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 SpecificityGenerating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes.
Soukup G, DeRose E, Koizumi M, Breaker R. Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes. RNA 2001, 7: 524-36. PMID: 11345431, PMCID: PMC1370106, DOI: 10.1017/s1355838201002175.Peer-Reviewed Original ResearchConceptsEffector-binding domainAllosteric ribozymesRandom mutagenesisMolecular switchLigand-binding RNAsRNA molecular switchCyclic nucleotide monophosphatesModular rational designSecondary structure organizationSpecific effector moleculesGenetic switchDirect mutational analysisNucleotide covariationsCatalytic domainPhylogeny dataMutational analysisModular engineeringCatalytic moduleNucleic acid structuresNucleotide monophosphatesEffector moleculesAffinity maturationRibozymeMutagenesisHammerhead ribozyme
2000
Altering molecular recognition of RNA aptamers by allosteric selection11Edited by D. E. Draper
Soukup G, Emilsson G, Breaker R. Altering molecular recognition of RNA aptamers by allosteric selection11Edited by D. E. Draper. Journal Of Molecular Biology 2000, 298: 623-632. PMID: 10788325, DOI: 10.1006/jmbi.2000.3704.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 ResearchRelationship between internucleotide linkage geometry and the stability of RNA.
Soukup G, Breaker R. Relationship between internucleotide linkage geometry and the stability of RNA. RNA 1999, 5: 1308-25. PMID: 10573122, PMCID: PMC1369853, DOI: 10.1017/s1355838299990891.Peer-Reviewed Original Research
1998
Mechanism for allosteric inhibition of an ATP-sensitive ribozyme
Tang J, Breaker R. Mechanism for allosteric inhibition of an ATP-sensitive ribozyme. Nucleic Acids Research 1998, 26: 4214-4221. PMID: 9722642, PMCID: PMC147823, DOI: 10.1093/nar/26.18.4214.Peer-Reviewed Original ResearchConceptsAllosteric ribozymesModular rational designFunctional modulationEffector moleculesSelf-cleaving ribozymesFunction of ribozymesSmall effector moleculesPresence of ATPAbsence of ATPAptamer domainStructural basisLigand bindingAllosteric inhibitionRibozyme domainPossible mechanismTertiary structureConformational changesRibozyme