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)]

The sequence of the target duplex and the TFOs, and the chemical structure of the drug–TFO 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 77 bp duplex target sequence was inserted between the BamHI and EcoRI sites of pBSK. The TFO is complementary to the oligopurine strand of the duplex and binds parallel to it. The target site is in boldface for the 20 nt TFO and is underlined for the 16 nt TFOs. , 5-methyl-2′-deoxycytidine; , 5-propynyl-2′-deoxyuridine. The structures of the VP16 derivatives-TFO conjugates used in this study are shown. The nomenclature of the conjugates is described in the Materials and Methods

Rational Design of Bisubstrate-Type Analogues as Inhibitors of DNA Methyltransferases in Cancer Cells

Aberrant DNA hypermethylation of promoter of tumor suppressor genes is commonly observed in cancer, and its inhibition by small molecules is promising for their reactivation. Here we designed bisubstrate analogues-based inhibitors, by mimicking each substrate, the <i>S</i>-adenosyl-l-methionine and the deoxycytidine, and linking them together. This approach resulted in quinazoline–quinoline derivatives as potent inhibitors of DNMT3A and DNMT1, some showing certain isoform selectivity. We highlighted the importance of (i) the nature and rigidity of the linker between the two moieties for inhibition, as (ii) the presence of the nitrogen on the quinoline group, and (iii) of a hydrophobic group on the quinazoline. The most potent inhibitors induced demethylation of <i>CDKN2A</i> promoter in colon carcinoma HCT116 cells and its reactivation after 7 days of treatment. Furthermore, in a leukemia cell model system, we found a correlation between demethylation of the promoter induced by the treatment, chromatin opening at the promoter, and the reactivation of a reporter gene

Supplementary Information from Hijacking DNA methyltransferase transition state analogues to produce chemical scaffolds for PRMTs inhibitors

NMR attribution, complementary Materials & Methods and Biological result

Supplementary Information from Hijacking DNA methyltransferase transition state analogues to produce chemical scaffolds for PRMTs inhibitors

NMR attribution, complementary Materials & Methods and Biological result