4.8 Article

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

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

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

Nandini Manickam et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

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

Thomas Philipp Hoernes et al.

NUCLEIC ACIDS RESEARCH (2016)

Review Chemistry, Multidisciplinary

Post-transcriptional Modifications Modulate rRNA Structure and Ligand Interactions

Jun Jiang et al.

ACCOUNTS OF CHEMICAL RESEARCH (2016)

Article Chemistry, Multidisciplinary

Facile Recoding of Selenocysteine in Nature

Takahito Mukai et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2016)

Article Biochemistry & Molecular Biology

Structural Basis for Translation Termination on a Pseudouridylated Stop Codon

Egor Svidritskiy et al.

JOURNAL OF MOLECULAR BIOLOGY (2016)

Article Biochemistry & Molecular Biology

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

Temple F. Smith et al.

FEBS LETTERS (2015)

Review Biochemistry & Molecular Biology

Codon Bias as a Means to Fine-Tune Gene Expression

Tessa E. F. Quax et al.

MOLECULAR CELL (2015)

Article Biochemistry & Molecular Biology

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

Patrick C. Thiaville et al.

MOLECULAR MICROBIOLOGY (2015)

Review Microbiology

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

Jiqiang Ling et al.

NATURE REVIEWS MICROBIOLOGY (2015)

Article Biochemistry & Molecular Biology

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

Yury S. Polikanov et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2015)

Article Biochemistry & Molecular Biology

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

Paul J. Sample et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Multidisciplinary Sciences

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

Jingji Zhang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Biochemistry & Molecular Biology

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

Benjamin H. Hudson et al.

Review Biochemistry & Molecular Biology

'View From A Bricge': A New Perspective on Eukaryotic rRNA Base Modification

Sunny Sharma et al.

TRENDS IN BIOCHEMICAL SCIENCES (2015)

Article Multidisciplinary Sciences

Structural insights into the translational infidelity mechanism

Alexey Rozov et al.

NATURE COMMUNICATIONS (2015)

Article Biochemistry & Molecular Biology

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

Yury S. Polikanov et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2015)

Article Chemistry, Multidisciplinary

Recoding the Genetic Code with Selenocysteine

Markus J. Broecker et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2014)

Review Biochemistry & Molecular Biology

Expanding and Reprogramming the Genetic Code of Cells and Animals

Jason W. Chin

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 83 (2014)

Article Biochemistry & Molecular Biology

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

Takeo Suzuki et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

Distribution and frequencies of post-transcriptional modifications in tRNAs

Magdalena A. Machnicka et al.

RNA BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Decoding Mechanism of Non-universal Genetic Codes in Loligo bleekeri Mitochondria

Takayuki Ohira et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2013)

Article Biochemistry & Molecular Biology

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

Prashant K. Khade et al.

JOURNAL OF MOLECULAR BIOLOGY (2013)

Article Biochemistry & Molecular Biology

A Realistic Model Under Which the Genetic Code is Optimal

Harry Buhrman et al.

JOURNAL OF MOLECULAR EVOLUTION (2013)

Article Multidisciplinary Sciences

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

Israel S. Fernandez et al.

NATURE (2013)

Article Biochemistry & Molecular Biology

MODOMICS: a database of RNA modification pathways-2013 update

Magdalena A. Machnicka et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

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

William A. Cantara et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemistry & Molecular Biology

tRNA residues evolved to promote translational accuracy

Irina Shepotinovskaya et al.

Article Biochemistry & Molecular Biology

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

Jonathan L. Chen et al.

BIOCHEMISTRY (2012)

Article Biochemistry & Molecular Biology

A Role for tRNA Modifications in Genome Structure and Codon Usage

Eva Maria Novoa et al.

Article Biochemistry & Molecular Biology

Human tRNALYs3UUU Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto-Enol Tautomerism

Franck A. P. Vendeix et al.

JOURNAL OF MOLECULAR BIOLOGY (2012)

Article Multidisciplinary Sciences

A new understanding of the decoding principle on the ribosome

Natalia Demeshkina et al.

NATURE (2012)

Article Multidisciplinary Sciences

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

Dan Dominissini et al.

NATURE (2012)

Article Biochemistry & Molecular Biology

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

Deepali Agarwal et al.

