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
Characterization of a DNA-Cleaving deoxyribozyme
Carmi N, Breaker R. Characterization of a DNA-Cleaving deoxyribozyme. Bioorganic & Medicinal Chemistry 2001, 9: 2589-2600. PMID: 11557347, DOI: 10.1016/s0968-0896(01)00035-9.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceCatalysisCopperDeoxyadenosinesDeoxyribonucleotidesDNADNA, CatalyticDNA, Single-StrandedElectrophoresis, Gel, Two-DimensionalModels, MolecularMolecular StructureNucleic Acid ConformationOxidation-ReductionSequence Analysis, DNAStructure-Activity RelationshipSubstrate SpecificityImmobilized 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
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 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 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 ResearchIn vitro selection of deoxyribozymes with DNA capping activity.
Li Y, Liu Y, Breaker R. In vitro selection of deoxyribozymes with DNA capping activity. Nucleic Acids Symposium Series 1999, 42: 237-8. PMID: 10780467, DOI: 10.1093/nass/42.1.237.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 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
Cleaving DNA with DNA
Carmi N, Balkhi S, Breaker R. Cleaving DNA with DNA. Proceedings Of The National Academy Of Sciences Of The United States Of America 1998, 95: 2233-2237. PMID: 9482868, PMCID: PMC19303, DOI: 10.1073/pnas.95.5.2233.Peer-Reviewed Original Research
1997
DNA 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
1995
A DNA enzyme with Mg2+-dependent RNA phosphoesterase activity
Breaker R, Joyce G. A DNA enzyme with Mg2+-dependent RNA phosphoesterase activity. Cell Chemical Biology 1995, 2: 655-660. PMID: 9383471, DOI: 10.1016/1074-5521(95)90028-4.Peer-Reviewed Original Research
1994
A DNA enzyme that cleaves RNA
Breaker R, Joyce G. A DNA enzyme that cleaves RNA. Cell Chemical Biology 1994, 1: 223-229. PMID: 9383394, DOI: 10.1016/1074-5521(94)90014-0.Peer-Reviewed Original ResearchConceptsDNA enzymeRNA enzymeDependent cleavageSimilarity of DNATypes of RNACatalytic domainDNA sequencesRandom nucleotidesRapid turnoverRNASuccessive roundsEnzymeDNACatalytic rateSelective amplificationBiological systemsTurnover rateSequenceCleavageIntermolecular contextNucleotidesPopulationTurnoverPhosphoesters