PuSH - Publication Server of Helmholtz Zentrum München: Kinetic FRET assay to measure binding-induced conformational changes of nucleic acids.

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Higuera-Rodriguez, R.A.* ; De Pascali, M.C.* ; Aziz, M. ; Sattler, M. ; Rant, U.* ; Kaiser, W.J.*

Kinetic FRET assay to measure binding-induced conformational changes of nucleic acids.

ACS sens. 8, 4597-4606 (2023)

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The interaction of small molecules or proteins with RNA or DNA often involves changes in the nucleic acid (NA) folding and structure. A biophysical characterization of these processes helps us to understand the underlying molecular mechanisms. Here, we propose kinFRET (kinetics Förster resonance energy transfer), a real-time ensemble FRET methodology to measure binding and folding kinetics. With kinFRET, the kinetics of conformational changes of NAs (DNA or RNA) upon analyte binding can be directly followed via a FRET signal using a chip-based biosensor. We demonstrate the utility of this approach with two representative examples. First, we monitored the conformational changes of different formats of an aptamer (MN19) upon interaction with small-molecule analytes. Second, we characterized the binding kinetics of RNA recognition by tandem K homology (KH) domains of the human insulin-like growth factor II mRNA-binding protein 3 (IMP3), which reveals distinct kinetic contributions of the two KH domains. Our data demonstrate that kinFRET is well suited to study the kinetics and conformational changes of NA-analyte interactions.

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