2023
8-oxoguanine riboswitches in bacteria detect and respond to oxidative DNA damage
Dhakal S, Kavita K, Panchapakesan S, Roth A, Breaker R. 8-oxoguanine riboswitches in bacteria detect and respond to oxidative DNA damage. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2307854120. PMID: 37748066, PMCID: PMC10556655, DOI: 10.1073/pnas.2307854120.Peer-Reviewed Original ResearchMeSH KeywordsAptamers, NucleotideBacteriaDeoxyguanosineGuanineLigandsNucleic Acid ConformationOxidative StressRiboswitchXanthineConceptsAptamer domainGene expressionLigand specificityOxidative damageLigand-binding pocketRiboswitch classesFamilies of bacteriaRare variantsRiboswitch aptamerCertain oxidative stressesExposure of cellsOxidative DNA damageRiboswitchGene associationsRNA aptamersDNA damageNucleotide poolBacteriaTarget ligandsOxidative stressMutationsNumerous alterationsPurine derivativesExpressionVariantsExploiting natural riboswitches for aptamer engineering and validation
Mohsen M, Midy M, Balaji A, Breaker R. Exploiting natural riboswitches for aptamer engineering and validation. Nucleic Acids Research 2023, 51: 966-981. PMID: 36617976, PMCID: PMC9881172, DOI: 10.1093/nar/gkac1218.Peer-Reviewed Original ResearchMeSH KeywordsAptamers, NucleotideCaffeineGenetic EngineeringGuanineLigandsNucleic Acid ConformationQuinineRiboswitchConceptsNatural riboswitchesRiboswitch aptamerReporter gene expressionSecondary structure featuresRNA poolExpression platformVivo functionGene expressionSurvival mechanismRNA sequencesStructural featuresRiboswitchAptamer selectionSmall moleculesSequenceAptamerCellsGuanineTest tubeFuture effortsSelectionSelection strategyExpressionPoolAptamer engineering
2009
Engineering ligand-responsive gene-control elements: lessons learned from natural riboswitches
Link K, Breaker R. Engineering ligand-responsive gene-control elements: lessons learned from natural riboswitches. Gene Therapy 2009, 16: 1189-1201. PMID: 19587710, PMCID: PMC5325117, DOI: 10.1038/gt.2009.81.Peer-Reviewed Original Research
2008
In Vitro Selection and Characterization of Cellulose-Binding RNA Aptamers Using isothermal Amplification
Boese B, Corbino K, Breaker R. In Vitro Selection and Characterization of Cellulose-Binding RNA Aptamers Using isothermal Amplification. Nucleosides Nucleotides & Nucleic Acids 2008, 27: 949-966. PMID: 18696364, PMCID: PMC5360192, DOI: 10.1080/15257770802257903.Peer-Reviewed Original ResearchConceptsRNA aptamersRibozyme cleavage productsCellulose affinity chromatographyIsolation of RNARapid amplificationVitro SelectionRibozyme functionRibozyme sequenceFunctional nucleic acidsNucleic acid amplification protocolsRNARobust bindingAffinity chromatographyCleavage productsNucleic acidsSequence replicationBindingSignificant bindingAptamerAmplification protocolAmplificationRiboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP
Sudarsan N, Lee E, Weinberg Z, Moy R, Kim J, Link K, Breaker R. Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP. Science 2008, 321: 411-413. PMID: 18635805, PMCID: PMC5304454, DOI: 10.1126/science.1159519.Peer-Reviewed Original ResearchConceptsCyclic di-GMPVirulence gene expressionGene expressionSecond messenger cyclic di-GMPNumerous fundamental cellular processesCyclic di-guanosine monophosphateFundamental cellular processesExpression of genesGMP riboswitchRiboswitch classesFlagellum biosynthesisBiofilm lifestyleCellular processesDiverse speciesPilus formationSecond messengerCell differentiationRiboswitchBacterial speciesMessenger RNARNA dinucleotideSpeciesExpressionPhysiological changesRegulon