Getting DNA and RNA out of the dark with 2CNqA: a bright adenine analogue and interbase FRET donor
Artikel i vetenskaplig tidskrift, 2020

With the central role of nucleic acids there is a need for development of fluorophores that facilitate the visualization of processes involving nucleic acids without perturbing their natural properties and behaviour. Here, we incorporate a new analogue of adenine, 2CNqA, into both DNA and RNA, and evaluate its nucleobase-mimicking and internal fluorophore capacities. We find that 2CNqA displays excellent photophysical properties in both nucleic acids, is highly specific for thymine/uracil, and maintains and slightly stabilises the canonical conformations of DNA and RNA duplexes. Moreover, the 2CNqA fluorophore has a quantum yield in single-stranded and duplex DNA ranging from 10% to 44% and 22% to 32%, respectively, and a slightly lower one (average 12%) inside duplex RNA. In combination with a comparatively strong molar absorptivity for this class of compounds, the resulting brightness of 2CNqA inside double-stranded DNA is the highest reported for a fluorescent base analogue. The high, relatively sequence-independent quantum yield in duplexes makes 2CNqA promising as a nucleic acid label and as an interbase Förster resonance energy transfer (FRET) donor. Finally, we report its excellent spectral overlap with the interbase FRET acceptors qAnitro and tCnitro, and demonstrate that these FRET pairs enable conformation studies of DNA and RNA.


Anna Wiktoria Wypijewska Del Nogal

Chalmers, Kemi och kemiteknik, Kemi och biokemi

Anders Foller Füchtbauer

Chalmers, Kemi och kemiteknik

Göteborgs universitet

Mattias Bood

Göteborgs universitet

AstraZeneca AB

Jesper Nilsson

Chalmers, Kemi och kemiteknik, Kemi och biokemi

Moa Sandberg Wranne

Chalmers, Kemi och kemiteknik, Kemi och biokemi

Sangamesh Sarangamath

Chalmers, Kemi och kemiteknik, Kemi och biokemi

Pauline Pfeiffer

Chalmers, Biologi och bioteknik, Kemisk biologi

Vinoth Sundar Rajan

Chalmers, Biologi och bioteknik, Kemisk biologi

Afaf El-Sagheer

Suez University

Anders Dahlén

AstraZeneca AB

Tom Brown

University of Oxford

Morten Grötli

Göteborgs universitet

Marcus Wilhelmsson

Chalmers, Kemi och kemiteknik, Kemi och biokemi

Nucleic Acids Research

0305-1048 (ISSN) 1362-4962 (eISSN)

Vol. 48 14 7640-7652


Nanovetenskap och nanoteknik (SO 2010-2017, EI 2018-)

Hälsa och teknik


Fysikalisk kemi

Biokemi och molekylärbiologi

Organisk kemi


Grundläggande vetenskaper





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