Poly(ADP-ribose) polymerase-1 (PARP-1) participates in DNA cleavage and rejoining-dependent reactions, such as DNA replication, recombination and repair. Its 46 kDa N-terminal DNA-binding domain contains two putative zinc-fingers and two helix-turn-helix motifs and acts as a detector of DNA strand breaks. PARP-1 is also important in transcriptional regulation, although the determinants for its binding to undamaged genomic DNA have not been defined. Together with Dr. Slava Soldatenkov, we have shown by low-resolution mapping that PARP-1 may bind to the promoter sequences of its own gene, which include sites of potential duplex bending and easy DNA unwinding, as well as cruciform-forming regions [1]. We proposed that PARP-1 may recognize the sites where DNA helices converge at an angle, such as bent DNA and cruciforms, and/or double/single-strand DNA boundaries, such as those at double-strand breaks in DNA where only an overhang of one strand over another and/or partial DNA unpairing due to fraying ends are expected [2]. Such double/single-strand DNA boundaries also exist in the locally unpaired DNA or at the hairpin loops. Using DNase I and nuclease P1 footprinting and atomic force microscopy we have shown that PARP-1 binds to stem/loop boundaries of cruciform hairpins (Figure 1). Cleavage of the cruciform by the junction resolvase, T4 endonuclease VII, is independent of PARP-1, which indicates that PARP-1 does not bind to the four-arm junctions of the cruciform [3]. Thus, PARP-1 differs from other cruciform-binding proteins by binding to hairpin tips rather than to junctions. Furthermore, it appears that one mechanism of PARP-1 interaction with the gene regulatory sequences is by binding to the promoter-localized cruciforms. PARP-1 interactions with the non-B-DNA structures are functional: DNA hairpins, cruciforms and stably unpaired regions are all effective activators of PARP-1 auto-modification and trans-poly(ADP-ribosyl)ation of histone H1 in the absence of free DNA ends [4]. One function of such modification in undamaged cells may be local chromatin loosening to provide access to DNA for regulatory factors, thus implicating PARP-1 in fundamental processes, such as DNA replication, recombination and transcription (Figure 2).

Publications

1. Soldatenkov VA, Chasovskikh S, Potaman VN, Trofimova I, Smulson ME, Dritschilo A. (2002) Transcriptional repression by binding of poly(ADP-ribose) polymerase to promoter sequences. J Biol Chem 277: 665-670 (link to PDF).
2. Soldatenkov VA, Potaman VN (2004) DNA-binding properties of poly(ADP-ribose) polymerase: a target for anti-cancer therapy. Curr Drug Targets 5: 357-365 (request a copy)
3. Potaman VN, Shlyakhtenko LS, Oussatcheva EA, Lyubchenko YL, Soldatenkov VA (2005) Specific binding of poly(ADP-ribose) polymerase to cruciform hairpins. J Mol Biol 348: 609-615 (request a copy)
4. Lonskaya I, Potaman VN, Shlyakhtenko LS, Oussatcheva EA, Lyubchenko YL, Soldatenkov VA (2005) Regulation of poly(ADP-ribose) polymerase-1 by DNA structure-specific binding. J Biol Chem 280: 17076-17083 (link to PDF)