Sequence-specific intercalating agents: intercalation at specific sequences on duplex DNA via major groove recognition by oligonucleotide-intercalator conjugates.

Abstract

An acridine derivative was covalently linked to the 5' end of a homopyrimidine oligonucleotide. Specific binding to a homopurine homopyrimidine sequence of duplex DNA was demonstrated by spectroscopic studies (absorption and fluorescence) and by "footprinting" experiments with a copper phenanthroline chelate used as an artificial nuclease. A hypochromism and a red shift of the acridine absorption were observed. Triple-helix formation was also accompanied by a hypochromism in the ultraviolet range. The fluorescence of the acridine ring was quenched by a stacking interaction with a GC base pair adjacent to the homopurine-homopyrimidine target sequence. The intercalating agent strongly stabilized the complex formed by the oligopyrimidine with its target duplex sequence. Cytosine methylation further increased the stability of the complexes. Footprinting studies revealed that the oligopyrimidine binds in a parallel orientation with respect to the homopurine-containing strand of the duplex. The intercalated acridine extended by 2 base pairs the region of the duplex protected by the oligopyrimidine against degradation by the nuclease activity of the copper phenanthroline chelate. Random intercalation of the acridine ring was lost due to the repulsive effect of the negatively charged oligonucleotide tail. Intercalation occurred only at those double-stranded sequences where the homopyrimidine oligonucleotide recognized the major groove of duplex DNA.

Prediction of the stability of DNA triplexes.

“…4B), with the exception of affinity cleavage data, even though the ionic conditions are not uniform. In many thermal melting and calorimetric experiments, we are able to predict the melting temperature (21,23,(26)(27)(28) within 6°C, only slightly worse than the members of our data set (Fig. 4B). Once again, the model shows no apparent bias in GC content or pH.…”

Interactions of cryptolepine and neocryptolepine with unusual DNA structures

“…At least three classes of triplexes exist which differ in sequence composition and relative orientations of the phosphodiester backbone of the third strand [14]. Nevertheless, triplex stability under physiological conditions is relatively low and this limitation led to the design of small molecules that interact with the triplex and stabilize it [15] or of chemical modifications that increase the affinity of the third strand for its target [16].…”

Inhibition of aromatase expression by a psoralen‐linked triplex‐forming oligonucleotide targeted to a coding sequence

“…Binding affinity can be increased by covalently linking third strand ODNs to intercalating groups such as acridine [4] or psoralens [5,6]. The latter are photoactive intercalating groups which on irradiation at 320-400 nm form stable covalent adducts with pyrimidine bases, preferably thymine, at one or both ends of the psoralen molecule.…”