Et sequence-specific bulges [8,9,10], mismatches [11,12] and loops [13]. However, it is not clear whether a particular disease is linked to only one sequence-specific DNA conformation; therefore, compounds able to universally target DNA unconventional structures within a duplex section of DNA could be appealing from both a therapeutic and diagnostic point of view. Clerocidin (CL) (Fig. 1A) is a natural product isolated from Oidiodendron truncatum, initially described as a gyrase inhibitor [14,15,16]. CL was subsequently shown to target DNA ss regions while being unreactive towards the 25033180 double-helix: CL directly reacts with three-base DNA bulges, with different mechanisms depending on the exposed nucleotide. In particular, CL electrophilic groups (i.e. a strained epoxy ring and an a-ketoaldehyde function in equilibrium with its hemi-acetalic form) target i) the nucleophilic N7 of guanine (G) inducing spontaneous depurination and DNA strand cleavage [17,18], ii) the NH2 and N3 of cytosine (C) with formation of a stable condensed ring system, which is degraded to induce DNA cleavage only after hot Epigenetics alkali treatmentClerocidin Dissects DNA Secondary StructureFigure 1. Reagents used in this study. A) Chemical structure of CL. B) Schematic representation of the single-stranded (ss) regions of the oligonucleotides used, subdivided according to the secondary structure category. Double-stranded regions flanking the ss moiety are shown, because CL reactivity was assayed and compared towards oligonucleotides with both G/C and A/T-rich flanking regions. Arrows indicate the position of CL alkylation and cleavage. The size of the arrows corresponds to the degree of reactivity. doi:10.1371/journal.pone.0052994.g[19], and iii) the NH2 and N1 of adenine (A) to generate an adduct that degrades upon alkali but does not result in DNA strand scission [20]. Due to lack of strong nucleophilic sites, thymine (T) does not react with CL. The bulky diterpenoid portion of CL modulates the accessibility of the epoxide and a-ketoaldehyde reactive groups towards the DNA. Here we sought to investigate the ability of CL to target bases embedded in different DNA conformational environments, such as mismatched bases and nicked DNA, loops and hairpins. Our results showed that CL was able to react with most ss structures within a duplex DNA; however, the Epigenetics number of ss bases was important to determine 
the accessibility 1326631 of the compound to the reactive site. Therefore CL, besides being able to target a wide range of ss structures in a double helix setting, can also be used as a tool to evaluate site accessibility and folding of ss areas of the DNA within a double helix environment.Materials and Methods Clerocidin and OligonucleotidesCL was a gift of Leo Pharmaceutical Products (Ballerup, Denmark). Molar extinction coefficients were experimentally determined to be 11818 M21 cm21 for CL. Working drug solutions were obtained by diluting fresh stocks in the appropriate buffer. T4 polynucleotide kinase was purchased from Fermentas (Burlington, Canada). [c-32P]ATP was from Perkin Elmer (MA, USA), while all oligonucleotides were from Sigma Aldrich (St Louis, MO, USA). Oligonucleotides used in this study are reported in Table 1.Alkylation by Clerocidin of Single Stranded Bases in a Duplex EnvironmentAll oligonucleotides were gel-purified before use and prepared in desalted/lyophilised form. Forward oligonucleotides were 59end-labelled with [c- 32P]ATP by T4 polynucleotide kinase and were.Et sequence-specific bulges [8,9,10], mismatches [11,12] and loops [13]. However, it is not clear whether a particular disease is linked to only one sequence-specific DNA conformation; therefore, compounds able to universally target DNA unconventional structures within a duplex section of DNA could be appealing from both a therapeutic and diagnostic point of view. Clerocidin (CL) (Fig. 1A) is a natural product isolated from Oidiodendron truncatum, initially described as a gyrase inhibitor [14,15,16]. CL was subsequently shown to target DNA ss regions while being unreactive towards the 25033180 double-helix: CL directly reacts with three-base DNA bulges, with different mechanisms depending on the exposed nucleotide. In particular, CL electrophilic groups (i.e. a 
strained epoxy ring and an a-ketoaldehyde function in equilibrium with its hemi-acetalic form) target i) the nucleophilic N7 of guanine (G) inducing spontaneous depurination and DNA strand cleavage [17,18], ii) the NH2 and N3 of cytosine (C) with formation of a stable condensed ring system, which is degraded to induce DNA cleavage only after hot alkali treatmentClerocidin Dissects DNA Secondary StructureFigure 1. Reagents used in this study. A) Chemical structure of CL. B) Schematic representation of the single-stranded (ss) regions of the oligonucleotides used, subdivided according to the secondary structure category. Double-stranded regions flanking the ss moiety are shown, because CL reactivity was assayed and compared towards oligonucleotides with both G/C and A/T-rich flanking regions. Arrows indicate the position of CL alkylation and cleavage. The size of the arrows corresponds to the degree of reactivity. doi:10.1371/journal.pone.0052994.g[19], and iii) the NH2 and N1 of adenine (A) to generate an adduct that degrades upon alkali but does not result in DNA strand scission [20]. Due to lack of strong nucleophilic sites, thymine (T) does not react with CL. The bulky diterpenoid portion of CL modulates the accessibility of the epoxide and a-ketoaldehyde reactive groups towards the DNA. Here we sought to investigate the ability of CL to target bases embedded in different DNA conformational environments, such as mismatched bases and nicked DNA, loops and hairpins. Our results showed that CL was able to react with most ss structures within a duplex DNA; however, the number of ss bases was important to determine the accessibility 1326631 of the compound to the reactive site. Therefore CL, besides being able to target a wide range of ss structures in a double helix setting, can also be used as a tool to evaluate site accessibility and folding of ss areas of the DNA within a double helix environment.Materials and Methods Clerocidin and OligonucleotidesCL was a gift of Leo Pharmaceutical Products (Ballerup, Denmark). Molar extinction coefficients were experimentally determined to be 11818 M21 cm21 for CL. Working drug solutions were obtained by diluting fresh stocks in the appropriate buffer. T4 polynucleotide kinase was purchased from Fermentas (Burlington, Canada). [c-32P]ATP was from Perkin Elmer (MA, USA), while all oligonucleotides were from Sigma Aldrich (St Louis, MO, USA). Oligonucleotides used in this study are reported in Table 1.Alkylation by Clerocidin of Single Stranded Bases in a Duplex EnvironmentAll oligonucleotides were gel-purified before use and prepared in desalted/lyophilised form. Forward oligonucleotides were 59end-labelled with [c- 32P]ATP by T4 polynucleotide kinase and were.
