2023
In vitro Selection and in vivo Testing of Riboswitch-inspired Aptamers
Mohsen M, Breaker R. In vitro Selection and in vivo Testing of Riboswitch-inspired Aptamers. Bio-protocol 2023, 13: e4775. PMID: 37456339, PMCID: PMC10338711, DOI: 10.21769/bioprotoc.4775.Peer-Reviewed Original ResearchAptamer candidatesSubsequent biochemical validationComplex cellular environmentVitro selection protocolSelfish sequencesRiboswitch aptamerNext-generation sequencingRNA poolBacterial cell cultureExpression platformCellular environmentBacterial cellsBiochemical validationStructural scaffoldLigand candidatesCell culturesSelection protocolAptamerRiboswitchNew ligandsSelectionBioinformaticsSequencingScaffold typesSequenceExploiting natural riboswitches for aptamer engineering and validation
Mohsen M, Midy M, Balaji A, Breaker R. Exploiting natural riboswitches for aptamer engineering and validation. Nucleic Acids Research 2023, 51: 966-981. PMID: 36617976, PMCID: PMC9881172, DOI: 10.1093/nar/gkac1218.Peer-Reviewed Original ResearchConceptsNatural riboswitchesRiboswitch aptamerReporter gene expressionSecondary structure featuresRNA poolExpression platformVivo functionGene expressionSurvival mechanismRNA sequencesStructural featuresRiboswitchAptamer selectionSmall moleculesSequenceAptamerCellsGuanineTest tubeFuture effortsSelectionSelection strategyExpressionPoolAptamer engineering
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 Specificity
1999
Phosphorylating 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