAMINASE | tRNA | MITOCHONDRIAL | BIOCHEMISTRY & MOLECULAR BIOLOGY | deaminase | tRF | TRANSLATION | CELLULAR STRESS | adenosine | FRAGMENTS | DATABASE | WOBBLE POSITION | ANTICODON | Anticodon - metabolism | Gene Expression | Adenosine Deaminase - genetics | Adenosine Deaminase - metabolism | Anticodon - genetics | Humans | Anticodon - chemistry | Substrate Specificity | Inosine - metabolism | RNA, Transfer, Ala - genetics | RNA, Transfer, Ala - metabolism | RNA, Transfer, Arg - genetics | Sequence Alignment | Deamination | Base Sequence | RNA, Transfer, Arg - chemistry | RNA, Transfer, Arg - metabolism | Adenosine - metabolism | RNA, Transfer, Ala - chemistry | Nucleic Acid Conformation | Evolution, Molecular | Anticodons | Enzymes | Adenosine deaminase | Ribonucleic acid--RNA | Transfer RNA | Index Medicus
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4. Full Text Ensemble cryo-EM elucidates the mechanism of translation fidelity
by Loveland, Anna B and Demo, Gabriel and Grigorieff, Nikolaus and Korostelev, Andrei A
Nature, ISSN 0028-0836, 06/2017, Volume 546, Issue 7656, pp. 113 - 117
Gene translation depends on accurate decoding of mRNA, the structural mechanism of which remains poorly understood. Ribosomes decode mRNA codons by selecting... 
EF-TU | ANGSTROM RESOLUTION | ESCHERICHIA-COLI RIBOSOME | AMINOACYL-TRANSFER-RNA | CRYSTAL-STRUCTURE | MULTIDISCIPLINARY SCIENCES | ELECTRON-MICROSCOPY | ELONGATION-FACTOR-TU | GENETIC-CODE TRANSLATION | GTP HYDROLYSIS | 16S RIBOSOMAL-RNA | Anticodon - ultrastructure | Ribosome Subunits - chemistry | Protein Biosynthesis | Anticodon - chemistry | Ribosomes - metabolism | RNA, Ribosomal, 16S - ultrastructure | GTP Phosphohydrolases - ultrastructure | Guanosine Triphosphate - metabolism | RNA, Transfer, Amino Acyl - metabolism | Protein Domains | Codon - genetics | RNA, Transfer, Amino Acyl - ultrastructure | RNA, Ribosomal, 16S - metabolism | Anticodon - genetics | Ribosomes - chemistry | Models, Molecular | RNA, Transfer, Amino Acyl - genetics | Escherichia coli - chemistry | Peptide Elongation Factor Tu - ultrastructure | Cryoelectron Microscopy | Hydrolysis | Peptide Elongation Factor Tu - metabolism | Codon - ultrastructure | Ribosomes - ultrastructure | Codon - chemistry | GTP Phosphohydrolases - metabolism | Escherichia coli - genetics | Ribosome Subunits - ultrastructure | RNA, Ribosomal, 16S - genetics | Escherichia coli - ultrastructure | Ribosome Subunits - metabolism | RNA sequencing | Messenger RNA | Physiological aspects | Observations | Genetic translation | Methods | Transfer RNA | Binding | Fidelity | Anticodons | GTP | High resolution | tRNA | Molecular structure | Ricin | Ribosomes | Elongation factor EF-Tu | Decoding | Ribonucleic acid--RNA | Intermediates | Proteins | Docks | Microscopy | Elongated structure | Accommodation | Codons | Molecular biology | Binding sites | Elongation | Conformation | Index Medicus
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5. Full Text Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit
by James M. Ogle and Ditlev E. Brodersen and William M. Clemons and Michael J. Tarry and Andrew P. Carter and V. Ramakrishnan
Science, ISSN 0036-8075, 5/2001, Volume 292, Issue 5518, pp. 897 - 902
Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the... 
