Published in Methods Enzymol on July 17, 2015
Detecting RNA modifications in the epitranscriptome: predict and validate. Nat Rev Genet (2017) 0.80
Mass spectrometry of modified RNAs: recent developments. Analyst (2015) 0.79
tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence. Nat Commun (2016) 0.78
Going global: the new era of mapping modifications in RNA. Wiley Interdiscip Rev RNA (2016) 0.76
Small RNA Modifications: Integral to Function and Disease. Trends Mol Med (2016) 0.75
Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions. Biomolecules (2017) 0.75
Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc Natl Acad Sci U S A (1972) 83.88
A procedure for the isolation of mammalian messenger ribonucleic acid. Biochemistry (1972) 14.47
The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol (2006) 13.13
On the lability of poly(A) sequences during extraction of messenger RNA from polyribosomes. Biochim Biophys Acta (1972) 6.05
The RNA Modification Database: 1999 update. Nucleic Acids Res (1999) 4.97
MODOMICS: a database of RNA modification pathways--2013 update. Nucleic Acids Res (2012) 4.43
tRNA's wobble decoding of the genome: 40 years of modification. J Mol Biol (2006) 4.06
Improvement of reading frame maintenance is a common function for several tRNA modifications. EMBO J (2001) 3.80
The RNA Modification Database, RNAMDB: 2011 update. Nucleic Acids Res (2010) 3.42
The role of modifications in codon discrimination by tRNA(Lys)UUU. Nat Struct Mol Biol (2004) 3.08
Metabolomic database annotations via query of elemental compositions: mass accuracy is insufficient even at less than 1 ppm. BMC Bioinformatics (2006) 3.02
Preparation and enzymatic hydrolysis of DNA and RNA for mass spectrometry. Methods Enzymol (1990) 3.02
Trm9-catalyzed tRNA modifications link translation to the DNA damage response. Mol Cell (2007) 2.94
Decoding the genome: a modified view. Nucleic Acids Res (2004) 2.90
Mouse Piwi-interacting RNAs are 2'-O-methylated at their 3' termini. Nat Struct Mol Biol (2007) 2.89
MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Res (2008) 2.84
Quantitative enzymatic hydrolysis of tRNAs: reversed-phase high-performance liquid chromatography of tRNA nucleosides. J Chromatogr (1982) 2.78
A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. PLoS Genet (2010) 2.73
The 3' termini of mouse Piwi-interacting RNAs are 2'-O-methylated. Nat Struct Mol Biol (2007) 2.71
Analysis of RNA hydrolyzates by liquid chromatography-mass spectrometry. Methods Enzymol (1990) 2.56
Hydrophilic-interaction chromatography for the separation of peptides, nucleic acids and other polar compounds. J Chromatogr (1990) 2.49
Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature (2014) 2.49
Stabilization of RNA stacking by pseudouridine. Nucleic Acids Res (1995) 2.46
Grand challenge commentary: RNA epigenetics? Nat Chem Biol (2010) 2.33
Complete analysis of tRNA-modified nucleosides by high-performance liquid chromatography: the 29 modified nucleosides of Salmonella typhimurium and Escherichia coli tRNA. Anal Biochem (1983) 2.29
Accurate translation of the genetic code depends on tRNA modified nucleosides. J Biol Chem (2002) 2.25
Ribonucleoside analysis by reversed-phase high-performance liquid chromatography. J Chromatogr (1989) 2.16
Streptavidin aptamers: affinity tags for the study of RNAs and ribonucleoproteins. RNA (2001) 2.11
tRNA stabilization by modified nucleotides. Biochemistry (2010) 2.10
Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications. EMBO Rep (2008) 1.98
Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins. Nat Commun (2012) 1.93
Analysis of the methylation sites in yeast ribosomal RNA. Eur J Biochem (1973) 1.82
The modification of the wobble base of tRNAGlu modulates the translation rate of glutamic acid codons in vivo. J Mol Biol (1998) 1.77
Translational misreading: a tRNA modification counteracts a +2 ribosomal frameshift. Genes Dev (2001) 1.76
