title: Quadracyclic adenine: a non-perturbing fluorescent adenine analogue.
abstract: Fluorescent-base analogues (FBAs) comprise a group of increasingly important molecules for the investigation of nucleic acid structure and dynamics as well as of interactions between nucleic acids and other molecules. Here, we report on the synthesis, detailed spectroscopic characterisation and base-pairing properties of a new environment-sensitive fluorescent adenine analogue, quadracyclic adenine (qA). After developing an efficient route of synthesis for the phosphoramidite of qA it was incorporated into DNA in high yield by using standard solid-phase synthesis procedures. In DNA qA serves as an adenine analogue that preserves the B-form and, in contrast to most currently available FBAs, maintains or even increases the stability of the duplex. We demonstrate that, unlike fluorescent adenine analogues, such as the most commonly used one, 2-aminopurine, and the recently developed triazole adenine, qA shows highly specific base-pairing with thymine. Moreover, qA has an absorption band outside the absorption of the natural nucleobases (>300 nm) and can thus be selectively excited. Upon excitation the qA monomer displays a fluorescence quantum yield of 6.8 % with an emission maximum at 456 nm. More importantly, upon incorporation into DNA the fluorescence of qA is significantly less quenched than most FBAs. This results in quantum yields that in some sequences reach values that are up to fourfold higher than maximum values reported for 2-aminopurine. To facilitate future utilisation of qA in biochemical and biophysical studies we investigated its fluorescence properties in greater detail and resolved its absorption band outside the DNA absorption region into distinct transition dipole moments. In conclusion, the unique combination of properties of qA make it a promising alternative to current fluorescent adenine analogues for future detailed studies of nucleic acid-containing systems.
authors.affiliation: Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, 41296 Gothenburg, Sweden.
authors.forename: Anke
authors.initials: A
authors.lastname: Dierckx
authors.forename: Francois-Alexandre
authors.initials: FA
authors.lastname: Miannay
authors.forename: Nouha
authors.initials: N
authors.lastname: Ben Gaied
authors.forename: Søren
authors.initials: S
authors.lastname: Preus
authors.forename: Markus
authors.initials: M
authors.lastname: Björck
authors.forename: Tom
authors.initials: T
authors.lastname: Brown
authors.forename: L Marcus
authors.initials: LM
authors.lastname: Wilhelmsson
mesh_terms: D000225:Adenine / Q000031:analogs & derivatives / Q000138:chemical synthesis / Q000737:chemistry; D000465:Algorithms; D020029:Base Pairing; D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000187:drug effects; D005453:Fluorescence; D005456:Fluorescent Dyes / Q000138:chemical synthesis / Q000737:chemistry; D015394:Molecular Structure
chemical_list: D005456:Fluorescent Dyes; D004247:DNA; D000225:Adenine