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 ResearchConceptsAptamer domainGene expressionLigand specificityOxidative damageLigand-binding pocketRiboswitch classesFamilies of bacteriaRare variantsRiboswitch aptamerCertain oxidative stressesExposure of cellsOxidative DNA damageRiboswitchGene associationsRNA aptamersDNA damageNucleotide poolBacteriaTarget ligandsOxidative stressMutationsNumerous alterationsPurine derivativesExpressionVariants
2006
Genetic control by riboswitches and ribozymes
Breaker R. Genetic control by riboswitches and ribozymes. The FASEB Journal 2006, 20: a455-a456. DOI: 10.1096/fasebj.20.4.a455-d.Peer-Reviewed Original ResearchGenetic switchGene expressionAptamer domainBacterial speciesCertain messenger RNAsControl gene expressionMessenger RNA stabilityNon-coding regionsComplex genetic elementsSelf-cleaving ribozymesRiboswitch classesReceptor-ligand interactionsTranscription elongationTranslation initiationRNA stabilityRNA transcriptionRiboswitchAllosteric changesGenetic controlGenetic elementsRNA structureMessenger RNATarget metabolitesRNARecent findingsRiboswitches: Natural Metabolite‐binding RNAs Controlling Gene Expression
Roth A, Welz R, Breaker R. Riboswitches: Natural Metabolite‐binding RNAs Controlling Gene Expression. 2006, 191-207. DOI: 10.1002/3527608192.ch8.Peer-Reviewed Original Research
1998
Mechanism for allosteric inhibition of an ATP-sensitive ribozyme
Tang J, Breaker R. Mechanism for allosteric inhibition of an ATP-sensitive ribozyme. Nucleic Acids Research 1998, 26: 4214-4221. PMID: 9722642, PMCID: PMC147823, DOI: 10.1093/nar/26.18.4214.Peer-Reviewed Original ResearchConceptsAllosteric ribozymesModular rational designFunctional modulationEffector moleculesSelf-cleaving ribozymesFunction of ribozymesSmall effector moleculesPresence of ATPAbsence of ATPAptamer domainStructural basisLigand bindingAllosteric inhibitionRibozyme domainPossible mechanismTertiary structureConformational changesRibozyme
1997
Rational design of allosteric ribozymes
Tang J, Breaker R. Rational design of allosteric ribozymes. Cell Chemical Biology 1997, 4: 453-459. PMID: 9224568, DOI: 10.1016/s1074-5521(97)90197-6.Peer-Reviewed Original ResearchConceptsAllosteric regulationAllosteric ribozymesEffector moleculesProtein enzymesActive siteCatalytic ratePresence of dATPSelf-cleaving ribozymesSmall effector moleculesPresence of ATPSmall molecule receptorRational design strategyCellular processesEnzyme active siteAptamer domainAllosteric controlAllosteric enzymeCatalytic RNARNA aptamersConformational changesLigand moleculesMetabolic pathwaysCatalytic activityAllosteric hammerheadCatalytic features