Lighting Up DNA with the Environment-Sensitive Bright Adenine Analogue qAN4
Journal article, 2020

The fluorescent adenine analogue qAN4 was recently shown to possess promising photophysical properties, including a high brightness as a monomer. Here we report the synthesis of the phosphoramidite of qAN4 and its successful incorporation into DNA oligonucleotides using standard solid-phase synthesis. Circular dichroism and thermal melting studies indicate that the qAN4-modification has a stabilizing effect on the B-form of DNA. Moreover, qAN4 base-pairs selectively with thymine with mismatch penalties similar to those of mismatches of adenine. The low energy absorption band of qAN4 inside DNA has its peak around 358 nm and the emission in duplex DNA is partly quenched and blue-shifted (ca. 410 nm), compared to the monomeric form. The spectral properties of the fluorophore also show sensitivity to pH; a property that may find biological applications. Quantum yields in single-stranded DNA range from 1-29 % and in duplex DNA from 1-7 %. In combination with the absorptive properties, this gives an average brightness inside duplex DNA of 275 M-1  cm-1 , more than five times higher than the most used environment-sensitive fluorescent base analogue, 2-aminopurine. Finally, we show that qAN4 can be used to advantage as a donor for interbase FRET applications in combination with adenine analogue qAnitro as an acceptor.

nucleobase analogues




base pairing


Anders Foller Füchtbauer

University of Gothenburg

Moa Sandberg Wranne

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry

Sangamesh Sarangamath

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry

Mattias Bood

AstraZeneca AB

University of Gothenburg

Afaf El-Sagheer

University of Oxford

Suez University

T. Brown

University of Oxford

Henrik Gradén

AstraZeneca AB

Morten Grötli

University of Gothenburg

Marcus Wilhelmsson

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry


2192-6506 (ISSN)

Vol. 85 2 319-326

Subject Categories

Polymer Chemistry

Physical Chemistry

Atom and Molecular Physics and Optics

Areas of Advance

Nanoscience and Nanotechnology (SO 2010-2017, EI 2018-)

Health Engineering





More information

Latest update

2/8/2021 8