JOURNAL OF MOLECULAR BIOLOGY (2011)

Article Biochemistry & Molecular Biology

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

Peter T. S. van der Gulik et al.

JOURNAL OF MOLECULAR EVOLUTION (2011)

Article Multidisciplinary Sciences

Converting nonsense codons into sense codons by targeted pseudouridylation

John Karijolich et al.

NATURE (2011)

Article Biochemistry & Molecular Biology

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

T. Martin Schmeing et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2011)

Article Biochemistry & Molecular Biology

The RNA modification database, RNAMDB: 2011 update

William A. Cantara et al.

NUCLEIC ACIDS RESEARCH (2011)

Review Biology

Evolutionary optimization of speed and accuracy of decoding on the ribosome

Ingo Wohlgemuth et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2011)

Review Biochemistry & Molecular Biology

tRNA Modification and Genetic Code Variations in Animal Mitochondria

Kimitsuna Watanabe et al.

JOURNAL OF NUCLEIC ACIDS (2011)

Review Biochemistry & Molecular Biology

Adding New Chemistries to the Genetic Code

Chang C. Liu et al.

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 79 (2010)

Article Biochemistry & Molecular Biology

tRNA Stabilization by Modified Nucleotides

Yuri Motorin et al.

BIOCHEMISTRY (2010)

Article Biochemistry & Molecular Biology

Optimization of speed and accuracy of decoding in translation

Ingo Wohlgemuth et al.

EMBO JOURNAL (2010)

Letter Genetics & Heredity

The Distinction Between Recoding and Codon Reassignment

John F. Atkins et al.

GENETICS (2010)

Article Biochemistry & Molecular Biology

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

Wenqi Ran et al.

MOLECULAR BIOLOGY AND EVOLUTION (2010)

Article Biochemistry & Molecular Biology

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

Hani S. Zaher et al.

MOLECULAR CELL (2010)

Article Biochemistry & Molecular Biology

Structural aspects of messenger RNA reading frame maintenance by the ribosome

Lasse B. Jenner et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2010)

Article Biochemistry & Molecular Biology

Structural rearrangements of the ribosome at the tRNA proofreading step

Lasse Jenner et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2010)

Article Biology

The fourfold way of the genetic code

Miguel Angel Jimenez-Montano

BIOSYSTEMS (2009)

Article Biochemistry & Molecular Biology

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

Michael Yarus et al.

JOURNAL OF MOLECULAR EVOLUTION (2009)

Article Biochemistry & Molecular Biology

Bases in the anticodon loop of tRNAGGCAla prevent misreading

Hiroshi Murakami et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)

Article Biochemistry & Molecular Biology

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

Sarah Ledoux et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)

Article Biochemistry & Molecular Biology

tRNAdb 2009: compilation of tRNA sequences and tRNA genes

Frank Juehling et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

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

Paul F. Agris

EMBO REPORTS (2008)

Article Biology

The role of alternative genetic codes in viral evolution and emergence

Laura A. Shackelton et al.

JOURNAL OF THEORETICAL BIOLOGY (2008)

Article Biochemistry & Molecular Biology

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

Pierre Barraud et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Biochemistry & Molecular Biology

Role of a tRNA base modification and its precursors in frameshifting in eukaryotes

William F. Waas et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2007)

Review Biochemistry & Molecular Biology

tRNA's wobble decoding of the genome: 40 years of modification

Paul F. Agris et al.

JOURNAL OF MOLECULAR BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Natural expansion of the genetic code

Alexandre Ambrogelly et al.

NATURE CHEMICAL BIOLOGY (2007)

Review Biochemistry & Molecular Biology

Comparative RNomics and modomics in mollicutes: Prediction of gene function and evolutionary implications

Valerie de Crecy-Lagard et al.

IUBMB LIFE (2007)

Article Biochemistry & Molecular Biology

Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines

Albert Weixlbaumer et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Diversity of tRNA genes in eukaryotes

Jeffrey M. Goodenbour et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Multidisciplinary Sciences

Structure of the 70S ribosome complexed with mRNA and tRNA

Maria Selmer et al.