Transfer RNA modification: influence on translational frameshifting and metabolism. FEBS Lett (1999) 1.73
Discovery and biological characterization of geranylated RNA in bacteria. Nat Chem Biol (2012) 1.70
Mass spectrometric identification and characterization of RNA-modifying enzymes. Methods Enzymol (2007) 1.58
Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine. Proc Natl Acad Sci U S A (2010) 1.57
A general method for rapid and nondenaturing purification of RNAs. RNA (2004) 1.57
Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells. Mol Cell (2012) 1.56
Histidylation by yeast HisRS of tRNA or tRNA-like structure relies on residues -1 and 73 but is dependent on the RNA context. Nucleic Acids Res (1994) 1.44
Detection of enzymatic activity of transfer RNA modification enzymes using radiolabeled tRNA substrates. Methods Enzymol (2007) 1.44
Conformational flexibility in RNA: the role of dihydrouridine. Nucleic Acids Res (1996) 1.41
A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification. Nat Chem Biol (2012) 1.37
A single methyl group prevents the mischarging of a tRNA. Nat Struct Biol (1994) 1.37
A truncated aminoacyl-tRNA synthetase modifies RNA. Proc Natl Acad Sci U S A (2004) 1.32
Identity elements of Saccharomyces cerevisiae tRNA(His). Nucleic Acids Res (1995) 1.30
Wobble position modified nucleosides evolved to select transfer RNA codon recognition: a modified-wobble hypothesis. Biochimie (1991) 1.30
Improved native affinity purification of RNA. RNA (2007) 1.29
LC/MS analysis of cellular RNA reveals NAD-linked RNA. Nat Chem Biol (2009) 1.29
Rapid purification of RNAs using fast performance liquid chromatography (FPLC). RNA (2006) 1.25
Choosing the best pulse sequences, acquisition parameters, postacquisition processing strategies, and probes for natural product structure elucidation by NMR spectroscopy. J Nat Prod (2002) 1.23
tRNA tKUUU, tQUUG, and tEUUC wobble position modifications fine-tune protein translation by promoting ribosome A-site binding. Proc Natl Acad Sci U S A (2013) 1.23
Detection of RNA modifications. RNA Biol (2010) 1.16
The many applications of acid urea polyacrylamide gel electrophoresis to studies of tRNAs and aminoacyl-tRNA synthetases. Methods (2008) 1.15
Chaplet column chromatography: isolation of a large set of individual RNAs in a single step. Methods Enzymol (2007) 1.15
Non-coding RNA and its potential role in Mycobacterium tuberculosis pathogenesis. RNA Biol (2012) 1.15
Identification of "known unknowns" utilizing accurate mass data and ChemSpider. J Am Soc Mass Spectrom (2011) 1.14
Chromatography of nucleosides. J Chromatogr (1980) 1.13
Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications. RNA Biol (2012) 1.13
Sephadex-binding RNA ligands: rapid affinity purification of RNA from complex RNA mixtures. Nucleic Acids Res (2001) 1.12
A chemical screen for biological small molecule-RNA conjugates reveals CoA-linked RNA. Proc Natl Acad Sci U S A (2009) 1.12
FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA. Nat Commun (2013) 1.10
Mass spectrometry-based detection of transfer RNAs by their signature endonuclease digestion products. RNA (2006) 1.10
Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry. Nat Protoc (2014) 1.09
Rapid, nondenaturing RNA purification using weak anion-exchange fast performance liquid chromatography. RNA (2010) 1.06
Absence of 2'-deoxyoxanosine and presence of abasic sites in DNA exposed to nitric oxide at controlled physiological concentrations. Chem Res Toxicol (2003) 1.06
Profiling of ribose methylations in RNA by high-throughput sequencing. Angew Chem Int Ed Engl (2014) 1.04
Precision of RNA separation by polyacrylamide gel electrophoresis. Anal Biochem (1970) 1.03
Identification of 5-hydroxycytidine at position 2501 concludes characterization of modified nucleotides in E. coli 23S rRNA. J Mol Biol (2011) 1.01
Thiolation of transfer RNA in Escherichia coli varies with growth rate. Nucleic Acids Res (1992) 1.00
