Molecular Recognition of Nucleic Acids: Structure and Fluorescent Probes
P.I.: Marie-Paule Teulade-Fichou
The targeting of nucleic acids for therapeutic or molecular biology purposes remains a challenge, due to the random distribution of most synthetic compounds on the complex architecture of chromatin. The recognition of DNA structure characteristics is an approach enabling to target the fixation of small molecules on strategic regions. This approach, based on the conception of specific probes constitutes the main topics of our research, organized in two directions: the structural probes, and the photoactive probes. The targeted structures are unusual (non-B) DNA conformations (quadruplex, loops), lesions (abasic sites, mismatches) and secondary structures of RNA (hairpins and pseudoknots). In fine the objectives are the detection of structures involved in pathologies and the establishement of interferences with DNA proteic machineries (repair enzymes, telomerase, telomere capping proteins).
G-quadruplex DNA ligands
G-quadruplex DNA (G4) represents a family of nucleic acid secondary that can be formed by certain guanine-rich sequences in the presence of monovalent cations and are stabilized by G- quartets. It has became apparent that G-quadruplex structures may play roles in key biological processes and can be targeted for therapeutic intervention. These structures may be involved in anticancer, antiviral and potentially anti-infectious strategies. Indeed, G-quadruplexes may have applications in areas ranging from supramolecular chemistry and nanotechnology to medicinal chemistry. The quadruplex field is now expanding at a fast rate but even if significant progresses have been made recently, it is clear that, for a fuller understanding of G- quadruplexes, better analytical tools must be developed Our goal is to provide new tools for the biologists that would help to probe and evidence quadruplex formation. However, one major issue resided in the poor selectivity of some of the first ligand generations towards quadruplex, which seriously limited their application. To make further advances in the current context, new generation of chemical tools are imperatively required that would either present new functions, exhibit selectivity for a subset of quadruplex structures and/or have interesting biological functions. In this context, we developed molecular tools along two main axis i) analogues of telomestatin a potent telomerase inhibitor and high affinity quadruplex binder ii) design of specifically tailored fluorescent probes and cross-linking ligands
Given the remarkable developments of multiphotonic microscopy, we recently turned our attention towards the design of fluorophores optimized for biphotonic absorption and compatible with the labelling of biomolecules (low molecular weight, water-solubility, chemical function for bioconjugation). Novel DNA markers have been elaborated, which combine criteria rarely met in usual markers: i) low quantum yield in the free state and red-emission with a high brightness when bound to DNA; ii) two-photon absorption cross sections 15-20-fold larger than that of usual markers iii) high photostability. The TP series represent a novel family of robust probes for optical tracking of DNA in cells by confocal and multiphotonic microscopy. (Patent WO 2008/055969 A1).