DNA transitions induced by binding of PARP-1 to cruciform structures in supercoiled plasmids

Background: Poly(ADP-ribose)polymerase-1 (PARP-1) binds to single and double-stranded breaks in DNA, but less well known is its affinity for undamaged DNA. Previously, we have shown that PARP-I also binds to the hairpin structures in DNA models. The mechanism underlying these interactions remains to be defined. Methods: We analyzed atomic force microscopy (AFM) images of complex of PARP-1 proteins with supercoiled plasmids containing cruciform structures. Using volume measurement analysis of molecules of PARP-1, we determined the numbers of PARP-I molecules interacting with supercoiled DNA plasmids containing one cruciform structure. We also determined the extent of supercoiling of plasmids. Results: Our observations show that PARP-I binds to sequences that transition from B-DNA to cruciform structures. PARP-1 is present at the ends of hairpin arms, sites containing a 4-base single-stranded DNA. Furthermore, interaction of PARP-1 with supercoiled plasmids leads to a more relaxed plasmid-DNA conformation. Conclusions: Binding of PARP-1 to cruciform DNA offers insight into possible mechanisms underlying with changes in DNA conformation. These observations may offer insight into mechanisms involving DNA conformation related to process such as DNA repair and transcription. (c) 2005 International Society for Analytical Cytology.