Featured Publications
Natural circularly permuted group II introns in bacteria produce RNA circles
Roth A, Weinberg Z, Vanderschuren K, Murdock MH, Breaker RR. Natural circularly permuted group II introns in bacteria produce RNA circles. IScience 2021, 24: 103431. PMID: 34901790, PMCID: PMC8637638, DOI: 10.1016/j.isci.2021.103431.Peer-Reviewed Original Research
2018
Large Noncoding RNAs in Bacteria
Harris K, Breaker R. Large Noncoding RNAs in Bacteria. 2018, 515-526. DOI: 10.1128/9781683670247.ch30.Peer-Reviewed Original ResearchNcRNA classesSelfish genetic elementsLarge noncoding RNAsGenetic information processingProtein-coding regionsGroup II intronsSelf-splicing ribozymesStructured ncRNAsPrecursor tRNAsRNA splicingCellular processesDNA genomeNoncoding RNAsGenetic elementsGene expressionExon flanksPeptide bond formationRNA cleavagePhysiological adaptationsBind ionsRibozyme structureEssential roleRibozymeIntriguing possibilityBacteria
2016
Prospects for Noncoding RNA Discovery in Bacteria
Breaker R. Prospects for Noncoding RNA Discovery in Bacteria. The FASEB Journal 2016, 30 DOI: 10.1096/fasebj.30.1_supplement.386.1.Peer-Reviewed Original ResearchNoncoding RNAsNovel biochemical functionLarge noncoding RNAsBacterial noncoding RNAsRNA world organismsSelf-cleaving ribozymesRiboswitch candidatesRNA discoveryBiological validation studiesBiochemical functionsBioinformatics analysisModern cellsWorld organismsRNAGreat diversityStructural diversityNovel ribozymesRibozymeDiversityBacteriaDiscoveryRiboswitchRNAsOrganismsCells
2007
Chapter 8
Link K, Breaker R. Chapter 8. 2007, 134-152. DOI: 10.1039/9781847557988-00134.Peer-Reviewed Original Research
2002
Deoxyribozymes: new activities and new applications
Emilsson G, Breaker R. Deoxyribozymes: new activities and new applications. Cellular And Molecular Life Sciences 2002, 59: 596-607. PMID: 12022469, PMCID: PMC11337523, DOI: 10.1007/s00018-002-8452-4.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 ribozymeCooperative binding of effectors by an allosteric ribozyme
Jose A, Soukup G, Breaker R. Cooperative binding of effectors by an allosteric ribozyme. Nucleic Acids Research 2001, 29: 1631-1637. PMID: 11266567, PMCID: PMC31269, DOI: 10.1093/nar/29.7.1631.Peer-Reviewed Original ResearchConceptsAllosteric ribozymesCooperative bindingModular rational designAbsence of effectorsAllosteric proteinsRNA modulesRNA structureMolecular switchAllosteric effectorsFirst bindsFunctional complexityEffectorsDifferent effectorsInduces formationFMNStructural studiesRNARibozymeRibozyme constructsBindingRational designProteinBindsSitesConcertImmobilized RNA switches for the analysis of complex chemical and biological mixtures
Seetharaman S, Zivarts M, Sudarsan N, Breaker R. Immobilized RNA switches for the analysis of complex chemical and biological mixtures. Nature Biotechnology 2001, 19: 336-341. PMID: 11283591, DOI: 10.1038/86723.Peer-Reviewed Original ResearchConceptsDrug analytesMetal ionsBiological mixturesBiosensor arrayAnalyte sensorRNA molecular switchComplex mixturesComplex chemicalMolecular switchEnzyme cofactorMixtureRNA switchesBacterial culture mediumAnalytesMoietyIonsGoldImmobilizationCorresponding effectorsChemicalsStatus of targetAddressable pixelsRibozymeCofactor
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 ribozymes sensitive to the second messengers cAMP and cGMP.
Koizumi M, Kerr J, Soukup G, Breaker R. Allosteric ribozymes sensitive to the second messengers cAMP and cGMP. Nucleic Acids Symposium Series 1999, 42: 275-6. PMID: 10780486, DOI: 10.1093/nass/42.1.275.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 strategiesEngineering precision RNA molecular switches
Soukup G, Breaker R. Engineering precision RNA molecular switches. Proceedings Of The National Academy Of Sciences Of The United States Of America 1999, 96: 3584-3589. PMID: 10097080, PMCID: PMC22337, DOI: 10.1073/pnas.96.7.3584.Peer-Reviewed Original ResearchConceptsRNA molecular switchMolecular switchGenetic control elementsEnzyme engineering strategiesRNA switchesReceptor domainConformational changesControl elementsEngineering strategiesStructural bridgeModular natureMolecular sensorsStructural reorganizationCorresponding ligandsRNARibozymeSwitchLigandsCatalyticReceptorsTripartite constructsReorganizationDomainIn Vitro Selection of Nucleic Acid Enzymes
Breaker R, Kurz M. In Vitro Selection of Nucleic Acid Enzymes. Current Topics In Microbiology And Immunology 1999, 243: 137-158. PMID: 10453642, DOI: 10.1007/978-3-642-60142-2_8.Peer-Reviewed Original ResearchConceptsDiversity of enzymesYears of evolutionNucleic acid enzymesEvolutionary historyNucleic acidsBiochemical functionsDNA substratesMetabolic machineryVitro SelectionProtein enzymesCatalytic functionBiological catalystsAcid enzymesHydrolysis reactionProteinEnzymeNatural functionRibozymeDistinct classesRNAEssential componentReactionMachineryCatalystDiversity
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
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 strategiesDNA aptamers and DNA enzymes
Breaker R. DNA aptamers and DNA enzymes. Current Opinion In Chemical Biology 1997, 1: 26-31. PMID: 9667831, DOI: 10.1016/s1367-5931(97)80105-6.Peer-Reviewed Original ResearchDNA enzymes
Breaker R. DNA enzymes. Nature Biotechnology 1997, 15: 427-431. PMID: 9131619, DOI: 10.1038/nbt0597-427.Peer-Reviewed Original Research
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
1995
Self-Incorporation of coenzymes by ribozymes
Breaker R, Joyce G. Self-Incorporation of coenzymes by ribozymes. Journal Of Molecular Evolution 1995, 40: 551-558. PMID: 7643406, DOI: 10.1007/bf00160500.Peer-Reviewed Original ResearchConceptsFunctional groupsCoenzyme analoguesAdditional functional groupsChemical functional groupsChemical moietiesTransfer reactionsCovalent attachmentRNA enzymeAbsence of proteinStandard nucleotidesCatalysisCatalytic functionRibozyme activityRNA worldRibozymeMoietyAnaloguesCoenzymeCoA-SHMoleculesReaction