Research topics
Our current research topics (partly covered in the following reviews: Org. Biomol. Chem., 2008, J. Nucleic Acids, 2010, Eur. J. Org. Chem. 2019, Nat. Rev. Chem. 2019 , Annu. Rep. Med. Chem. 2020, RSC Chem. Biol. 2020, Cell Chem. Biol. 2021, Nucleic Acids Res. 2022, Acc. Chem. Res. 2023 & Handbook of Chemical Biology of Nucleic Acids 2023) are divided in three main themes:
1) The study of synthetic G-quartets:
Guanine (G) is a fascinating nucleobase thanks to its highly versatile H-bond creating capability: it can be classically involved in GC base pair, under standard Watson-Crick conditions, but also in G-quartet, a cyclic array of four G held together via Hoogsteen H-bonds. Naturally occurring G-quartets have attracted recently an intensified interest for their ability to be formed intramolecularly in G-rich DNA ad RNA sequences. These G-rich DNA or RNA stretches thus give rise to corresponding G-quadruplex structures, whose stability results from the self-stacking of contiguous G-quartets. The discovery of quadruplex-forming sequences in key regions of the chromosomes or mRNA spurred investigations into the possibility of controlling the corresponding cellular events (i.e., regulation of gene expression, etc.) by the stabilization of G-quadruplex with small-molecules (so called G-quadruplex ligands).
Non-naturally occurring G-quartets, also named synthetic G-quartets (SQ), have been intensively studied, mostly for bionanotechnological applications. In sharp contrast, intramolecular synthetic G-quartets (iSQ) have been more sparingly studied. The simplest way to obtain iSQ is to assemble four G in a single scaffold, as pioneeringly demonstrated by John C. Sherman with the studies of TASQ (for template-assembled synthetic G-quartet). We have taken a further leap along that road with the synthesis of water-soluble TASQ, including DOTASQ, PorphySQ, PNADOTASQ, PNAPorphySQ, PyroTASQ, N-TASQ, BioTASQ, CyTASQ and BioCyTASQ, TriazoTASQ and BioTriazoTASQ, and the MultiTASQ series (MultiTASQ, azidoMultiTASQ and photoMultiTASQ). This water-solubility, along with their quite unique structural features (i.e. their ability to adopt alternatively an “open” (in which the guanines are independent) and a “closed” conformation (in which the guanines are involved in the SQ)), lead us to develop biologically directed applications, including the studies of our TASQ as G-quadruplex ligands, which interact with its DNA target according to a ‘like likes like’ process driven by the nature-inspired assembly of two G-quartets, one from the TASQ, the other one from the G-quadruplex. Other prototypes of TASQ, the so-called twice-as-smart quadruplex ligands (being both smart quadruplex ligands and smart fluorescent probes), were implemented to visualize both DNA and RNA quadruplexes in human cells in a straightforward and unbiased manner. Recently, biotinylated TASQ were used to fish quadruplexes out from human cells prior to be identified by sequencing (G4RP-seq & G4DP-seq protocols).
More information on DOTASQ: Chem. Commun. 2011; PorphySQ: Org. Biomol. Chem. 2012; PNADOTASQ: J. Am. Chem. Soc. 2013, Chem. Eur. J. 2013 & J. Mol. Biol 2017; PNAPorphySQ: ChemMedChem, 2014; PyroTASQ: J. Am. Chem. Soc. 2014 & Sci. Rep. 2016; N-TASQ: J. Am. Chem. Soc. 2015, Sci. Rep. 2016, Biochim. Biophys. Acta 2017, eLife 2020, Autophagy 2020, Aging 2021 & NAR Cancer 2021; BioTASQ: Nat. Commun. 2018 & Nucleic Acids Res. 2019, Nat. Protoc. 2022 & Biochimie 2023; CyTASQ & BioCyTASQ: ACS Chem. Biol. 2021 & iScience 2023; TriazoTASQ and BioTriazoTASQ: JACS Au 2022, MultiTASQ and azidoMultiTASQ: RSC Chem. Biol. 2023.
For other quadruplex ligands, see AuTMX2: Inorg. Chem. 2014; TEGPy: Org. Biomol. Chem. 2015; Pd.TEGPy: New J. Chem. 2016; and Ru(II) complexes: Chem. Eur. J. 2017.