SCIENCE (2006)

Article Biochemistry & Molecular Biology

tRNA residues that have coevolved with their anticodon to ensure uniform and accurate codon recognition

Mikolaj Olejniczak et al.

BIOCHIMIE (2006)

Article Multidisciplinary Sciences

Collective evolution and the genetic code

Kalin Vetsigian et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biochemistry & Molecular Biology

Quantitative analysis of deoxynucleotide substitutions in the codon-anticodon helix

RP Fahlman et al.

JOURNAL OF MOLECULAR BIOLOGY (2006)

Review Biochemistry & Molecular Biology

Evolution of the genetic code in yeasts

I Miranda et al.

YEAST (2006)

Article Multidisciplinary Sciences

An active role for tRNA in decoding beyond codon:anticodon pairing

L Cochella et al.

SCIENCE (2005)

Review Microbiology

Horizontal gene transfer: Perspectives at a crossroads of scientific disciplines

BF Smets et al.

NATURE REVIEWS MICROBIOLOGY (2005)

Review Biochemistry & Molecular Biology

Reprogrammed genetic decoding in cellular gene expression

O Namy et al.

MOLECULAR CELL (2004)

Article Biochemistry & Molecular Biology

Aminoacylation of the anticodon stem by a tRNA-synthetase paralog:: relic of an ancient code?

H Grosjean et al.

TRENDS IN BIOCHEMICAL SCIENCES (2004)

Article Biochemistry & Molecular Biology

Uniform binding of aminoacylated transfer RNAs to the ribosomal A and P sites

RP Fahlman et al.

MOLECULAR CELL (2004)

Article Biochemistry & Molecular Biology

The role of modifications in codon discrimination by tRNALys UUU

FV Murphy et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2004)

Article Biochemistry & Molecular Biology

Structure of a purine-purine wobble base pair in the decoding center of the ribosome

FV Murphy et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2004)

Article Biology

Amino acid biogenesis, evolution of the genetic code and aminoacyl-tRNA synthetases

L Klipcan et al.

JOURNAL OF THEORETICAL BIOLOGY (2004)

Article Biochemistry & Molecular Biology

A new classification scheme of the genetic code

T Wilhelm et al.

JOURNAL OF MOLECULAR EVOLUTION (2004)

Review Biology

The case for an error minimizing standard genetic code

SJ Freeland et al.

ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES (2003)

Article Biochemistry & Molecular Biology

tRNAT1Ser(G34)with the anticodon GGA can recognize not only UCC and UCU codons but also UCA and UCG codons

Y Yamada et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION (2003)

Review Biochemistry & Molecular Biology

Molecular evolution from abiotic scratch

EN Trifonov et al.

FEBS LETTERS (2002)

Review Biochemistry & Molecular Biology

Misreading of termination codons in eukaryotes by natural nonsense suppressor tRNAs

H Beier et al.

NUCLEIC ACIDS RESEARCH (2001)

Article Biochemistry & Molecular Biology

The path of messenger RNA through the ribosome

GZ Yusupova et al.

Article Multidisciplinary Sciences

Recognition of cognate transfer RNA by the 30S ribosomal subunit

JM Ogle et al.

SCIENCE (2001)

Article Biochemistry & Molecular Biology

A universal mode of helix packing in RNA

EA Doherty et al.

NATURE STRUCTURAL BIOLOGY (2001)

Letter Biochemistry & Molecular Biology

An extended structural signature for the tRNA anticodon loop

P Auffinger et al.

Article Biochemistry & Molecular Biology

Molecular evolution: Please release me, genetic code

N Lehman

CURRENT BIOLOGY (2001)

Article Biochemistry & Molecular Biology

A primordial tRNA modification required for the evolution of life?

GR Björk et al.

EMBO JOURNAL (2001)

Review Genetics & Heredity

Rewiring the keyboard evolvability of the genetic code

RD Knight et al.

NATURE REVIEWS GENETICS (2001)

Article Multidisciplinary Sciences

Testing a biosynthetic theory of the genetic code: Fact or artifact?

TA Ronneberg et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)

Article Biochemistry & Molecular Biology

Codon usage tabulated from international DNA sequence databases: status for the year 2000

Y Nakamura et al.

NUCLEIC ACIDS RESEARCH (2000)