title: AFM studies of lambda repressor oligomers securing DNA loops.
abstract: Large, cooperative assemblies of proteins that wrap and/or loop genomic DNA may "epigenetically" shift configurational equilibria that determine developmental pathways. Such is the case of the lambda bacteriophage which may exhibit virulent (lytic) or quiescent (lysogenic) growth. The lysogenic state of lambda prophages is maintained by the lambda repressor (CI), which binds to tripartite operator sites in each of the O(L) and O(R) control regions located about 2.3 kbp apart on the phage genome and represses lytic promoters. Dodd and collaborators have suggested that an initial loop formed by interaction between CI bound at O(R) and O(L) provides the proper scaffold for additional CI binding to attenuate the P(RM) promoter and avoid over production of CI. Recently, the looping equilibrium as a function of CI concentration was measured using tethered particle motion analysis, but the oligomerization of CI in looped states could not be determined. Scanning force microscopy has now been used to probe these details directly. An equilibrium distribution of looped and unlooped molecules confined to a plane was found to be commensurate to that for tethered molecules in solution, and the occupancies of specific operator sites for several looped and unlooped conformations were determined. Some loops appeared to be sealed by oligomers of 6-8, most by oligomers of 10-12, and a few by oligomers of 14-16.
authors.affiliation: Department of Cell Biology, Emory University, Atlanta, GA 30322, USA.
authors.forename: Haowei
authors.initials: H
authors.lastname: Wang
authors.forename: Laura
authors.initials: L
authors.lastname: Finzi
authors.forename: Dale E A
authors.initials: DE
authors.lastname: Lewis
authors.forename: David
authors.initials: D
authors.lastname: Dunlap
mesh_terms: D010582:Bacteriophage lambda / Q000737:chemistry* / Q000648:ultrastructure; D001665:Binding Sites; D002138:Calibration; D053938:DNA Fragmentation; D004279:DNA, Viral / Q000737:chemistry* / Q000648:ultrastructure; D018625:Microscopy, Atomic Force; D008970:Molecular Weight; D009690:Nucleic Acid Conformation; D012097:Repressor Proteins / Q000737:chemistry*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry*
chemical_list: D004279:DNA, Viral; D012097:Repressor Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins
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