2024
Engineered Branaplam Aptamers Exploit Structural Elements from Natural Riboswitches
Mohsen M, Midy M, Balaji A, Breaker R. Engineered Branaplam Aptamers Exploit Structural Elements from Natural Riboswitches. ACS Chemical Biology 2024, 19: 1447-1452. PMID: 38954594, PMCID: PMC11267568, DOI: 10.1021/acschembio.4c00358.Peer-Reviewed Original ResearchRNA poolRiboswitch aptamerAptamer candidatesPaired elementsIn vitro selectionNatural riboswitchesHuntington's diseaseThiamine pyrophosphateAptamer developmentRiboswitchDrug candidatesAptamerStructural scaffoldBranaplamRNASpinal muscular atrophyImproved bindingTreat spinal muscular atrophySmall moleculesBioavailability characteristicsDissociation constantPseudoknotMuscular atrophyStructural elementsPool
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
1997
Examination of the catalytic fitness of the hammerhead ribozyme by in vitro selection.
Tang J, Breaker R. Examination of the catalytic fitness of the hammerhead ribozyme by in vitro selection. RNA 1997, 3: 914-25. PMID: 9257650, PMCID: PMC1369536.Peer-Reviewed Original ResearchConceptsConsensus sequenceATP-binding RNA aptamerCatalytic fitnessHammerhead ribozymeAbsence of ATPRNA poolAllosteric ribozymesVitro SelectionRNA aptamersCatalytic functionSequence variantsAllosteric interactionsCombinatorial poolsRibozymeTranscriptionATPRNACatalytic rateSequenceHammerhead domainRibozyme constructsFitnessAllosteric delayPoolSimilar strategies