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

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 e...

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Autores principales: Wypijewska del Nogal, Anna, Füchtbauer, Anders F, Bood, Mattias, Nilsson, Jesper R, Wranne, Moa S, Sarangamath, Sangamesh, Pfeiffer, Pauline, Rajan, Vinoth Sundar, El-Sagheer, Afaf H, Dahlén, Anders, Brown, Tom, Grøtli, Morten, Wilhelmsson, L Marcus
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7641321/
https://www.ncbi.nlm.nih.gov/pubmed/32558908
http://dx.doi.org/10.1093/nar/gkaa525
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author Wypijewska del Nogal, Anna
Füchtbauer, Anders F
Bood, Mattias
Nilsson, Jesper R
Wranne, Moa S
Sarangamath, Sangamesh
Pfeiffer, Pauline
Rajan, Vinoth Sundar
El-Sagheer, Afaf H
Dahlén, Anders
Brown, Tom
Grøtli, Morten
Wilhelmsson, L Marcus
author_facet Wypijewska del Nogal, Anna
Füchtbauer, Anders F
Bood, Mattias
Nilsson, Jesper R
Wranne, Moa S
Sarangamath, Sangamesh
Pfeiffer, Pauline
Rajan, Vinoth Sundar
El-Sagheer, Afaf H
Dahlén, Anders
Brown, Tom
Grøtli, Morten
Wilhelmsson, L Marcus
author_sort Wypijewska del Nogal, Anna
collection PubMed
description 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 qA(nitro) and tC(nitro), and demonstrate that these FRET pairs enable conformation studies of DNA and RNA.
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spelling pubmed-76413212020-11-10 Getting DNA and RNA out of the dark with 2CNqA: a bright adenine analogue and interbase FRET donor Wypijewska del Nogal, Anna Füchtbauer, Anders F Bood, Mattias Nilsson, Jesper R Wranne, Moa S Sarangamath, Sangamesh Pfeiffer, Pauline Rajan, Vinoth Sundar El-Sagheer, Afaf H Dahlén, Anders Brown, Tom Grøtli, Morten Wilhelmsson, L Marcus Nucleic Acids Res Chemical Biology and Nucleic Acid Chemistry 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 qA(nitro) and tC(nitro), and demonstrate that these FRET pairs enable conformation studies of DNA and RNA. Oxford University Press 2020-06-19 /pmc/articles/PMC7641321/ /pubmed/32558908 http://dx.doi.org/10.1093/nar/gkaa525 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Chemical Biology and Nucleic Acid Chemistry
Wypijewska del Nogal, Anna
Füchtbauer, Anders F
Bood, Mattias
Nilsson, Jesper R
Wranne, Moa S
Sarangamath, Sangamesh
Pfeiffer, Pauline
Rajan, Vinoth Sundar
El-Sagheer, Afaf H
Dahlén, Anders
Brown, Tom
Grøtli, Morten
Wilhelmsson, L Marcus
Getting DNA and RNA out of the dark with 2CNqA: a bright adenine analogue and interbase FRET donor
title Getting DNA and RNA out of the dark with 2CNqA: a bright adenine analogue and interbase FRET donor
title_full Getting DNA and RNA out of the dark with 2CNqA: a bright adenine analogue and interbase FRET donor
title_fullStr Getting DNA and RNA out of the dark with 2CNqA: a bright adenine analogue and interbase FRET donor
title_full_unstemmed Getting DNA and RNA out of the dark with 2CNqA: a bright adenine analogue and interbase FRET donor
title_short Getting DNA and RNA out of the dark with 2CNqA: a bright adenine analogue and interbase FRET donor
title_sort getting dna and rna out of the dark with 2cnqa: a bright adenine analogue and interbase fret donor
topic Chemical Biology and Nucleic Acid Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7641321/
https://www.ncbi.nlm.nih.gov/pubmed/32558908
http://dx.doi.org/10.1093/nar/gkaa525
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