Messenger RNA | Hydrogen bonds | RNA | Antibiotics | Protein synthesis | Ribosomes | Crystals | Research Articles | Codons | Anticodon | Transfer RNA | P-SITE | ANGSTROM RESOLUTION | ELONGATION-FACTOR TU | ESCHERICHIA-COLI RIBOSOME | AMINOACYL-TRANSFER-RNA | PHENYLALANINE TRANSFER-RNA | CRYSTAL-STRUCTURE | MULTIDISCIPLINARY SCIENCES | A-SITE | 70S RIBOSOME | DNA-REPLICATION | Codon - metabolism | Anticodon - metabolism | Protein Biosynthesis | Peptide Chain Elongation, Translational | RNA, Transfer, Phe - chemistry | Anticodon - chemistry | RNA, Transfer, Amino Acid-Specific - metabolism | Ribosomes - metabolism | Thermus thermophilus - metabolism | Crystallography, X-Ray | Thermus thermophilus - ultrastructure | Guanosine Triphosphate - metabolism | RNA, Messenger - metabolism | Paromomycin - pharmacology | Thermodynamics | Nucleic Acid Conformation | RNA, Transfer - chemistry | Binding Sites | RNA, Bacterial - metabolism | RNA, Ribosomal, 16S - metabolism | RNA, Transfer, Phe - metabolism | Thermus thermophilus - chemistry | RNA, Transfer - metabolism | Ribosomes - chemistry | Models, Molecular | Anti-Bacterial Agents - metabolism | Peptide Elongation Factor Tu - metabolism | RNA, Transfer, Amino Acid-Specific - chemistry | RNA, Ribosomal, 16S - chemistry | Ribosomes - ultrastructure | Codon - chemistry | Base Pairing | Hydrogen Bonding | RNA, Bacterial - chemistry | RNA, Messenger - chemistry | Anti-Bacterial Agents - pharmacology | Paromomycin - metabolism | Protein research | Usage | Polypeptides | Amino acids | Research | Molecular biology | Statistics | Ribonucleic acid--RNA | Ribonucleic acid | ribosomal subunit 30S | paromomysin | Index Medicus
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6. Full Text Human tRNALys3UUU Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto–Enol Tautomerism
by Vendeix, Franck A.P and Murphy, Frank V and Cantara, William A and Leszczyńska, Grażyna and Gustilo, Estella M and Sproat, Brian and Malkiewicz, Andrzej and Agris, Paul F and Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Journal of Molecular Biology, ISSN 0022-2836, 03/2012, Volume 416, Issue 4, pp. 467 - 485
Human tRNA (htRNA ) decodes the lysine codons AAA and AAG during translation and also plays a crucial role as the primer for HIV-1 (human immunodeficiency... 
wobble decoding | anticodon structure | tRNALys3 | modifications | tRNA
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7. Full Text Favored and less favored codon-anticodon duplexes arising from the GC codon family box encoding for alanine: some computational perspectives
by Devi, Martina and Lyngdoh, R.H. Duncan
Journal of Biomolecular Structure and Dynamics, ISSN 0739-1102, 03/2018, Volume 36, Issue 4, pp. 1029 - 1049
Alanine is encoded by the four codons of the GC box (GCA, GCG, GCU, and GCC). Known alanine anticodons include the UGC, IGC, and VGC triplets (I = inosine;... 
codon-anticodon duplex stability | favored codons | alanine anticodons | Alanine GC codon box | wobble base pair configuration | codon–anticodon duplex stability | STRUCTURAL INSIGHTS | WOBBLE BASE-PAIRS | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | 1ST POSITION | GENETIC-CODE | BIOPHYSICS | MINOR CONSTITUENT | MODIFIED NUCLEOSIDES | MODIFIED URIDINE | TRANSFER-RNA | NUCLEOTIDE-SEQUENCE | Codon - chemistry | Alanine - genetics | Base Pairing | Hydrogen Bonding | Anticodon - genetics | Anticodon - chemistry | Computational Biology | Alanine - chemistry | Codon - genetics | Nucleic Acid Conformation | Index Medicus
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8. Full Text Structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem loops
by Tatsuya Maehigashi and Jack A. Dunkle and Stacey J. Miles and Christine M. Dunham
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 9/2014, Volume 111, Issue 35, pp. 12740 - 12745
Maintenance of the correct reading frame on the ribosome is essential for accurate protein synthesis. Here, we report structures of the 70S ribosome bound to... 
