2023
Exploiting 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
2005
Gene expression control: Harnessing RNA switches
Breaker R. Gene expression control: Harnessing RNA switches. Gene Therapy 2005, 12: 725-726. PMID: 19202632, DOI: 10.1038/sj.gt.3302461.Peer-Reviewed Original Research
2001
Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes.
Soukup G, DeRose E, Koizumi M, Breaker R. Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes. RNA 2001, 7: 524-36. PMID: 11345431, PMCID: PMC1370106, DOI: 10.1017/s1355838201002175.Peer-Reviewed Original ResearchConceptsEffector-binding domainAllosteric ribozymesRandom mutagenesisMolecular switchLigand-binding RNAsRNA molecular switchCyclic nucleotide monophosphatesModular rational designSecondary structure organizationSpecific effector moleculesGenetic switchDirect mutational analysisNucleotide covariationsCatalytic domainPhylogeny dataMutational analysisModular engineeringCatalytic moduleNucleic acid structuresNucleotide monophosphatesEffector moleculesAffinity maturationRibozymeMutagenesisHammerhead ribozyme
2000
Altering 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
1999
Nucleic acid molecular switches
Soukup G, Breaker R. Nucleic acid molecular switches. Trends In Biotechnology 1999, 17: 469-476. PMID: 10557159, DOI: 10.1016/s0167-7799(99)01383-9.Peer-Reviewed Original ResearchAllosteric selection of ribozymes that respond to the second messengers cGMP and cAMP
Koizumi M, Soukup G, Kerr J, Breaker R. Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP. Nature Structural & Molecular Biology 1999, 6: 1062-1071. PMID: 10542100, DOI: 10.1038/14947.Peer-Reviewed Original ResearchConceptsRNA molecular switchGenetic control elementsMolecular recognition characteristicsEmergence of ribozymesSecond messenger cGMPRNAs exhibitAllosteric ribozymesRNA transcriptsCellular RNASelective sensorCAMP additionMolecular switchFold activationCatalytic rateRecognition characteristicsRibozymeControl elementsEffector compoundsHammerhead ribozymeChemical agentsCompoundsStructural characteristicsSpecific nucleosideNew combinatorial strategyCombinatorial strategies
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 featuresDNA enzymes
Breaker R. DNA enzymes. Nature Biotechnology 1997, 15: 427-431. PMID: 9131619, DOI: 10.1038/nbt0597-427.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceCatalysisDNADNA ReplicationEnzymesGenetic EngineeringGenomeMolecular Sequence DataNucleic Acid ConformationRNA, Catalytic
1996
In vitro selection of self-cleaving DNAs
Carmi N, Shultz L, Breaker R. In vitro selection of self-cleaving DNAs. Cell Chemical Biology 1996, 3: 1039-1046. PMID: 9000012, DOI: 10.1016/s1074-5521(96)90170-2.Peer-Reviewed Original ResearchConceptsIndividual catalystsCatalytic DNAEnzyme-like activityChemical transformationsSole cofactorRate enhancementAdditional reactionsCu2DNA enzymeCatalystDNA cleavageBiological contextVitro SelectionUncatalyzed rateOxidative mechanismsDNAFurther optimizationDistinct classesRibozymeHydroxylDeoxyribozymesBiocatalystReactionCleavageCofactor