Fluorescent nucleobase analogues for base-base FRET in nucleic acids: Synthesis, photophysics and applications
Reviewartikel, 2017

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, tC O -tC nitro , has recently been complemented with among others the adenine analogue FRET pair, qAN1-qA nitro , 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, κ 2 , 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.



B-to-Z-DNA transition

Tricyclic cytosines


Nucleic acid structure and dynamics

Quadracyclic adenines

Fluorescent base analogues


[Person ee0acd8e-b5e3-4c37-82c7-b682748f54d8 not found]

Göteborgs universitet

[Person 8f546a07-d36f-4233-b64e-79d7d8dbfdc8 not found]

Chalmers, Kemi och kemiteknik, Kemi och biokemi, Fysikalisk kemi

[Person 816c39b9-0364-4ae3-b827-f169976f8de4 not found]

Chalmers, Kemi och kemiteknik, Kemi och biokemi, Fysikalisk kemi

[Person 1ce813ce-fd8b-4550-9456-285b715f3e5f not found]

Göteborgs universitet

[Person 45da4d76-7d00-4b8c-898a-74782e12be3e not found]

Chalmers, Kemi och kemiteknik, Kemi och biokemi, Fysikalisk kemi

Beilstein Journal of Organic Chemistry

1860-5397 (ISSN)

Vol. 14 114-129


Nanovetenskap och nanoteknik (SO 2010-2017, EI 2018-)

Livsvetenskaper och teknik (2010-2018)


Fysikalisk kemi


Organisk kemi



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