Reading frames | Electronic structure | Messenger RNA | RNA | Ribosomes | Nucleotides | Codons | Electron density | Anticodon | Transfer RNA | Near cognate | Processivity | GLYCINE TRANSFER-RNA | MULTIDISCIPLINARY SCIENCES | READING FRAME MAINTENANCE | ESCHERICHIA-COLI | 30S RIBOSOMAL-SUBUNIT | CODON RECOGNITION | processivity | SACCHAROMYCES-CEREVISIAE | SUPPRESSOR SUFJ | near cognate | MESSENGER-RNA | SALMONELLA-TYPHIMURIUM | EXTENDED ANTICODON | Inverted Repeat Sequences - genetics | Salmonella typhimurium - genetics | Anticodon - genetics | RNA, Messenger - genetics | Anticodon - chemistry | Genes, Suppressor | Ribosomes - chemistry | Crystallography, X-Ray | Frameshifting, Ribosomal - genetics | Thermus thermophilus - genetics | Ribosomes - genetics | Escherichia coli - genetics | RNA, Transfer - genetics | RNA, Messenger - chemistry | Nucleic Acid Conformation | RNA, Transfer - chemistry | RNA sequencing | Physiological aspects | Genetic research | Research | Ribonucleic acid--RNA | Molecular biology | Protein synthesis | Correlation analysis | Index Medicus | Biological Sciences
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9. Full Text Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment
by Jiqiang Ling and Kaitlyn M. Peterson and Ivana Simonović and Chris Cho and Dieter Söll and Miljan Simonović and Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 2/2012, Volume 109, Issue 9, pp. 3281 - 3286
Aminoacyl-tRNA synthetases (aaRSs) ensure faithful translation of mRNA into protein by coupling an amino acid to a set of tRNAs with conserved anticodon... 
Yeasts | Enzymes | Active sites | Crystals | Amino acids | Biochemistry | Codons | Anticodon | Transfer RNA | Crystal structure | Protein synthesis | Anticodon recognition | DOMAIN | PROTEIN | ZINC ION | MULTIDISCIPLINARY SCIENCES | protein synthesis | DUAL-MODE RECOGNITION | QUALITY-CONTROL | IDENTITY | IN-VITRO | MISTRANSLATION | DISCRIMINATION | anticodon recognition | ANTICODON LOOP | Mitochondria - enzymology | Staphylococcus aureus - enzymology | Species Specificity | RNA Editing | Saccharomyces cerevisiae - genetics | Molecular Sequence Data | Substrate Specificity | Crystallography, X-Ray | Threonine-tRNA Ligase - genetics | Leucine | Threonine-tRNA Ligase - chemistry | RNA, Transfer, Amino Acyl - metabolism | Codon - genetics | Protein Structure, Tertiary | Amino Acid Sequence | Catalytic Domain | Escherichia coli - enzymology | Threonine | Anticodon - genetics | Models, Molecular | RNA, Transfer, Amino Acyl - genetics | Saccharomyces cerevisiae Proteins - genetics | Sequence Alignment | Saccharomyces cerevisiae Proteins - metabolism | Aeropyrum - enzymology | Saccharomyces cerevisiae - enzymology | Protein Conformation | Threonine-tRNA Ligase - metabolism | Evolution, Molecular | Saccharomyces cerevisiae Proteins - chemistry | Mitochondria | Yeast fungi | RNA | Physiological aspects | Protein biosynthesis | Genetic aspects | Research | Molecular structure | Binding sites | Anticodons | Aminoacylation | Isoacceptors | Translation | Threonine-tRNA ligase | tRNA | Data processing | Genetic code | Aminoacyl-tRNA ligase | Index Medicus | ESCHERICHIA COLI | TRIPLETS | BASIC BIOLOGICAL SCIENCES | MITOCHONDRIA | SACCHAROMYCES CEREVISIAE | CRYSTAL STRUCTURE | SIMULATION | 60 APPLIED LIFE SCIENCES | CODONS | GENETICS | AMINO ACIDS | ENZYMES | YEASTS | LIGASES | SYNTHESIS | LEUCINE | PROTEINS | THREONINE | Biological Sciences
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10. Full Text ALKBH1 is an RNA dioxygenase responsible for cytoplasmic and mitochondrial tRNA modifications
by Kawarada, Layla and Suzuki, Takeo and Ohira, Takayuki and Hirata, Shoji and Miyauchi, Kenjyo and Suzuki, Tsutomu
Nucleic Acids Research, ISSN 0305-1048, 07/2017, Volume 45, Issue 12, pp. 7401 - 7415
ALKBH1 is a 2-oxoglutarate-and Fe2+-dependent dioxygenase responsible for multiple cellular functions. Here, we show that ALKBH1 is involved in biogenesis of... 
