An integrated, structure- and energy-based view of the genetic code

Post-transcriptional Modifications Modulate rRNA Structure and Ligand Interactions

(2016) Jun Jiang et al.   ACCOUNTS OF CHEMICAL RESEARCH

Facile Recoding of Selenocysteine in Nature

(2016) Takahito Mukai et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Structural Basis for Translation Termination on a Pseudouridylated Stop Codon

(2016) Egor Svidritskiy et al.   JOURNAL OF MOLECULAR BIOLOGY

Expanding the amino acid repertoire of ribosomal polypeptide synthesis via the artificial division of codon boxes

(2016) Yoshihiko Iwane et al.   Nature Chemistry

The evolution of Class II Aminoacyl-tRNA synthetases and the first code

(2015) Temple F. Smith et al.   FEBS LETTERS

Codon Bias as a Means to Fine-Tune Gene Expression

(2015) Tessa E.F. Quax et al.   MOLECULAR CELL

Essentiality of threonylcarbamoyladenosine (t6A), a universal tRNA modification, in bacteria

(2015) Patrick C. Thiaville et al.   MOLECULAR MICROBIOLOGY

Genetic code flexibility in microorganisms: novel mechanisms and impact on physiology

(2015) Jiqiang Ling et al.   NATURE REVIEWS MICROBIOLOGY

Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly

(2015) Yury S Polikanov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A common tRNA modification at an unusual location: the discovery of wyosine biosynthesis in mitochondria

(2015) Paul J. Sample et al.   NUCLEIC ACIDS RESEARCH

Effects of tRNA modification on translational accuracy depend on intrinsic codon–anticodon strength

(2015) Nandini Manickam et al.   NUCLEIC ACIDS RESEARCH

Nucleotide modifications within bacterial messenger RNAs regulate their translation and are able to rewire the genetic code

(2015) Thomas Philipp Hoernes et al.   NUCLEIC ACIDS RESEARCH

Accuracy of initial codon selection by aminoacyl-tRNAs on the mRNA-programmed bacterial ribosome

(2015) Jingji Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

O6-Methylguanosine leads to position-dependent effects on ribosome speed and fidelity

(2015) Benjamin H. Hudson et al.   RNA

‘View From A Bridge’: A New Perspective on Eukaryotic rRNA Base Modification

(2015) Sunny Sharma et al.   TRENDS IN BIOCHEMICAL SCIENCES

Structural insights into the translational infidelity mechanism

(2015) Alexey Rozov et al.   Nature Communications

Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly

(2015) Yury S Polikanov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Distribution and frequencies of post-transcriptional modifications in tRNAs

(2015) Magdalena A Machnicka et al.   RNA Biology

Expanding and Reprogramming the Genetic Code of Cells and Animals

(2014) Jason W. Chin   Annual Review of Biochemistry

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA

(2014) Schraga Schwartz et al.   CELL

A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs

(2014) T. Suzuki et al.   NUCLEIC ACIDS RESEARCH

Predicting the Minimal Translation Apparatus: Lessons from the Reductive Evolution of Mollicutes

(2014) Henri Grosjean et al.   PLoS Genetics

Recoding the Genetic Code with Selenocysteine

(2013) Markus J. Bröcker et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Decoding Mechanism of Non-universal Genetic Codes inLoligo bleekeriMitochondria

(2013) Takayuki Ohira et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Steric Complementarity in the Decoding Center Is Important for tRNA Selection by the Ribosome

(2013) Prashant K. Khade et al.   JOURNAL OF MOLECULAR BIOLOGY

A Realistic Model Under Which the Genetic Code is Optimal

(2013) Harry Buhrman et al.   JOURNAL OF MOLECULAR EVOLUTION

Unusual base pairing during the decoding of a stop codon by the ribosome

(2013) Israel S. Fernández et al.   NATURE

Expanded use of sense codons is regulated by modified cytidines in tRNA

(2013) W. A. Cantara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

tRNA residues evolved to promote translational accuracy

(2013) I. Shepotinovskaya et al.   RNA

Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides

(2013) G. A. Hudson et al.   RNA

The central role of protein S12 in organizing the structure of the decoding site of the ribosome

(2013) H. Demirci et al.   RNA

Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters

(2012) Jonathan L. Chen et al.   BIOCHEMISTRY

A Role for tRNA Modifications in Genome Structure and Codon Usage

(2012) Eva Maria Novoa et al.   CELL

A new understanding of the decoding principle on the ribosome

(2012) Natalia Demeshkina et al.   NATURE

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids

(2012) Naama Wald et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways—2013 update

