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 SpecificityIn 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 ResearchConceptsDNA ligationModern living systemsDNA kinaseEnzymatic functionRandom sequence populationVitro SelectionProtein enzymesConstruction of DNADNA constructsDNA phosphorylationDNADeoxyribozymesKinaseLiving systemsFundamental roleChemical reactionsAdenylationFundamental questionsBiocatalysisPhosphorylationEnzymeBiotechnologySelection strategyDiscoveryDetailed overview
1999
Deoxyribozymes: 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 systemReactionChemicalsPhosphorylating 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
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
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
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 contextNucleotidesPopulationTurnoverPhosphoestersEmergence of a replicating species from an in vitro RNA evolution reaction.
Breaker R, Joyce G. Emergence of a replicating species from an in vitro RNA evolution reaction. Proceedings Of The National Academy Of Sciences Of The United States Of America 1994, 91: 6093-6097. PMID: 7517040, PMCID: PMC44144, DOI: 10.1073/pnas.91.13.6093.Peer-Reviewed Original ResearchConceptsRNA polymeraseDNA-dependent RNA polymeraseRNA polymerase promoter sequencePromoter sequencesEvolution experimentsRNA moleculesAcid sequenceRNA transcriptsSpecific nucleic acid sequencesTarget chemical reactionNucleic acid sequencesRNA replicationPolymeraseRNADNAReverse transcriptaseSelective amplificationDNA hairpinsSequence replicationChemical reactionsUnique classReplicationSequenceTranscriptaseParticular chemical reaction