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Development of bright fluorescent quadracyclic adenine analogues: TDDFT-calculation supported rational design

Journal article
Authors Anders Foller Larsen
Blaise Dumat
Moa Sandberg Wranne
Christopher P. Lawson
S. Preus
Mattias Bood
Henrik Gradén
Marcus Wilhelmsson
Morten Grøtli
Published in Scientific Reports
Volume 5
Pages art. no. 12653
ISSN 2045-2322
Publication year 2015
Published at Department of Chemistry and Molecular Biology
Pages art. no. 12653
Language en
Keywords Nucleic-Acid, Photophysical Properties, Cytosine Analog, Base Analog, Pyrrolo-Dc, Nucleoside, Density, Oligonucleotides, Probes, Fluorophore
Subject categories Biochemistry and Molecular Biology, Physical Chemistry, Biophysical chemistry, Spectroscopy, Bioorganic chemistry, Physical organic chemistry


Fluorescent base analogues (FBAs) comprise a family of increasingly important molecules for the investigation of nucleic acid structure and dynamics. We recently reported the quantum chemical calculation supported development of four microenvironment sensitive analogues of the quadracyclic adenine (qA) scaffold, the qANs, with highly promising absorptive and fluorescence properties that were very well predicted by TDDFT calculations. Herein, we report on the efficient synthesis, experimental and theoretical characterization of nine novel quadracyclic adenine derivatives. The brightest derivative, 2-CNqA, displays a 13-fold increased brightness (epsilon Phi(F) = 4500) compared with the parent compound qA and has the additional benefit of being a virtually microenvironment-insensitive fluorophore, making it a suitable candidate for nucleic acid incorporation and use in quantitative FRET and anisotropy experiments. TDDFT calculations, conducted on the nine novel qAs a posteriori, successfully describe the relative fluorescence quantum yield and brightness of all qA derivatives. This observation suggests that the TDDFT-based rational design strategy may be employed for the development of bright fluorophores built up from a common scaffold to reduce the otherwise costly and time-consuming screening process usually required to obtain useful and bright FBAs.

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