The Scope of Application of Macrocyclic Polyamines Beyond Metal Chelation

Recent advances in the use of radiometals for both imaging and therapy has spurred on the development of an original chemistry that endows radionuclide-chelating molecular cages with ever sharper physicochemical properties. Macrocyclic polyamines (MPAs) such as cyclen and DOTA are among the most frequently encountered cages for the design of new radiotracers, owing to their versatile chemistry that makes them customizable molecular tools. The idea of using MPAs for alternative purposes has recently emerged, with an eye towards benefiting from their unique topology, versatility, symmetry and water-solubility. This review summarizes strategies that have been recently implemented in which MPAs…

Transcriptome-wide identification of transient RNA G-quadruplexes in human cells

Guanine-rich RNA sequences can fold into four-stranded structures, termed G-quadruplexes (G4-RNAs), whose biological roles are poorly understood, and in vivo existence is debated. To profile biologically relevant G4-RNA in the human transcriptome, we report here on G4RP-seq, which combines G4-RNA-specific precipitation (G4RP) with sequencing. This protocol comprises a chemical crosslinking step, followed by affinity capture with the G4-specific small-molecule ligand/probe BioTASQ, and target identification by sequencing, allowing for capturing global snapshots of transiently folded G4-RNAs. We detect widespread G4-RNA targets within the transcriptome, indicative of transient G4 formation in…

Identifying three-way DNA junction-specific small-molecules

Three-way junction DNA (TWJ-DNA, also known as 3WJ-DNA) is an alternative secondary DNA structure comprised of three duplex-DNAs that converge towards a single point, termed the branch point. This point is characterized by unique geometrical properties that make its specific targeting by synthetic small-molecules possible. Such a targeting has already been demonstrated in the solid state but not thoroughly biophysically investigated in solution. Herein, a set of simple biophysical assays has been developed to identify TWJ-specific small-molecule ligands; these assays, inspired by the considerable body of work that has been reported to characterize the interactions between small-molecules an…

Biomimetic G-quartet compounds

Small-molecule affinity capture of DNA/RNA quadruplexes and their identification in vitro and in vivo through the G4RP protocol

International audience; Guanine-rich DNA and RNA sequences can fold into higher-order structures known as G-quadruplexes (or G4-DNA and G4-RNA, respectively). The prevalence of the G4 landscapes in the human genome, transcriptome and ncRNAome (non-coding RNA), collectively known as G4ome, is strongly suggestive of biological relevance at multiple levels (gene expression , replication). Small-molecules can be used to track G4s in living cells for the functional characterization of G4s in both normal and disease-associated changes in cell biology. Here, we describe biotinylated biomimetic ligands referred to as Bio-TASQ and their use as molecular tools that allow for isolating G4s through aff…

The Scope of Application of Macrocyclic Polyamines Beyond Metal Chelation

International audience; Recent advances in the use of radiometals for both imaging and therapy has spurred on the development of an original chemistry that endows radionuclide-chelating molecular cages with ever sharper physicochemical properties. Macrocyclic polyamines (MPAs) such as cyclen and DOTA are among the most frequently encountered cages for the design of new radiotracers, owing to their versatile chemistry that makes them customizable molecular tools. The idea of using MPAs for alternative purposes has recently emerged, with an eye towards benefiting from their unique topology, versatility, symmetry and water-solubility. This review summarizes strategies that have been recently i…

Front Cover: The Scope of Application of Macrocyclic Polyamines Beyond Metal Chelation (Eur. J. Org. Chem. 36/2019)

International audience

Disclosing the actual efficiency of G-quadruplex-DNA–disrupting small molecules

AbstractThe quest for small molecules that avidly bind to G-quadruplex-DNA (G4-DNA, or G4), so called G4-ligands, has invigorated the G4 research field from its very inception. Massive efforts have been invested to i- screen or design G4-ligands, ii- evaluate their G4-interacting properties in vitro through a series of now widely accepted and routinely implemented assays, and iii- use them as unique chemical biology tools to interrogate cellular networks that might involve G4s. In sharp contrast, only uncoordinated efforts at developing small molecules aimed at destabilizing G4s have been invested to date, even though it is now recognized that such molecular tools would have tremendous appl…

DNA Junction Ligands Trigger DNA Damage and Are Synthetic Lethal with DNA Repair Inhibitors in Cancer Cells.

International audience; Translocation of DNA and RNA polymerases along their duplex substrates results in DNA supercoiling. This torsional stress promotes the formation of plectonemic structures, including three-way DNA junction (TWJ), which can block DNA transactions and lead to DNA damage. While cells have evolved multiple mechanisms to prevent the accumulation of such structures, stabilizing TWJ through ad hoc ligands offer an opportunity to trigger DNA damage in cells with high level of transcription and replication, such as cancer cells. Here, we develop a series of azacryptand-based TWJ ligands, we thoroughly characterize their TWJ-interacting properties in vitro and demonstrate their…

How to untie G-quadruplex knots and why?

International audience; For over two decades, the prime objective of the chemical biology community studying G-quadruplexes (G4s) has been to use chemicals to interact with and stabilize G4s in cells to obtain mechanistic interpretations. This strategy has been undoubtedly successful, as demonstrated by recent advances. However, these insights have also led to a fundamental rethinking of G4-targeting strategies: due to the prevalence of G4s in the human genome, transcriptome, and ncRNAome (collectively referred to as the G4ome), and their involvement in human diseases, should we continue developing G4-stabilizing ligands or should we invest in designing molecular tools to unfold G4s? Here, …

CCDC 829826: Experimental Crystal Structure Determination

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CCDC 1952718: Experimental Crystal Structure Determination

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