title: G-quadruplex fluorescence sensing by core-extended naphthalene diimides.
abstract: Fluorescent sensing of G-quadruplex nucleic acids (G4s) is an effective strategy to elucidate their role in vitro and in vivo. Small molecule ligands have often been exploited, producing an emission light up upon binding. Naphthalene diimides (NDIs), although potent G4 binders exhibiting red-NIR fluorophores, have only been marginally exploited, as they are usually quenched upon binding. Contrary, aggregating core-extended naphthalene diimides (cex-NDIs) proved to be effective probes.
  
  
  
  We prepared a library of eighteen cex-NDIs by organic synthesis, characterising their aggregation-dependent absorption and emission properties. Absorption and emission titrations, fluorescent intercalator displacement assay (FID) and circular dichroism (CD) analysis were performed to elucidate their behavior as G4 fluorescent sensors, selectivity and binding mode.
  
  
  
  cex-NDIs aggregate under aqueous solvents and as a result, their fluorescence is mostly quenched under physiological conditions. Upon G4 binding, they disaggregate into binding monomers, producing a fluorescent light-up with anti-parallel and hybrid G4s. Contrary, with parallel G4s a light-off was recorded. For the formers a groove-like interaction was inferred by ICD signals, while for the latter an end-stacking interaction mode was hypothesized by G4-FID data.
  
  
  
  cex-NDIs G4 sensing mechanism works via a induced disaggregation. The emission response depends on the G4 topology, which dictates the prevailing -groove or end-stacking- binding mode.
  
  
  
  This study highlights the potential of cex-NDIs as G4 fluorescent probes. Besides being readily synthesized and conveniently emitting above 600nm, they light-up upon binding to anti-parallel and hybrid G4, complementing a number of other probes' selectivity for the parallel topology. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
authors.affiliation: Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy. Electronic address: michela.zuffo01@universitadipavia.it.
authors.forename: Michela
authors.initials: M
authors.lastname: Zuffo
authors.affiliation: Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy. Electronic address: filippo.doria@unipv.it.
authors.forename: Filippo
authors.initials: F
authors.lastname: Doria
authors.affiliation: Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy. Electronic address: sil.botti89@gmail.com.
authors.forename: Silvia
authors.initials: S
authors.lastname: Botti
authors.affiliation: Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy. Electronic address: gretabergamaschi@gmail.com.
authors.forename: Greta
authors.initials: G
authors.lastname: Bergamaschi
authors.affiliation: Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy. Electronic address: mauro.freccero@unipv.it.
authors.forename: Mauro
authors.initials: M
authors.lastname: Freccero
mesh_terms: D001665:Binding Sites; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D005456:Fluorescent Dyes / Q000138:chemical synthesis / Q000378:metabolism*; D054856:G-Quadruplexes; D006151:Guanosine / Q000737:chemistry / Q000378:metabolism*; D006863:Hydrogen-Ion Concentration; D007094:Imides / Q000138:chemical synthesis / Q000378:metabolism*; D008024:Ligands; D009281:Naphthalenes / Q000138:chemical synthesis / Q000378:metabolism*; D009994:Osmolar Concentration; D012997:Solvents / Q000737:chemistry; D013050:Spectrometry, Fluorescence; D013329:Structure-Activity Relationship
chemical_list: D005456:Fluorescent Dyes; D007094:Imides; D008024:Ligands; D009281:Naphthalenes; D012997:Solvents; D006151:Guanosine; C542131:naphthalenediimide; D004247:DNA
keywords: Aggregation; Binding; Fluorescent probes; G-quadruplex sensing; Induced circular dichroism; Topology based selectivity