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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...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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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. |
format | Online Article Text |
id | pubmed-7641321 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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