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Fluorescent nucleobase analogues for base-base FRET in nucleic acids: Synthesis, photophysics and applications

Journal article
Authors Mattias Bood
Sangamesh Sarangamath
Moa S. Wranne
Morten Grøtli
Marcus Wilhelmsson
Published in Beilstein Journal of Organic Chemistry
Volume 14
Pages 114-129
ISSN 1860-5397
Publication year 2017
Published at Department of Chemistry and Molecular Biology
Pages 114-129
Language en
Keywords B-to-Z-DNA transition, Fluorescent base analogues, FRET, Netropsin, Nucleic acid structure and dynamics, Quadracyclic adenines, Tricyclic cytosines, Z-DNA
Subject categories Biochemistry and Molecular Biology, Organic Chemistry


Forster resonance energy transfer (FRET) between a donor nucleobase analogue and an acceptor nucleobase analogue, base-base FRET, works as a spectroscopic ruler and protractor. With their firm stacking and ability to replace the natural nucleic acid bases inside the base-stack, base analogue donor and acceptor molecules complement external fluorophores like the Cy-, Alexa- and ATTO-dyes and enable detailed investigations of structure and dynamics of nucleic acid containing systems. The first base-base FRET pair, tCO-tCnitro, has recently been complemented with among others the adenine analogue FRET pair, qAN1-qAnitro, increasing the flexibility of the methodology. Here we present the design, synthesis, photophysical characterization and use of such base analogues. They enable a higher control of the FRET orientation factor, κ2, have a different distance window of opportunity than external fluorophores, and, thus, have the potential to facilitate better structure resolution. Netropsin DNA binding and the B-to-Z-DNA transition are examples of structure investigations that recently have been performed using base.base FRET and that are described here. Base-base FRET has been around for less than a decade, only in 2017 expanded beyond one FRET pair, and represents a highly promising structure and dynamics methodology for the field of nucleic acids. Here we bring up its advantages as well as disadvantages and touch upon potential future applications. © 2018 Bood et al.

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