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

Bood, MattiasGothenburg University,Göteborgs universitet,Institutionen för kemi och molekylärbiologi,Department of Chemistry and Molecular Biology,University of Gothenburg (författare)

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.

Sarangamath, Sangamesh,1992Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)sansar (författare)
Sandberg Wranne, Moa,1986Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)moasan (författare)
Grøtli, Morten,1966Gothenburg University,Göteborgs universitet,Institutionen för kemi och molekylärbiologi,Department of Chemistry and Molecular Biology,University of Gothenburg(Swepub:cth)grotli (författare)
Wilhelmsson, Marcus,1974Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)mawi (författare)
Göteborgs universitetInstitutionen för kemi och molekylärbiologi (creator_code:org_t)

Ingår i:Beilstein Journal of Organic Chemistry: Beilstein Institut14, s. 114-1291860-5397

Av författaren/redakt...: Bood, Mattias; Sarangamath, San ...; Sandberg Wranne, ...; Grøtli, Morten, ...; Wilhelmsson, Mar ...

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