2009
Closing the Loop on Protein-DNA Interactions: Interplay Between Shape and Flexibility in Nucleoprotein Assemblies Having Implications for Biological Regulation
Levene S, Zhang Y. Closing the Loop on Protein-DNA Interactions: Interplay Between Shape and Flexibility in Nucleoprotein Assemblies Having Implications for Biological Regulation. The IMA Volumes In Mathematics And Its Applications 2009, 150: 195-212. DOI: 10.1007/978-1-4419-0670-0_10.Peer-Reviewed Original ResearchDNA loop formationProtein-DNA interactionsProtein-binding sitesArchitectural proteinsGene repressionLoop formationGene regulationProtein domainsDNA replicationDNA loopsNucleoprotein assembliesBiological regulationLac repressorBiological processesBiological importanceConformational flexibilityProteinEssential mechanistic aspectsDNARegulationSingle moleculesRepressorMechanistic aspectsDistant sitesRepression
2006
Analysis of In-Vivo LacR-Mediated Gene Repression Based on the Mechanics of DNA Looping
Zhang Y, McEwen AE, Crothers DM, Levene SD. Analysis of In-Vivo LacR-Mediated Gene Repression Based on the Mechanics of DNA Looping. PLOS ONE 2006, 1: e136. PMID: 17205140, PMCID: PMC1762422, DOI: 10.1371/journal.pone.0000136.Peer-Reviewed Original ResearchConceptsGene regulationNucleoprotein complexesNon-specific DNA-binding proteinE. coli lac repressorWild-type E. coli strainDNA-binding proteinsSmall DNA loopsSame DNA moleculeGene repressionDNA loopingDNA loopsOperator sitesOperator affinityDNA rigidityLac repressorE. coli strainsProtein conformationDNA persistence lengthDNA moleculesRepressor concentrationRepressionColi strainsDNARegulationVivo