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Second-Generation Fluorescent Quadracyclic Adenine Analogues: Environment-Responsive Probes with Enhanced Brightness

Journal article
Authors B. Dumat
Mattias Bood
Moa Sandberg Wranne
Christopher P. Lawson
Anders Foller Larsen
S. Preus
J. Streling
H. Gradén
E. Wellner
Morten Grøtli
Marcus Wilhelmsson
Published in Chemistry - A European Journal
Volume 21
Issue 10
Pages 4039-4048
ISSN 0947-6539
Publication year 2015
Published at Department of Chemistry and Molecular Biology
Pages 4039-4048
Language en
Keywords Aromatic substitution , C-C coupling , Fluorescent probes , Nucleic acids , Nucleobases
Subject categories Bioorganic chemistry, Physical organic chemistry, Spectroscopy, Biophysical chemistry, Physical Chemistry, Chemical Sciences


Fluorescent base analogues comprise a group of increasingly important molecules for the investigation of nucleic acid structure, dynamics, and interactions with other molecules. Herein, we report on the quantum chemical calculation aided design, synthesis, and characterization of four new putative quadracyclic adenine analogues. The compounds were efficiently synthesized from a common intermediate through a two-step pathway with the Suzuki-Miyaura coupling as the key step. Two of the compounds, qAN1 and qAN4, display brightnesses (εΦF) of 1700 and 2300, respectively, in water and behave as wavelength-ratiometric pH probes under acidic conditions. The other two, qAN2 and qAN3, display lower brightnesses but exhibit polarity-sensitive dual-band emissions that could prove useful to investigate DNA structural changes induced by DNA-protein or -drug interactions. The four qANs are very promising microenvironment-sensitive fluorescent adenine analogues that display considerable brightness for such compounds. Polarity and pH probes: 2-Aminopurine has long been the standard for fluorescent base analogues. Four new fluorescent probes suitable for the replacement of adenine in nucleic acids are presented. Based on their high structural similarity to their parent compound, quadracyclic adenine, they have the potential to be excellent A analogues. Their improved photophysical properties also suggest that they could be significantly brighter than 2-aminopurine inside nucleic acid systems (see figure; ΦF: fluorescence quantum yield).

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