(2012) Magdalena A. Machnicka et al.   NUCLEIC ACIDS RESEARCH

Taurine-containing Uridine Modifications in tRNA Anticodons Are Required to Decipher Non-universal Genetic Codes in Ascidian Mitochondria

(2011) Takeo Suzuki et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Error-Prone and Error-Restrictive Mutations Affecting Ribosomal Protein S12

(2011) Deepali Agarwal et al.   JOURNAL OF MOLECULAR BIOLOGY

Human tRNALys3UUU Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto–Enol Tautomerism

(2011) Franck A.P. Vendeix et al.   JOURNAL OF MOLECULAR BIOLOGY

Unassigned Codons, Nonsense Suppression, and Anticodon Modifications in the Evolution of the Genetic Code

(2011) Peter T. S. van der Gulik et al.   JOURNAL OF MOLECULAR EVOLUTION

Converting nonsense codons into sense codons by targeted pseudouridylation

(2011) John Karijolich et al.   NATURE

How mutations in tRNA distant from the anticodon affect the fidelity of decoding

(2011) T Martin Schmeing et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Evolutionary optimization of speed and accuracy of decoding on the ribosome

(2011) I. Wohlgemuth et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Adding New Chemistries to the Genetic Code

(2010) Chang C. Liu et al.   Annual Review of Biochemistry

tRNA Stabilization by Modified Nucleotides

(2010) Yuri Motorin et al.   BIOCHEMISTRY

Optimization of speed and accuracy of decoding in translation

(2010) Ingo Wohlgemuth et al.   EMBO JOURNAL

The Distinction Between Recoding and Codon Reassignment

(2010) J. F. Atkins et al.   GENETICS

The Influence of Anticodon-Codon Interactions and Modified Bases on Codon Usage Bias in Bacteria

(2010) W. Ran et al.   MOLECULAR BIOLOGY AND EVOLUTION

Hyperaccurate and Error-Prone Ribosomes Exploit Distinct Mechanisms during tRNA Selection

(2010) Hani S. Zaher et al.   MOLECULAR CELL

Structural aspects of messenger RNA reading frame maintenance by the ribosome

(2010) Lasse B Jenner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural rearrangements of the ribosome at the tRNA proofreading step

(2010) Lasse Jenner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The RNA modification database, RNAMDB: 2011 update

(2010) W. A. Cantara et al.   NUCLEIC ACIDS RESEARCH

The fourfold way of the genetic code

(2009) Miguel Angel Jiménez-Montaño   BIOSYSTEMS

Deciphering synonymous codons in the three domains of life: Co-evolution with specific tRNA modification enzymes

(2009) Henri Grosjean et al.   FEBS LETTERS

RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code

(2009) Michael Yarus et al.   JOURNAL OF MOLECULAR EVOLUTION

Bases in the anticodon loop of tRNAAlaGGC prevent misreading

(2009) Hiroshi Murakami et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A sequence element that tunes Escherichia coli tRNAAlaGGC to ensure accurate decoding

(2009) Sarah Ledoux et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Unconventional decoding of the AUA codon as methionine by mitochondrial tRNA Met with the anticodon f 5 CAU as revealed with a mitochondrial in vitro translation system

(2009) Chie Takemoto et al.   NUCLEIC ACIDS RESEARCH

An extension of the coevolution theory of the origin of the genetic code

(2008) Massimo Di Giulio   Biology Direct

Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications

(2008) Paul F Agris   EMBO REPORTS

Modified Uridines with C5-methylene Substituents at the First Position of the tRNA Anticodon Stabilize U·G Wobble Pairing during Decoding

(2008) Shinya Kurata et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The role of alternative genetic codes in viral evolution and emergence

(2008) Laura A. Shackelton et al.   JOURNAL OF THEORETICAL BIOLOGY

A unique conformation of the anticodon stem-loop is associated with the capacity of tRNAfMet to initiate protein synthesis

(2008) Pierre Barraud et al.   NUCLEIC ACIDS RESEARCH

tRNAdb 2009: compilation of tRNA sequences and tRNA genes

(2008) F. Juhling et al.   NUCLEIC ACIDS RESEARCH

Degeneracy of the genetic code and stability of the base pair at the second position of the anticodon

(2008) J. Lehmann et al.   RNA