Getting DNA and RNA out of the dark with 2CNqA: a bright adenine analogue and interbase FRET donor
Journal article, 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.

Author

Anna Wiktoria Wypijewska Del Nogal

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry

Anders Foller Füchtbauer

Chalmers, Chemistry and Chemical Engineering

University of Gothenburg

Mattias Bood

University of Gothenburg

AstraZeneca AB

Jesper Nilsson

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry

Moa Sandberg Wranne

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry

Sangamesh Sarangamath

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry, Physical Chemistry

Pauline Pfeiffer

Chalmers, Biology and Biological Engineering, Chemical Biology

Vinoth Sundar Rajan

Chalmers, Biology and Biological Engineering, Chemical Biology

Afaf El-Sagheer

Suez University

Anders Dahlén

AstraZeneca AB

Tom Brown

University of Oxford

Morten Grötli

University of Gothenburg

Marcus Wilhelmsson

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry

Nucleic Acids Research

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

Vol. 48 14 7640-7652

Areas of Advance

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

Health Engineering

Subject Categories

Physical Chemistry

Biochemistry and Molecular Biology

Organic Chemistry

Roots

Basic sciences

DOI

10.1093/nar/gkaa525

PubMed

32558908

More information

Latest update

11/22/2020