title: Regulation of poly(ADP-ribose) polymerase-1 by DNA structure-specific binding.
abstract: Poly(ADP-ribose) polymerase-1 (PARP-1) is an intracellular sensor of DNA strand breaks and plays a critical role in cellular responses to DNA damage. In normally functioning cells, PARP-1 enzymatic activity has been linked to the alterations in chromatin structure associated with gene expression. However, the molecular determinants for PARP-1 recruitment to specific sites in chromatin in the absence of DNA strand breaks remain obscure. Using gel shift and enzymatic footprinting assays and atomic force microscopy, we show that PARP-1 recognizes distortions in the DNA helical backbone and that it binds to three- and four-way junctions as well as to stably unpaired regions in double-stranded DNA. PARP-1 interactions with non-B DNA structures are functional and lead to its catalytic activation. DNA hairpins, cruciforms, and stably unpaired regions are all effective co-activators of PARP-1 auto-modification and poly(ADP-ribosyl)ation of histone H1 in the absence of free DNA ends. Enzyme kinetic analyses revealed that the structural features of non-B form DNA co-factors are important for PARP-1 catalysis activated by undamaged DNA. K0.5 constants for DNA co-factors, which are structurally different in the degree of base pairing and spatial DNA organization, follow the order: cruciform<or=hairpin<<loop. DNA structure also influenced the reaction rate; when a hairpin was substituted with a stably unpaired region, the maximum reaction velocity decreased almost 2-fold. These data suggest a link between PARP-1 binding to non-B DNA structures in genome and its function in the dynamics of local modulation of chromatin structure in the normal physiology of the cell.
authors.affiliation: Department of Radiation Medicine, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, D. C. 20057, USA.
authors.forename: Irina
authors.initials: I
authors.lastname: Lonskaya
authors.forename: Vladimir N
authors.initials: VN
authors.lastname: Potaman
authors.forename: Luda S
authors.initials: LS
authors.lastname: Shlyakhtenko
authors.forename: Elena A
authors.initials: EA
authors.lastname: Oussatcheva
authors.forename: Yuri L
authors.initials: YL
authors.lastname: Lyubchenko
authors.forename: Viatcheslav A
authors.initials: VA
authors.lastname: Soldatenkov
mesh_terms: D001665:Binding Sites; D001710:Biotin / Q000737:chemistry; D002384:Catalysis; D002843:Chromatin / Q000378:metabolism; D004247:DNA / Q000737:chemistry / Q000378:metabolism* / Q000648:ultrastructure*; D004305:Dose-Response Relationship, Drug; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D018625:Microscopy, Atomic Force; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization; D010957:Plasmids / Q000378:metabolism; D000071137:Poly (ADP-Ribose) Polymerase-1; D011065:Poly(ADP-ribose) Polymerases / Q000096:biosynthesis* / Q000737:chemistry*; D011485:Protein Binding; D011994:Recombinant Proteins / Q000737:chemistry; D012266:Ribose / Q000737:chemistry
chemical_list: D002843:Chromatin; D006657:Histones; D011994:Recombinant Proteins; D012266:Ribose; D001710:Biotin; D004247:DNA; C499320:PARP1 protein, human; D000071137:Poly (ADP-Ribose) Polymerase-1; D011065:Poly(ADP-ribose) Polymerases