For our brand new prototype of G4-unfolding molecule (or G4-unfolder), see PhpC: J. Am. Chem. Soc. 2021 & Chem. Commun. 2024
2) The bio-inspired catalysis:
Since the initial discovery of the catalytic capability of short DNA fragments, this peculiar pseudo-enzymatic property (termed DNAzyme) has continued to garner much interest in the scientific community because of the virtually unlimited applications in developing new molecular devices. Alongside the exponential rise in the number of DNAzyme applications in the last past years, researches aiming both deciphering its actual mechanism and finding convenient ways to improve its overall efficiency have only started to emerge. Credence has been lent to this strategy by the recent demonstration that the quadruplex-based DNAzyme proficiency can be enhanced by ATP supplements. We have made a further leap along this path, trying first of all to decipher the actual DNAzyme catalytic cycle (to gain insights into the steps the ATP may influence), and subsequently investigating in detail the influence of all the parameters that govern the catalytic efficiency.
We have also reported on the substitution of DNA pre-catalyst for TASQ, in a process that has been consequently termed TASQzyme. We indeed reported that DOTASQs are interesting biocatalyst-mimicking small molecules, since its intramolecular G-quartet fold offer a binding site to hemin, therefore paving the way for a reduction of the complexity of the DNAzyme system (neither DNA syntheses nor purification or folding steps). We also showed that DOTASQ can be used not only instead of but also along with DNA, in a quite unprecedented role of DNAzyme boosting agent. More recently, a series of applications have been developped with G4-based DNAzymes, ranging from the decontamination of waste waters (textile industry) to a quite innovative in situ photodynamic therapy (PDT) approach to treat hypoxic cancers.
See: Chem. Eur. J. 2011, J. Am. Chem. Soc. 2011, Nucleic Acids Res. 2012, Chem. Commun. 2013, Nanoscale 2014, Chem. Eur. J. 2016, Angew. Chem. Int. Ed. 2017, ACS Catal. 2018, Int. J. Biol. Macromol. 2020, Chem. Commun. 2020, Chem. Sci. 2020, CCS Chem. 2020, Chinese J. Catal. 2021, J. Chem. Theory Comput. 2021, Anal. Chem. 2022, J. Am. Chem. Soc. 2023 , ACS Catal. 2023 & Adv. Healthc. Mat. 2023.
3) The recognition of alternative DNA structures:
Many antitumor agents derive their effects through interaction with double-stranded DNA (duplex-DNA, or B-DNA). However, the success of small-molecule DNA binders as anticancer agents has been dampened by their inability to recognize specific sequences of duplex-DNA, thereby being poorly selective (and thus, responsible for serious and unwanted adverse events). This has led to the emergence of more complex molecular constructs (e.g. the conjugation of cytotoxic DNA binders to cancer-specific vectors), at the expense of simple DNA-interacting agents.
With an eye toward benefiting from the practical convenience of using small molecules as anticancer drugs, an important breakthrough came with the discovery that DNA does not solely exist as duplex-DNA (i.e. an helical architecture in which two DNA strands mutually stabilize each other in a anti-parallel fashion via Watson-Crick base-pairing) in cells: DNA may adopt locally some alternative structures like the compact duplex-DNA (or A-DNA), a duplex of inverted helicity (zigzag DNA, or Z-DNA), a triplex-DNA (hinged-DNA, or H-DNA), G-quadruplex-DNA (G4, or G-DNA) or a C-quadruplex-DNA (i-motif, or I-DNA), a three-way DNA junction (slipped DNA or S-DNA) or a four-way DNA junctions (cruciform DNA, or C-DNA), or a more complex structure gathering DNA and RNA (DNA:RNA hybrid, R-loop, or R-DNA). This discovery opens up an unprecedented and virtually unlimited playground for chemists: it indeed offers them new putative DNA targets and so, new possibilities for designing creative molecules to interact with them.
We believe that it is of utmost importance to identify small molecules selective to each sub-category of DNA aternative structures. To gain further insights into the actual biological consequences of these DNA binders, it is of crucial interest to evaluate in cellulo only compounds that display an exquisite selectivity for a unique alternative DNA structure. To this end, we need to precisely map the interactions that take place between a given molecule and an array of nonusual structures: we have developed a HTS screening assay, using oligonucleotides falling in four different DNA structure categories (duplex- and quadruplex-DNA, three- and four-way DNA junction). We have also introduced an index, the BONDS (for Branched & Other Nonusual DNAs Selectivity) index, which enables an easy quantification of the differential affinity of a molecule for a panel of alternative DNA architectures. We are now looking for new selective DNA binders.
See: Biochimie 2012, ChemBioChem 2012, Org. Biomol. Chem. 2015, Nucleic Acids Res. 2018, J. Med. Chem. 2019, J. Am. Chem. Soc. 2020 & Nucleic Acids Res. 2021