Comparison of Different Footprinting Methodologies for Detecting Binding Sites for a Small Ligand on DNA

Bailly, Christian; Waring, Michael J.

doi:10.1080/07391102.1995.10508782

Cited by 72 publications

(64 citation statements)

References 57 publications

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“…Experiments were performed essentially as described previously (Bailly and Waring, 1995). Briefly, reactions were conducted in a total volume of 10 l. Samples (3 l) of the labeled DNA fragments were incubated with 5 l of the buffered solution containing the ligand at appropriate concentration.…”

Section: Methodsmentioning

confidence: 99%

DNA Binding and Topoisomerase I Poisoning Activities of Novel Disaccharide Indolocarbazoles

et al. 2002

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The antibiotics AT2433-A1 and AT2433-B1 are two indolocarbazole diglycosides related to the antitumor drug rebeccamycin known to stabilize topoisomerase I-DNA complexes. This structural analogy prompted us to explore the binding of four indolocarbazole diglycosides with DNA and their capacity to interfere with the DNA cleavage-reunion reaction catalyzed by topoisomerase I. The molecular basis of the drug interaction with double-stranded DNA and with purified chromatin, with particular emphasis on the role of the carbohydrate moiety, was investigated by means of complementary spectroscopic techniques, including surface plasmon resonance and electric linear dichroism. We compared the DNA binding properties, sequence recognition, and effects on topoisomerase I-mediated DNA relaxation and cleavage of AT2433-A1 bearing a 2,4-dideoxy-4-methylamino-L-xylose residue, its dechlorinated analog AT2433-B1, the diastereoisomer iso-AT2433-B1 with an inverted aminosugar residue, and compounds 5H-indolo [2,3-a]pyrrolo [3,4-c]carbazole-5,7(6H)-dione, 12-␤-D-glucopyranosyl-12,13-dihydro-6-methyl (JDC-108) and 5H-indolo[2,3-a]pyrrolo[3, 4-c]carbazole-5,7(6H)-dione, 12-(6-O-␣-D-galacto-pyranosyl-␤-Dglucopyranosyl)-12,13-dihydro-6-methyl (JDC-277) with an uncharged mono-and disaccharide, respectively. The two antibiotics AT2433-A1 and AT2433-B1 proved to be highly cytotoxic to leukemia cells and this may be a consequence of their tight intercalative binding to DNA, preferentially into GC-rich sequences as inferred from DNase I footprinting studies and surface plasmon resonance measurements. Like the diastereoisomer iso-AT2433-B1, they have no inhibitory effect on topoisomerase I, in contrast to the uncharged diglycoside JDC-277, which stimulates DNA cleavage by the enzyme mainly at TG sites, as observed with camptothecin. Cytotoxicity measurements with CEM and CEM/C2 human leukemia cell lines sensitive and resistant to camptothecin, respectively, also suggested that topoisomerase I contributes, at least partially, to the mechanism of action of the neutral diglycoside JDC-277 but not to that of the cationic AT2433 compounds. Together, the results indicate that sequence-selective DNA interaction and topoisomerase I inhibition is controlled to a large extent by the stereochemistry of the diglycoside moiety.

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Section: Methodsmentioning

confidence: 99%

DNA Binding and Topoisomerase I Poisoning Activities of Novel Disaccharide Indolocarbazoles

et al. 2002

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“…DNase I (EC 3.1.21.1) footprinting experiments were performed essentially as described previously (Bailly and Waring, 1995b). Briefly, reactions were conducted in a total volume of 10 l. Samples (3 l) of the labeled DNA fragment were incubated with 5 l of the buffer solution containing the ligand at appropriate concentration.…”

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confidence: 99%

Recognition of Specific Sequences in DNA by a Topoisomerase I Inhibitor Derived from the Antitumor Drug Rebeccamycin

