Localized Chemical Reactivity in Double‐Stranded DNA Associated with the Intercalative Binding of Benzo[e]Pyridoindole and Benzo[g]Pyridoindole Triple‐Helix‐Stabilizing Ligands

Abstract

Footprinting with methidiumpropyl-EDTA . Fe" has been used to map the binding sites on duplex DNA of two closely related benzopyridoindole derivatives which selectively stabilize triple-helical DNA-oligonucleotide complexes. Both ligands bind to many sites, including certain oligopurine . oligopyrimidine tracts, with a weak preference for some (but not all) sequences rich in A . (BgPI) affect the reaction of dimethyl sulphate or potassium tetrachloropalladinate with the N7 of purines in the major groove, but both enhance the reactivity of purines (mostly adenine residues) towards diethylpyrocarbonate, both proximal and distal to their identified binding sites. With potassium permanganate and osmium tetroxidelpyridine, probes for the accessibility of the 5,6 double bond of pyrimidine residues, BgPI has a more potent effect than BePI and, generally, the reaction with KMnO, is more pronounced than that with OsO,. BgPI conspicuously potentiates the oxidation of pyrimidines in the triplet sequences 3'-ATA, 3'-GTA and 3'-GCA, whereas BePI enhances the reactivity of OsO, towards thymine in sequences 3'-ATYR, with no effect on cytosine residues. Thus, despite their structural homology and common lack of specific sequence preferences, the two benzopyridoindole derivatives induce distinct conformational changes in duplex DNA, not just within the sites where footprints can be detected.Keywords: drug-DNA interactions ; DNA footprinting; DNA recognition ; benzopyridoindole derivatives ; DNA triple helices.The interactions between DNA triple helices and drugs have been investigated by several groups in recent years [l-81. Part of the motivation derives from the fact that DNA triplexes are generally less stable than the corresponding duplexes, so that the stability of the triplex structure may need enhancing to increase the efficacy of the oligonucleotide. This goal can be achieved either by attaching the oligonucleotide directly to a DNA-binding agent (e.g. oligonucleotide-intercalator conjugates, [9]) or by use of a triple-helix-specific ligand (for review see [lo]).Among the most powerful triple-helix-stabilizing agents reported to date are the two benzopyridoindole derivatives 3-me- (Fig. 1) [2]. These two drugs were shown to intercalate into both DNA duplexes and triplexes but they selectively stabilize triple-

Ligand binding mode to duplex and triplex dna assessed by combining electrospray tandem mass spectrometry and molecular modeling

“…All drugs interact with the three DNA duplexes. Although intercalators usually show a preference for GC base pairs, this is not the case here, where even a small preference for AT-rich sequences is observed for some ligands, in agreement with footprinting studies [36]. The two benzopyridoindoles, 1 and 2, have the highest duplex and triplex affinities compared with the other drugs.…”

“…The benzopyridoindole (BPI) ligands 1 and 2 are representatives of the benzo-[e]pyridoindole (BePI, 1) and of the benzo[g]pyridoindole (BgPI, 2) families [33,34]. These molecules interact with duplex DNA [35], triplex DNA [34,36,37], and inhibit topoisomerases I and II [38]. Benzo-[f]pyridoquinoxaline derivatives (BPQs, 3-5) were developed to target triplex DNA more specifically [39,40], while pyridoquinoxaline derivatives (PQ, 7) served to assess the role of the extra benzo ring.…”

The effects of DNA supercoiling on G-quadruplex formation

“…Permanganate reacts with exposed thymines, by out-of-plane attack on the 5,6 double bond ( 55 ). Fully base paired thymines in B-DNA are unreactive to this probe, but it is has been widely used to detect the presence of single-stranded regions, unpaired thymines or distortions in the DNA helix ( 56 – 58 ). We therefore anticipated that it would be able to react with thymines in the loops of the quadruplexes.…”

Responses of DNA Mismatch Repair Proteins to a Stable G-Quadruplex Embedded into a DNA Duplex Structure

“…Potassium permanganate in combination with tetraethylammonium chloride was found to oxidize all mismatched or bulged T residues (including those in G4 loops) to thymine glycol by an out-of-plane attack on the 5,6 double bond and to induce DNA cleavage at these DNA sites. In contrast, thymine residues involved in Watson-Crick base pairing are not the targets of the KMnO4 attack [33,35,36].…”