tRNA modifications regulate translation during cellular stress. FEBS Lett (2014) 0.98
A system of RNA modifications and biased codon use controls cellular stress response at the level of translation. Chem Res Toxicol (2014) 0.98
Absolute and relative quantification of RNA modifications via biosynthetic isotopomers. Nucleic Acids Res (2014) 0.97
Study of the mass spectrometric fragmentation of pseudouridine: comparison of fragmentation data obtained by matrix-assisted laser desorption/ionisation post-source decay, electrospray ion trap multistage mass spectrometry, and by a method utilising electrospray quadrupole time-of-flight tandem mass spectrometry and in-source fragmentation. Rapid Commun Mass Spectrom (2005) 0.96
Partial methylation at Am100 in 18S rRNA of baker's yeast reveals ribosome heterogeneity on the level of eukaryotic rRNA modification. PLoS One (2014) 0.96
RNA affinity tags for the rapid purification and investigation of RNAs and RNA-protein complexes. Methods Mol Biol (2008) 0.96
Dynamic RNA modifications in posttranscriptional regulation. Mol Cell (2014) 0.95
Decoding system for the AUA codon by tRNAIle with the UAU anticodon in Mycoplasma mobile. Nucleic Acids Res (2013) 0.95
Retention behavior of small polar compounds on polar stationary phases in hydrophilic interaction chromatography. J Chromatogr A (2005) 0.93
A coordinated codon-dependent regulation of translation by Elongator. Cell Cycle (2012) 0.92
Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes. Chem Res Toxicol (2015) 0.92
Profiling of RNA modifications by multiplexed stable isotope labelling. Chem Commun (Camb) (2014) 0.91
Non-coding RNAs in hepatitis B or C-associated hepatocellular carcinoma: potential diagnostic and prognostic markers and therapeutic targets. Cancer Lett (2012) 0.91
RNA analysis by ion-pair reversed-phase high performance liquid chromatography. Nucleic Acids Res (2001) 0.91
Reversed-phase ion-pair liquid chromatography analysis and purification of small interfering RNA. Anal Biochem (2009) 0.90
Sprouts of RNA epigenetics: the discovery of mammalian RNA demethylases. RNA Biol (2013) 0.90
Purification of a synthetic oligonucleotide by anion exchange chromatography: method optimisation and scale-up. J Biochem Biophys Methods (2005) 0.89
Identity elements of tRNA(Thr) towards Saccharomyces cerevisiae threonyl-tRNA synthetase. Nucleic Acids Res (1995) 0.89
Evaluating the reproducibility of quantifying modified nucleosides from ribonucleic acids by LC-UV-MS. J Chromatogr B Analyt Technol Biomed Life Sci (2013) 0.88
The gene-specific codon counting database: a genome-based catalog of one-, two-, three-, four- and five-codon combinations present in Saccharomyces cerevisiae genes. Database (Oxford) (2012) 0.88
A multidimensional platform for the purification of non-coding RNA species. Nucleic Acids Res (2013) 0.88
Studying the mechanism of RNA separations using RNA chromatography and its application in the analysis of ribosomal RNA and RNA:RNA interactions. J Chromatogr A (2008) 0.87
Accurate mass measurement for the determination of elemental formula--a tutorial. Mass Spectrom Rev (2005) 0.86
Isotope-based analysis of modified tRNA nucleosides correlates modification density with translational efficiency. Angew Chem Int Ed Engl (2012) 0.86
Identification of N6,N6-dimethyladenosine in transfer RNA from Mycobacterium bovis Bacille Calmette-Guérin. Molecules (2011) 0.86
Separation of transfer RNA and 5S ribosomal RNA using capillary electrophoresis. J Chromatogr A (1995) 0.86
Metabolite identification by data-dependent accurate mass spectrometric analysis at resolving power of 60,000 in external calibration mode using an LTQ/Orbitrap. Rapid Commun Mass Spectrom (2007) 0.85
m(6)A-LAIC-seq reveals the census and complexity of the m(6)A epitranscriptome. Nat Methods (2016) 0.84
Oxidation of phosphorothioate DNA modifications leads to lethal genomic instability. Nat Chem Biol (2017) 0.75