Quantification of topo II-mediated DNA cleavage in the presence of TFO–drug conjugates

<p><b>Copyright information:</b></p><p>Taken from "Molecular basis of the targeting of topoisomerase II-mediated DNA cleavage by VP16 derivatives conjugated to triplex-forming oligonucleotides"</p><p>Nucleic Acids Research 2006;34(6):1900-1911.</p><p>Published online 5 Apr 2006</p><p>PMCID:PMC1447649.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> The analysis was as in and the gels were quantified after normalization relative to total radioactivity loaded. () Scheme showing the enhanced cleavage site of each conjugate: the 5′ conjugates are depicted in green as the corresponding cleavage site a; the 3′ 16TFO conjugates are depicted in red as the corresponding cleavage site f; the 3′ 20TFO conjugates are depicted in blue as the corresponding cleavage site g. The other topo II-mediated DNA cleavage sites described in the text are also labeled with letters. () Quantification of the specific cleavage for 20TFO-L- on both strands compared to free 20TFO-L. The cleavage intensity was normalized to the cleavage intensity of the free drug (at 1 µM) on a logarithmic scale at each cleavage site. The oligopyrimidine strand is in gray and the oligopurine strand is in black, the conjugate in filled bars and the 20TFO-L alone in hatched bars. () Specific cleavage intensities of the conjugates on the oligopyrimidine-containing strand of the duplex (Y). The 5′ 16TFO conjugates are depicted in light green (hatched bars -L-16TFO, squares -L-16TFO, horizontal bars -L-16TFO, vertical bars -L-16TFO), the 5′ 20TFO conjugates are depicted in dark green (hatched bars -L-20TFO, vertical bars -L-20TFO), the 3′ 16TFO conjugates are in red [hatched bars 16TFO-L-, squares 16TFO-L-, horizontal bars 16TFO-L-, vertical bars 16TFO-L-, crosses 16TFO-L-(4)] and the 3′ 20TFO ones are in blue [hatched bars 20TFO-L-, vertical bars 20TFO-L-, crosses 20TFO-L-(4), dots 20TFO-L-(4)]