OBESITY-ASSOCIATED FTO | LINKED MENTAL-RETARDATION | MESSENGER-RNA | DNA ALKYLATION DAMAGE | WOBBLE POSITION | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | IDENTIFICATION | SACCHAROMYCES-CEREVISIAE | RECESSIVE INTELLECTUAL DISABILITY | ANTICODON LOOP | AlkB Homolog 1, Histone H2a Dioxygenase - genetics | Anticodon - metabolism | Protein Biosynthesis | Oxidation-Reduction | Humans | Methyltransferases - metabolism | RNA, Transfer, Met - metabolism | Anticodon - chemistry | Methyltransferases - genetics | Oxidative Phosphorylation | Mitochondria - metabolism | Cytidine - analogs & derivatives | Gene Knockout Techniques | Genetic Complementation Test | RNA, Transfer, Met - genetics | AlkB Homolog 1, Histone H2a Dioxygenase - deficiency | Base Sequence | CRISPR-Cas Systems | HEK293 Cells | Cytidine - metabolism | Cytosol - metabolism | Nucleic Acid Conformation | Index Medicus | RNA
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11. Full Text Unusual base pairing during the decoding of a stop codon by the ribosome
by Fernández, Israel S and Ng, Chyan Leong and Kelley, Ann C and Wu, Guowei and Yu, Yi-Tao and Ramakrishnan, V
Nature, ISSN 0028-0836, 2013, Volume 500, Issue 7460, pp. 107 - 110
During normal translation, the binding of a release factor to one of the three stop codons (UGA, UAA or UAG) results in the termination of protein synthesis.... 
REFINEMENT | AMINOACYL-TRANSFER-RNA | MECHANISM | MULTIDISCIPLINARY SCIENCES | TARGETED PSEUDOURIDYLATION | Codon, Terminator - chemistry | Pseudouridine - chemistry | Anticodon - metabolism | Ribosome Subunits, Small, Bacterial - metabolism | Anticodon - genetics | Codon, Terminator - genetics | Anticodon - chemistry | Ribosomes - chemistry | Models, Molecular | Ribosomes - metabolism | Crystallography, X-Ray | Ribosome Subunits, Small, Bacterial - genetics | Codon, Terminator - metabolism | Pseudouridine - metabolism | Pseudouridine - genetics | Base Pairing | Ribosomes - genetics | Base Sequence | RNA, Transfer, Ser - genetics | Protein Conformation | RNA, Transfer, Ser - metabolism | Ribosome Subunits, Small, Bacterial - chemistry | Nucleic Acid Conformation | RNA, Transfer, Ser - chemistry | Purines | Protein biosynthesis | Codon | Properties | Ribosomes | Transfer RNA | Geometry | Mutation | Genes | Deoxyribonucleic acid--DNA | Index Medicus
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12. Full Text MODOMICS: a database of RNA modification pathways. 2017 update
by Boccaletto, Pietro and Machnicka, Magdalena A and Purta, Elzbieta and Piątkowski, Paweł and Bagiński, Błażej and Wirecki, Tomasz K and de Crécy-Lagard, Valérie and Ross, Robert and Limbach, Patrick A and Kotter, Annika and Helm, Mark and Bujnicki, Janusz M
Nucleic Acids Research, ISSN 0305-1048, 01/2018, Volume 46, Issue D1, pp. D303 - D307
Abstract MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides,... 
POSITION | BIOGENESIS | MITOCHONDRIAL | LANDSCAPE | BIOCHEMISTRY & MOLECULAR BIOLOGY | POSTTRANSCRIPTIONAL MODIFICATIONS | GENERATION | ANTICODON | RIBOSOMAL-RNA | IDENTIFICATION | Database Issue
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13. Full Text Eukaryotic Wobble Uridine Modifications Promote a Functionally Redundant Decoding System
by Marcus J. O. Johansson and Anders Esberg and Bo Huang and Glenn R. Björk and Anders S. Byström and Umeå universitet and Teknisk-naturvetenskapliga fakulteten and Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet)
Molecular and Cellular Biology, ISSN 0270-7306, 05/2008, Volume 28, Issue 10, pp. 3301 - 3312
Article Usage Stats Services MCB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley... 
