Recent Developments in Mass Spectrometry for the Characterization of Nucleosides, Nucleotides, Oligonucleotides, and Nucleic Acids

Banoub, Joseph; Newton, Russell P.; Esmans, Eddy L.; Ewing, David F.; Mackenzie, Grahame

doi:10.1021/cr030040w

Cited by 124 publications

(97 citation statements)

References 356 publications

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“…However in recent times, with the development of LC coupled to MS and on-going technological advances in ionization methods, in particular ESI as well as ion transmission and detection, MS has become a viable method for the quantitation of DNA adducts levels in animal and human samples obtained after exposure to exogenous and endogenous genotoxic compounds. Comprehensive reviews describing the application of LC coupled to MS for the study of DNA adducts have been published by Esmans et al (41)(42)(43)(44)(45). Figure 2 highlights the guanine and phosphate backbone adducts formed in DNA following exposure to various genotoxic chemicals that have been studied using LC-ESI-MS.…”

Section: Mass Spectrometry In the Analysis Of Dna Adductsmentioning

confidence: 99%

Liquid chromatography-electrospray ionization-mass spectrometry: the future of DNA adduct detection

2005

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Section: Mass Spectrometry In the Analysis Of Dna Adductsmentioning

confidence: 99%

Liquid chromatography-electrospray ionization-mass spectrometry: the future of DNA adduct detection

2005

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“…To properly characterize the products of Cfr modification, we developed an online nanoliquid chromatography electrospray ionization tandem mass spectrometry (nano-LC-ESI-MS n ) approach on an Agilent 6340 ion trap mass spectrometer. Mass spectrometry has successfully been employed in the structural characterization of nucleobases and nucleosides (for reviews, see Crain 1990a;Banoub et al 2005). Mass spectrometric studies of RNA nucleosides involve collisioninduced dissociation (CID) in multiple tandem MS steps (MS n ), which typically commences with neutral loss of ribose followed by a concerted ring opening and elimination of ammonia from the protonated nucleobase.…”

Section: Introductionmentioning

confidence: 99%

Identification of 8-methyladenosine as the modification catalyzed by the radical SAM methyltransferase Cfr that confers antibiotic resistance in bacteria

Giessing¹,

Jensen²,

Rasmussen³

et al. 2009

RNA

129

142

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The Cfr methyltransferase confers combined resistance to five different classes of antibiotics that bind to the peptidyl transferase center of bacterial ribosomes. The Cfr-mediated modification has previously been shown to occur on nucleotide A2503 of 23S rRNA and has a mass corresponding to an additional methyl group, but its specific identity and position remained to be elucidated. A novel tandem mass spectrometry approach has been developed to further characterize the Cfr-catalyzed modification. Comparison of nucleoside fragmentation patterns of A2503 from Escherichia coli cfr+ and cfrÀ strains with those of a chemically synthesized nucleoside standard shows that Cfr catalyzes formation of 8-methyladenosine. In addition, analysis of RNA derived from E. coli strains lacking the m 2 A2503 methyltransferase reveals that Cfr also has the ability to catalyze methylation at position 2 to form 2,8-dimethyladenosine. The mutation of single conserved cysteine residues in the radical SAM motif CxxxCxxC of Cfr abolishes its activity, lending support to the notion that the Cfr modification reaction occurs via a radical-based mechanism. Antibiotic susceptibility data confirm that the antibiotic resistance conferred by Cfr is provided by methylation at the 8 position and is independent of methylation at the 2 position of A2503. This investigation is, to our knowledge, the first instance where the 8-methyladenosine modification has been described in natural RNA molecules.

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“…More detailed descriptions of mass spectrometer configurations, especially as used in small and large molecule biological research, can be found in a number of recent reviews. 4,9,31,[33][34][35]101,102 The most common mass spectrometry platform for nucleoside analysis depends on the analytical goals of the experiment.…”

Section: High-performance Liquid Chromatography -Oligonucleotidesmentioning

confidence: 99%

“…For a more historical description of this area, a number of excellent reviews and book chapters can be consulted. [3][4][5][6][7][8][9][10] When RNA modifications are viewed through the lens of MS, there are essentially 3 different sample types one could analyze: nucleosides and nucleotides (treated in MS as small molecules), oligonucleotides, and intact nucleic acids (the latter 2 both treated as larger biopolymers). Techniques and strategies in small molecule MS -usually arising from developments in organic mass spectrometry -have not only been applied to nucleosides and nucleotides, but also to oligonucleotides.…”

Section: Introductionmentioning

confidence: 99%

The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry

Gaston

Limbach

2014

RNA Biology

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The analysis of ribonucleic acids (RNA) by mass spectrometry has been a valuable analytical approach for more than 25 years. In fact, mass spectrometry has become a method of choice for the analysis of modified nucleosides from RNA isolated out of biological samples. This review summarizes recent progress that has been made in both nucleoside and oligonucleotide mass spectral analysis. Applications of mass spectrometry in the identification, characterization and quantification of modified nucleosides are discussed. At the oligonucleotide level, advances in modern mass spectrometry approaches combined with the standard RNA modification mapping protocol enable the characterization of RNAs of varying lengths ranging from low molecular weight short interfering RNAs (siRNAs) to the extremely large 23 S rRNAs. New variations and improvements to this protocol are reviewed, including top-down strategies, as these developments now enable qualitative and quantitative measurements of RNA modification patterns in a variety of biological systems.

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Recent Developments in Mass Spectrometry for the Characterization of Nucleosides, Nucleotides, Oligonucleotides, and Nucleic Acids

Cited by 124 publications

References 356 publications

Liquid chromatography-electrospray ionization-mass spectrometry: the future of DNA adduct detection

Liquid chromatography-electrospray ionization-mass spectrometry: the future of DNA adduct detection

Identification of 8-methyladenosine as the modification catalyzed by the radical SAM methyltransferase Cfr that confers antibiotic resistance in bacteria

The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry

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