2023
Exploiting 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
2016
Prospects for Noncoding RNA Discovery in Bacteria
Breaker R. Prospects for Noncoding RNA Discovery in Bacteria. The FASEB Journal 2016, 30 DOI: 10.1096/fasebj.30.1_supplement.386.1.Peer-Reviewed Original ResearchNoncoding RNAsNovel biochemical functionLarge noncoding RNAsBacterial noncoding RNAsRNA world organismsSelf-cleaving ribozymesRiboswitch candidatesRNA discoveryBiological validation studiesBiochemical functionsBioinformatics analysisModern cellsWorld organismsRNAGreat diversityStructural diversityNovel ribozymesRibozymeDiversityBacteriaDiscoveryRiboswitchRNAsOrganismsCells
2010
The large, noncoding OLE RNA is associated with membrane biochemistry
Block K, Wallace J, Puerta‐Fernandez E, Breaker R. The large, noncoding OLE RNA is associated with membrane biochemistry. The FASEB Journal 2010, 24: 493.2-493.2. DOI: 10.1096/fasebj.24.1_supplement.493.2.Peer-Reviewed Original ResearchOLE RNAB. haloduransMembrane biochemistryMembrane-spanning proteinsHigh-throughput sequencingEnergy-generating pathwaysEscherichia coli cellsGel shift assaysNorthern blot analysisRNA fluorescenceSpecific ribonucleoproteinGram-positive bacteriaShift assaysColi cellsUnknown functionProbable binding siteSitu hybridizationBlot analysisBinding sitesHaloduransHoward Hughes Medical InstituteRNAProteinBiochemistryCells
2006
Riboswitches: Regulators of modern and ancient metabolism
Kim J, Breaker R. Riboswitches: Regulators of modern and ancient metabolism. The Biochemist 2006, 28: 11-15. DOI: 10.1042/bio02802011.Peer-Reviewed Original ResearchComplex biochemical pathwaysPrimitive life formsNucleic acid biochemistryAncient metabolismPrimitive organismsModern cellsLife formsStructured RNAsBiochemical pathwaysBiological processesEfficient enzymeRNARecent findingsMolecular sensorsSpecific receptorsSuch moleculesRiboswitchOrganismsRegulatorEnormous potentialEnzymePathwayBiochemistryMetabolismCells
1997
DNA enzymes
Breaker R. DNA enzymes. Nature Biotechnology 1997, 15: 427-431. PMID: 9131619, DOI: 10.1038/nbt0597-427.Peer-Reviewed Original Research