Issue 7, 2021

Single-molecule fluorescence detection of a tricyclic nucleoside analogue


Fluorescent nucleobase surrogates capable of Watson–Crick hydrogen bonding are essential probes of nucleic acid structure and dynamics, but their limited brightness and short absorption and emission wavelengths have rendered them unsuitable for single-molecule detection. Aiming to improve on these properties, we designed a new tricyclic pyrimidine nucleoside analogue with a push–pull conjugated system and synthesized it in seven sequential steps. The resulting C-linked 8-(diethylamino)benzo[b][1,8]naphthyridin-2(1H)-one nucleoside, which we name ABN, exhibits ε442 = 20 000 M−1 cm−1 and Φem,540 = 0.39 in water, increasing to Φem = 0.50–0.53 when base paired with adenine in duplex DNA oligonucleotides. Single-molecule fluorescence measurements of ABN using both one-photon and two-photon excitation demonstrate its excellent photostability and indicate that the nucleoside is present to > 95% in a bright state with count rates of at least 15 kHz per molecule. This new fluorescent nucleobase analogue, which, in duplex DNA, is the brightest and most red-shifted known, is the first to offer robust and accessible single-molecule fluorescence detection capabilities.

Graphical abstract: Single-molecule fluorescence detection of a tricyclic nucleoside analogue

Supplementary files

Article information

Article type
Edge Article
17 Jul 2020
28 Dec 2020
First published
28 Dec 2020
This article is Open Access

All publication charges for this article have been paid for by the Royal Society of Chemistry
Creative Commons BY license

Chem. Sci., 2021,12, 2623-2628

Single-molecule fluorescence detection of a tricyclic nucleoside analogue

G. N. Samaan, M. K. Wyllie, J. M. Cizmic, L. Needham, D. Nobis, K. Ngo, S. Andersen, S. W. Magennis, S. F. Lee and B. W. Purse, Chem. Sci., 2021, 12, 2623 DOI: 10.1039/D0SC03903A

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