2022
Internally controlled RNA sequencing comparisons using nucleoside recoding chemistry
Courvan MCS, Niederer RO, Vock IW, Kiefer L, Gilbert WV, Simon MD. Internally controlled RNA sequencing comparisons using nucleoside recoding chemistry. Nucleic Acids Research 2022, 50: e110-e110. PMID: 36018791, PMCID: PMC9638901, DOI: 10.1093/nar/gkac693.Peer-Reviewed Original ResearchConceptsBiochemical manipulationRNA polymerase II inhibitionSodium arsenite stressSet of transcriptsNew biological understandingTranscript regulationArsenite stressMRNA associationRNA transcriptsBiological insightsHeat shockMetabolic labelBiological understandingRNA contentRNA levelsTranscriptsCell culturesII inhibitionBiological variationDDX5RibosomesMCM2RNAAbundanceRegulation
2019
Reengineering a tRNA Methyltransferase To Covalently Capture New RNA Substrates
Smith TS, Zoltek MA, Simon MD. Reengineering a tRNA Methyltransferase To Covalently Capture New RNA Substrates. Journal Of The American Chemical Society 2019, 141: 17460-17465. PMID: 31626536, DOI: 10.1021/jacs.9b08529.Peer-Reviewed Original ResearchConceptsSubstrate specificityRNA substratesSubstrate RNARNA substrate specificityWild-type proteinCovalent RNA modificationsHigh-throughput sequencing assaysDouble mutantRNA modificationsTriple mutantSubstrate mutantsTRNA methyltransferaseProtein engineeringRNA transcriptsMutantsRational engineeringRNASubstrate screeningTRMASequencing assaysMethyltransferaseEnzymeProteinPowerful toolSpecificity