Featured Publications
Discovering riboswitches: the past and the future
Kavita K, Breaker RR. Discovering riboswitches: the past and the future. Trends In Biochemical Sciences 2022, 48: 119-141. PMID: 36150954, PMCID: PMC10043782, DOI: 10.1016/j.tibs.2022.08.009.Peer-Reviewed Original Research
2024
Genetic disruption of the bacterial raiA motif noncoding RNA causes defects in sporulation and aggregation
Soares L, King C, Fernando C, Roth A, Breaker R. Genetic disruption of the bacterial raiA motif noncoding RNA causes defects in sporulation and aggregation. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2318008121. PMID: 38306478, PMCID: PMC10861870, DOI: 10.1073/pnas.2318008121.Peer-Reviewed Original ResearchConceptsMotif RNAsGenetic disruptionSecondary structure modelKnock-out strainTrans-acting factorsNoncoding RNAsCell differentiation processAbundant RNATransfer RNANcRNA classesRibosomal RNASpore formationMotif genesCellular processesBacterial speciesCellular functionsBioinformatics analysisExpression analysisMotifRNAGenesBiochemical mechanismsNcRNAsDifferentiation processStructural probes
2023
Evidence that OLE RNA is a component of a major stress‐responsive ribonucleoprotein particle in extremophilic bacteria
Breaker R, Harris K, Lyon S, Wencker F, Fernando C. Evidence that OLE RNA is a component of a major stress‐responsive ribonucleoprotein particle in extremophilic bacteria. Molecular Microbiology 2023, 120: 324-340. PMID: 37469248, DOI: 10.1111/mmi.15129.Peer-Reviewed Original ResearchConceptsOLE RNAPrecise biochemical functionFundamental cellular processesCell growthTOR complexesProtein partnersRibonucleoprotein complexesCellular processesRNP complexesBiochemical functionsGram-positive bacteriaNoncoding RNAsRibonucleoprotein particleExtremophilic bacteriaBacterial speciesGenetic disruptionStress conditionsDiverse pathwaysRNAMetabolic adaptationCell membraneExtreme environmentsCarbon sourceBacteriaComplexesRiboswitches
Salvail H, Breaker R. Riboswitches. Current Biology 2023, 33: r343-r348. PMID: 37160088, PMCID: PMC11207198, DOI: 10.1016/j.cub.2023.03.069.Peer-Reviewed Original ResearchScreening for small molecule inhibitors of SAH nucleosidase using an SAH riboswitch
Sadeeshkumar H, Balaji A, Sutherland A, Mootien S, Anthony K, Breaker R. Screening for small molecule inhibitors of SAH nucleosidase using an SAH riboswitch. Analytical Biochemistry 2023, 666: 115047. PMID: 36682579, PMCID: PMC11149561, DOI: 10.1016/j.ab.2023.115047.Peer-Reviewed Original ResearchConceptsHigh-throughput screenAutoinducer-2Reporter geneBacterial processesEssential bacterial processesGram-negative bacterial cellsQuorum sensing signalsΒ-galactosidase reporter geneSmall molecule inhibitorsAntibiotic drug discoveryNatural riboswitchesAntimicrobial drug developmentRNA elementsPhysiological signalingRiboswitchBacterial cellsMolecule inhibitorsS-adenosylmethionineEscherichia coliCritical functionsNew targetsGenesDrug discoverySmall moleculesPromising target
2022
Ornate, large, extremophilic (OLE) RNA forms a kink turn necessary for OapC protein recognition and RNA function
Lyon S, Harris K, Odzer N, Wilkins S, Breaker R. Ornate, large, extremophilic (OLE) RNA forms a kink turn necessary for OapC protein recognition and RNA function. Journal Of Biological Chemistry 2022, 298: 102674. PMID: 36336078, PMCID: PMC9723947, DOI: 10.1016/j.jbc.2022.102674.Peer-Reviewed Original ResearchConceptsOLE RNARNP complexesRNA-protein binding assaysPrecise biochemical functionRNA structural motifsInability of cellsNatural binding sitesRibonucleoprotein complexesRNA functionBiochemical functionsExhibit phenotypesBacterial proteinsK-turnKink turnBacillus haloduransDisruptive mutationsSame proteinBacterial speciesProtein recognitionAnaerobic bacterial speciesFunctional roleSecondary structureRNAProteinOapB
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
Immobilized 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 pixelsRibozymeCofactorCooperative 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 designProteinBindsSitesConcert
2000
Tech.Sight. Molecular biology. Making catalytic DNAs.
Breaker R. Tech.Sight. Molecular biology. Making catalytic DNAs. Science 2000, 290: 2095-6. PMID: 11187837, DOI: 10.1126/science.290.5499.2095.Peer-Reviewed Original ResearchMolecular 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 ResearchAllosteric nucleic acid catalysts
Soukup G, Breaker R. Allosteric nucleic acid catalysts. Current Opinion In Structural Biology 2000, 10: 318-325. PMID: 10851196, DOI: 10.1016/s0959-440x(00)00090-7.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 ResearchRelationship 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 ResearchCatalytic 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 ResearchEngineering 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 ResearchConceptsSubstrate recognition patternRandom sequence poolsKinase-like activityStandard NTPsATP hydrolysisSpecific target DNAVitro SelectionIndividual DNAProtein enzymesDNADNTP substratesMultiple turnoversDeoxyribozymesEnzymeTarget DNABiological systemsDeoxyribose moietyGTPNTPsRNAATPDNTPsCatalytic potentialSelectionRibose
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
1996
Are engineered proteins getting competition from RNA?
Breaker R. Are engineered proteins getting competition from RNA? Current Opinion In Biotechnology 1996, 7: 442-448. PMID: 8768905, DOI: 10.1016/s0958-1669(96)80122-4.Peer-Reviewed Original Research
1994
Production of RNA by a polymerase protein encapsulated within phospholipid vesicles
Chakrabarti A, Breaker R, Joyce G, Deamer D. Production of RNA by a polymerase protein encapsulated within phospholipid vesicles. Journal Of Molecular Evolution 1994, 39: 555-559. PMID: 7528810, DOI: 10.1007/bf00160400.Peer-Reviewed Original ResearchConceptsRNA polymeraseTemplate-independent RNA polymeraseProduction of RNACatalyzed polymerization reactionsBoundary membraneMacromolecular catalystsRNA productsPolymerization reactionPolymerase proteinDimyristoyl phosphatidylcholine vesiclesPolyacrylamide gel electrophoresisEthidium bromide fluorescenceEarly cellsRNA polymersPhase transition temperatureSubstrate fluxPhospholipid vesiclesVesiclesFree enzymeSuch reactionsGel electrophoresisPhosphatidylcholine vesiclesComponent lipidsPolymeraseCatalyst