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
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 ResearchMeSH KeywordsAnimalsBase SequenceBiotechnologyDNADNA, CatalyticGenomeKineticsMetalsModels, GeneticMolecular Sequence DataRNA
2001
Cooperative 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 ResearchMeSH KeywordsBase SequenceBinding SitesFlavin MononucleotideKineticsMolecular Sequence DataNucleic Acid ConformationOligonucleotidesRNARNA, CatalyticTheophyllineConceptsAllosteric ribozymesCooperative bindingModular rational designAbsence of effectorsAllosteric proteinsRNA modulesRNA structureMolecular switchAllosteric effectorsFirst bindsFunctional complexityEffectorsDifferent effectorsInduces formationFMNStructural studiesRNARibozymeRibozyme constructsBindingRational designProteinBindsSitesConcertGenerating 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 ribozymeIn Vitro Selection of Kinase and Ligase Deoxyribozymes
Li Y, Breaker R. In Vitro Selection of Kinase and Ligase Deoxyribozymes. Methods 2001, 23: 179-190. PMID: 11181037, DOI: 10.1006/meth.2000.1119.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine MonophosphateBase SequenceCopperDNA LigasesDNA, CatalyticGenetic TechniquesModels, ChemicalMolecular Sequence DataPhosphotransferasesConceptsDNA ligationModern living systemsDNA kinaseEnzymatic functionRandom sequence populationVitro SelectionProtein enzymesConstruction of DNADNA constructsDNA phosphorylationDNADeoxyribozymesKinaseLiving systemsFundamental roleChemical reactionsAdenylationFundamental questionsBiocatalysisPhosphorylationEnzymeBiotechnologySelection strategyDiscoveryDetailed overview
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 ResearchStructural diversity of self-cleaving ribozymes
Tang J, Breaker R. Structural diversity of self-cleaving ribozymes. Proceedings Of The National Academy Of Sciences Of The United States Of America 2000, 97: 5784-5789. PMID: 10823936, PMCID: PMC18511, DOI: 10.1073/pnas.97.11.5784.Peer-Reviewed Original ResearchCapping DNA with DNA †
Li Y, Liu Y, Breaker R. Capping DNA with DNA †. Biochemistry 2000, 39: 3106-3114. PMID: 10715132, DOI: 10.1021/bi992710r.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 strategiesRelationship between internucleotide linkage geometry and the stability of RNA.
Soukup G, Breaker R. Relationship between internucleotide linkage geometry and the stability of RNA. RNA 1999, 5: 1308-25. PMID: 10573122, PMCID: PMC1369853, DOI: 10.1017/s1355838299990891.Peer-Reviewed Original ResearchDesign of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization
Soukup G, Breaker R. Design of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization. Structure 1999, 7: 783-791. PMID: 10425680, DOI: 10.1016/s0969-2126(99)80102-6.Peer-Reviewed Original ResearchDeoxyribozymes: New players in the ancient game of biocatalysis
Li Y, Breaker R. Deoxyribozymes: New players in the ancient game of biocatalysis. Current Opinion In Structural Biology 1999, 9: 315-323. PMID: 10361095, DOI: 10.1016/s0959-440x(99)80042-6.Peer-Reviewed Original ResearchConceptsSubstrate recognitionGenetic informationIdeal storage systemBiological catalysisRNA counterpartsInert characterChemical reactionsDNANovel chemicalRate enhancementSubstantial untapped potentialNew playersArtificial DNAHelical structurePolynucleotide chainSurprising varietyDeoxyribozymesRecent studiesStructure formationProteinCatalysisBiocatalysisStorage systemReactionChemicalsCatalytic DNA: in training and seeking employment
Breaker R. Catalytic DNA: in training and seeking employment. Nature Biotechnology 1999, 17: 422-423. PMID: 10331790, DOI: 10.1038/8588.Peer-Reviewed Original ResearchAnimalsBase SequenceDNA, CatalyticDNA, Single-StrandedHumansMolecular Sequence DataRatsRNARNA, MessengerEngineering 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 constructsReorganizationDomainPhosphorylating DNA with DNA
Li Y, Breaker R. Phosphorylating DNA with DNA. Proceedings Of The National Academy Of Sciences Of The United States Of America 1999, 96: 2746-2751. PMID: 10077582, PMCID: PMC15840, DOI: 10.1073/pnas.96.6.2746.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceDNAHydrolysisMolecular Sequence DataPhosphorylationRNASubstrate SpecificityConceptsSubstrate recognition patternRandom sequence poolsKinase-like activityStandard NTPsATP hydrolysisSpecific target DNAVitro SelectionIndividual DNAProtein enzymesDNADNTP substratesMultiple turnoversDeoxyribozymesEnzymeTarget DNABiological systemsDeoxyribose moietyGTPNTPsRNAATPDNTPsCatalytic potentialSelectionRiboseIn 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 changesRibozymeAn amino acid as a cofactor for a catalytic polynucleotide
Roth A, Breaker R. An amino acid as a cofactor for a catalytic polynucleotide. Proceedings Of The National Academy Of Sciences Of The United States Of America 1998, 95: 6027-6031. PMID: 9600911, PMCID: PMC27579, DOI: 10.1073/pnas.95.11.6027.Peer-Reviewed Original ResearchMeSH KeywordsAmino AcidsBase SequenceDNA, Single-StrandedHistidineMolecular Sequence DataPolynucleotidesRNA, CatalyticConceptsAmino acidsRate enhancementDramatic rate enhancementMetal ion cofactorsAbsence of enzymeGeneral base catalystSuperior polymerChemical catalysisBiological catalystsRNA cleavage reactionCatalytic potentialOrganic cofactorImidazole groupsNatural ribozymesRNA worldBase catalystChemical groupsCatalytic mechanismCatalytic DNACleavage reactionIon cofactorProtein enzymesStructural foldingSubstrate cleavageConstituent amino acids