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.
Författare
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 7640-7652Styrkeområden
Nanovetenskap och nanoteknik (SO 2010-2017, EI 2018-)
Hälsa och teknik
Ämneskategorier
Fysikalisk kemi
Biokemi och molekylärbiologi
Organisk kemi
Fundament
Grundläggande vetenskaper
DOI
10.1093/nar/gkaa525
PubMed
32558908