Sequence-directed single strand cleavage of DNA by a netropsin-flavin hybrid molecule

Abstract

In an attempt to obtain sequence specific DNA-cleaving molecules, we have synthesized a series of hybrid minor groove binders composed of a photoactiveable isoalloxazine (flavin) chromophore linked through a polymethylenic chain to a bis-pyrrolecarboxamide moiety related to netropsin. Like netropsin, the hybrid derivatives preferentially bind to A+T-rich sequences. Activation of the flavin chromophore by visible light results in the appearance of single strand breaks in the vicinity of the DNA binding site. We have further investigated the cleavage affinity properties of one of these compounds referred to as netropsin-flavin (Net-Fla) and considered as representative of the series. Net-Fla cleaves only one strand at a specific locus downstream of 5'-AAAT-3', upstream of 5'-TAAA-3' and on either side of a 5'-AAAA-3' sequence. Net-Fla cleaves both strands downstream to 5'-AATT-3'. This makes the properties of Net-Fla similar to that of a restriction endonuclease and provides additional insight into establishing the rules for the readout of B-DNA helix by non-nucleotidic compounds. Using molecular modeling, we show that Net-Fla binds to an asymmetric site in one orientation. The values of the energetic minima lie in the same order as expected from the cleavage patterns, which suggests that the oriented cleavage is a consequence of a sequence-oriented binding of Net-Fla in the DNA minor groove.

DNA Minor Groove Binders: an Overview on Molecular Modeling and QSAR Approaches

“…Later a series of mGB hybrids have been synthesized and studied, by Bouziane et al with the aim of obtaining sequence specific DNA-cleaving molecules, which require the linkage of the cleaving moiety to a DNA binding molecule [54]. Targeted cleavage of double helical polynucleotides has been attempted by several research groups through the years, and it appeared that functionalized hybrid molecules may act as artificial nucleases and can serve as models for the design of pharmacologically active molecules [55].…”

Sequence-Specific DNA Minor Groove Binders. Design and Synthesis of Netropsin and Distamycin Analogues

“…Upon photoactivation in the presence of molecular oxygen, the flavin chromophore oxidizes and generates oxy radicals capable of causing DNA breaks. The linkage of netropsin to a flavin chromophore leads to AT selective strand cleavage reaction (195,196). Quinone-netropsin hybrids (e.g., 52) have been also designed.…”

Flavin-oligonucleotide conjugates: sequence specific photocleavage of DNA

“…4 Flavin-TFOs might also be useful tools for in vitro studies: riboflavin is one of the most efficient natural photosensitizers, and has previously been shown to induce DNA oxidation 5 and selective RNA cleavage. 6 Upon irradiation, netropsin-flavin conjugates are sequence-specific DNAcleaving molecules, 7 and flavin-peptide conjugates are able to repair a cyclobutane uracil dimer incorporated into an oligonucleotide. 8 Here, we show that flavin-oligonucleotide conjugates selectively photocleave a double stranded DNA target present in the HIV-1 genome and display original DNA photosensitisation properties.…”