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
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 protocolAmplification
2000
Molecular Recognition of cAMP by an RNA Aptamer †
Koizumi M, Breaker R. Molecular Recognition of cAMP by an RNA Aptamer †. Biochemistry 2000, 39: 8983-8992. PMID: 10913311, DOI: 10.1021/bi000149n.Peer-Reviewed Original ResearchAltering molecular recognition of RNA aptamers by allosteric selection11Edited by D. E. Draper
Soukup G, Emilsson G, Breaker R. Altering molecular recognition of RNA aptamers by allosteric selection11Edited by D. E. Draper. Journal Of Molecular Biology 2000, 298: 623-632. PMID: 10788325, DOI: 10.1006/jmbi.2000.3704.Peer-Reviewed Original Research
1997
Examination of the catalytic fitness of the hammerhead ribozyme by in vitro selection.
Tang J, Breaker R. Examination of the catalytic fitness of the hammerhead ribozyme by in vitro selection. RNA 1997, 3: 914-25. PMID: 9257650, PMCID: PMC1369536.Peer-Reviewed Original ResearchConceptsConsensus sequenceATP-binding RNA aptamerCatalytic fitnessHammerhead ribozymeAbsence of ATPRNA poolAllosteric ribozymesVitro SelectionRNA aptamersCatalytic functionSequence variantsAllosteric interactionsCombinatorial poolsRibozymeTranscriptionATPRNACatalytic rateSequenceHammerhead domainRibozyme constructsFitnessAllosteric delayPoolSimilar strategiesRational 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