et al. 1998

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We investigated the interaction with DNA of two synthetic derivatives of the antitumor antibiotic rebeccamycin: R-3, which is a potent topoisomerase I inhibitor and contains a methoxyglucose moiety appended to the indolocarbazole chromophore, and its aglycone, R-4. Spectroscopic measurements indicate that R-3 intercalates into DNA and that its carbohydrate domain contributes significantly to reinforce the affinity for DNA. Two complementary ligation assays concur that R-3, but not its aglycone counterpart, exerts a significant effect on the curvature and/or the flexibility of DNA. The sugar moiety may be responsible for preferential binding of R-3 to circular (or bent) DNA molecules as opposed to linear DNA fragments. The sequence selectivity of binding to DNA has been studied thoroughly by footprinting with DNase I and two other nucleases. The glycosylated compound is highly selective for nucleotide sequences containing GpT (ApC) and TpG (CpA) steps. The derivative lacking the sugar moiety on the indolocarbazole chromophore binds at essentially identical sites but with considerably lower affinity, so it seems that the chromophore rather than the carbohydrate is responsible for the preferential binding to sequences surrounding GpT and TpG steps. The influence of the exocyclic substituents present on the bases at the recognition sites (i.e., the 2-amino group of guanine and the 5-methyl group of thymine) was evaluated using two series of modified DNA molecules prepared by polymerase chain reaction containing inosine and/or 2,6-diaminopurine and uridine and/or 5-methylcytosine residues. The introduction of the amino group onto purine residues or the addition of a methyl group to pyrimidine residues suffices to create new drug binding sites. Therefore, unlike most DNA-binding small molecules, the rebeccamycin analogue seems to be highly sensitive to any modification of the exocyclic substituents on the bases in both the major and minor grooves of the double helix. The footprinting profiles with the different DNA fragments bear a remarkable resemblance to those determined for nogalamycin and bisnaphthalimide compounds known to recognize their preferred GpT and TpG sites via intercalation from the major groove. The unique DNA binding characteristics of the rebeccamycin analogue correlate well with its inhibitory effects on topoisomerase I .The camptothecin derivatives irinotecan (CPT-11) and topotecan recently introduced in cancer chemotherapy are arguably the best characterized topoisomerase I poisons (Pommier and Tanizawa, 1993). These drugs interfere with the breakage-rejoining reaction by stabilizing a covalent topoisomerase I/DNA intermediate (usually referred to as cleavable complex), which can be detected by the appearance of DNA strand breaks on denaturation of the protein with a detergent. So far, relatively few other drugs have been shown to promote topoisomerase I-mediated DNA cleavage. Intoplicine, saintopins, and related naphthacene-dione antibiotics as well as alkaloids such as bulgarein and cor...

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“…Evidently, the size of the footprints detected with DNase I does not vary with the number ofN-methylpyrrole residues but this is probably due to the inherent inaccuracy of the enzyme in defining the exact size of drug binding sites. There exists a general consensus that DNase I detects sequence-specific interactions between drugs and DNA with high sensitivity but tends to overestimate the size of the binding sites (discussed in Bailly & Waring, 1995a). Affinity cleaving studies using oligopyrrolecarboxamides (containing up to six N-methylpyrrolecarboxamide residues) linked to an EDTA-Fe ll group have revealed that the size of the drug binding site is directly proportional to the number of amide units in the molecule (Youngquist & Dervan, 1985).…”

Section: Antiviral Chemistryand Chemotherapy 8(3)mentioning

confidence: 99%

“…The PCR protocol used to incorporate inosine and 2,6-diaminopurine (DAP) residues into DNA has been recently described (Bailly & Waring, 1995a). Briefly, PCR reaction mixtures contained 10 ng of tyrT (A93 …”

Section: Preparation and Labelling Of Dna Fragments Containing Modifimentioning

confidence: 99%

Biological activity and DNA Sequence Specificity of Synthetic Carbamoyl Analogues of Distamycin

Alfieri

Animati

Arcamone

et al. 1997

Antivir Chem Chemother

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A new penta(N-methylpyrrole carboxamide) analogue of the antibiotic distamycin has been synthesized in which the N-terminal formylamino group was replaced by a carbamoyl moiety. It was substantially more stable than distamycin in aqueous solution and bound to DNA with about the same affinity constant. It had an exemplary margin of selectivity against herpes simplex virus type 1-infected HEp-2 cells in culture compared to uninfected control cells, and was equipotent with distamycin. For comparison, data for analogues containing fewer N-methylpyrrole carboxamide units and/or lacking the carbamoyl replacement are presented. Extensive DNase I footprinting experiments were conducted and revealed that all the distamycin analogues bound to AT-rich nucleotide sequences in three different restriction fragments, irrespective of how many pyrrole rings or which terminal moiety they contained. However, the relative strength of footprints differed significantly among the various compounds, though the apparent size of the binding site did not. With semi-synthetic DNA containing inosine and 2,6-diaminopurine residues in place of guanosine and adenine, respectively, the compounds recognized new binding sites composed of IC-rich clusters and were excluded from binding to their canonical sites. This showed that the process of specific sequence recognition was critically dominated by the placement of the purine 2-amino group in the minor groove of the double helix.

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Comparison of Different Footprinting Methodologies for Detecting Binding Sites for a Small Ligand on DNA

Cited by 72 publications

References 57 publications

DNA Binding and Topoisomerase I Poisoning Activities of Novel Disaccharide Indolocarbazoles

DNA Binding and Topoisomerase I Poisoning Activities of Novel Disaccharide Indolocarbazoles

Recognition of Specific Sequences in DNA by a Topoisomerase I Inhibitor Derived from the Antitumor Drug Rebeccamycin

Biological activity and DNA Sequence Specificity of Synthetic Carbamoyl Analogues of Distamycin

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