YEAST | POSITION | TRANSFER-RNA GENES | SHUTTLE VECTORS | BIOCHEMISTRY & MOLECULAR BIOLOGY | CODONS IN-VIVO | ESCHERICHIA-COLI | MODIFIED NUCLEOSIDES | SACCHAROMYCES-CEREVISIAE | ELONGATOR COMPLEX | ANTICODON LOOP | CELL BIOLOGY | Transfer RNA Aminoacylation | Protein Biosynthesis | Anticodon - genetics | Saccharomyces cerevisiae - genetics | RNA, Fungal - chemistry | Anticodon - chemistry | Saccharomyces cerevisiae - metabolism | Base Sequence | Plasmids - genetics | RNA, Transfer - genetics | Genes, Fungal | RNA, Fungal - genetics | Codon - genetics | RNA, Transfer - chemistry | Uridine - chemistry | Index Medicus
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14. Full Text Structural insights into translational recoding by frameshift suppressor tRNASufJ
by Fagan, Crystal E and Maehigashi, Tatsuya and Dunkle, Jack A and Miles, Stacey J and Dunham, Christine M and Emory Univ., Atlanta, GA (United States)
RNA, ISSN 1355-8382, 12/2014, Volume 20, Issue 12, pp. 1944 - 1954
The three-nucleotide mRNA reading frame is tightly regulated during translation to ensure accurate protein expression. Translation errors that lead to aberrant... 
Reading frame | X-ray crystal structure | Ribosome | Decoding | MRNA | Anticodon stem-loop | Anticodon - ultrastructure | Anticodon - genetics | Escherichia coli | RNA, Messenger - genetics | Genes, Suppressor | Nucleotides - genetics | Crystallography, X-Ray | RNA, Ribosomal, 16S - ultrastructure | RNA, Transfer - ultrastructure | Nucleotides - chemistry | Thermus thermophilus - genetics | RNA, Ribosomal, 16S - chemistry | Ribosomes - genetics | RNA, Ribosomal, 16S - genetics | RNA, Transfer - genetics | Protein Biosynthesis - genetics | Nucleic Acid Conformation | RNA, Transfer - chemistry | Index Medicus | reading frame | anticodon stem–loop | BASIC BIOLOGICAL SCIENCES | ribosome | mRNA | 60 APPLIED LIFE SCIENCES | decoding
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15. Full Text A DNA segment encoding the anticodon stem/loop of tRNA determines the specific recombination of integrative-conjugative elements in Acidithiobacillus species
by Castillo, Andrés and Tello, Mario and Ringwald, Kenneth and Acuña, Lillian G and Quatrini, Raquel and Orellana, Omar
RNA Biology, ISSN 1547-6286, 05/2018, Volume 15, Issue 4-5, pp. 492 - 499
Horizontal gene transfer is crucial for the adaptation of microorganisms to environmental cues. The acidophilic, bioleaching bacterium Acidithiobacillus... 
integration site | prokaryotes | transfer RNA | TRNA | specificity | ICEs | integrase | Anticodon stem/loop | acidophilic bacteria | ACTIVE-SITE | BIOCHEMISTRY & MOLECULAR BIOLOGY | Anticodon stem | EXCISION PROTEINS | MOBILE GENETIC ELEMENTS | LAMBDA-INTEGRASE | PREDICTION | SITE-SPECIFIC RECOMBINATION | EVOLUTION | FERROOXIDANS | CTNDOT | WEB | loop | Attachment Sites, Microbiological | Anticodon - metabolism | Mutagenesis, Site-Directed | DNA, Bacterial - metabolism | Chromosomes, Bacterial - chemistry | Anticodon - chemistry | Synteny | Acidithiobacillus - metabolism | Chromosome Mapping | Gene Transfer, Horizontal | RNA, Transfer, Ala - genetics | RNA, Transfer, Ala - metabolism | DNA Transposable Elements | Chromosomes, Bacterial - metabolism | DNA, Bacterial - genetics | Escherichia coli - genetics | Recombination, Genetic | Base Sequence | Acidithiobacillus - genetics | Escherichia coli - metabolism | Integrases - metabolism | DNA Damage | Nucleic Acid Conformation | Integrases - genetics | Index Medicus
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