title: Direct demonstration and quantification of long-range DNA looping by the lambda bacteriophage repressor.
abstract: Recently, it was proposed that DNA looping by the lambda repressor (CI protein) strengthens repression of lytic genes during lysogeny and simultaneously ensures efficient switching to lysis. To investigate this hypothesis, tethered particle motion experiments were performed and dynamic CI-mediated looping of single DNA molecules containing the lambda repressor binding sites separated by 2317 bp (the wild-type distance) was quantitatively analyzed. DNA containing all three intact operators or with mutated o3 operators were compared. Modeling the thermodynamic data established the free energy of CI octamer-mediated loop formation as 1.7 kcal/mol, which decreased to -0.7 kcal/mol when supplemented by a tetramer (octamer+tetramer-mediated loop). These results support the idea that loops secured by an octamer of CI bound at oL1, oL2, oR1 and oR2 operators must be augmented by a tetramer of CI bound at the oL3 and oR3 to be spontaneous and stable. Thus the o3 sites are critical for loops secured by the CI protein that attenuate cI expression.
authors.affiliation: Physics Department, Emory University, Atlanta, GA 30322, USA.
authors.forename: Chiara
authors.initials: C
authors.lastname: Zurla
authors.forename: Carlo
authors.initials: C
authors.lastname: Manzo
authors.forename: David
authors.initials: D
authors.lastname: Dunlap
authors.forename: Dale E A
authors.initials: DE
authors.lastname: Lewis
authors.forename: Sankar
authors.initials: S
authors.lastname: Adhya
authors.forename: Laura
authors.initials: L
authors.lastname: Finzi
mesh_terms: D010582:Bacteriophage lambda / Q000235:genetics*; D001665:Binding Sites; D004279:DNA, Viral / Q000737:chemistry* / Q000378:metabolism; D009690:Nucleic Acid Conformation; D009875:Operator Regions, Genetic; D012097:Repressor Proteins / Q000378:metabolism*; D013816:Thermodynamics; D054334:Viral Regulatory and Accessory Proteins / Q000378:metabolism*
chemical_list: D004279:DNA, Viral; D012097:Repressor Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins