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A practical guide to studying G-quadruplex structures using single-molecule FRET

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Abstract

In this article, we summarize the knowledge and best practices learned from bulk and single-molecule measurements to address some of the frequently experienced difficulties in single-molecule Förster resonance energy transfer (smFRET) measurements on G-quadruplex (GQ) structures. The number of studies that use smFRET to investigate the structure, function, dynamics, and interactions of GQ structures has grown significantly in the last few years, with new applications already in sight. However, a number of challenges need to be overcome before reliable and reproducible smFRET data can be obtained in measurements that include GQ. The annealing and storage conditions, the location of fluorophores on the DNA construct, and the ionic conditions of the experiment are some of the factors that are of critical importance for the outcome of measurements, and many of these manifest themselves in unique ways in smFRET assays. By reviewing these aspects and providing a summary of best practices, we aim to provide a practical guide that will help in successfully designing and performing smFRET studies on GQ structures.

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Acknowledgements

We thank Prof. Victoria Birkedal and Prof. Michael Stone for sharing extensive information regarding their experimental protocols with us. This study was funded by the US National Institutes of Health (Grant Number 1R15GM109386 to H.B.).

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  1. Department of Physics, Kent State University, Kent, OH, 44242, USA

    Parastoo Maleki, Jagat B. Budhathoki, William A. Roy & Hamza Balci

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  1. Parastoo Maleki
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Maleki, P., Budhathoki, J.B., Roy, W.A. et al. A practical guide to studying G-quadruplex structures using single-molecule FRET. Mol Genet Genomics 292, 483–498 (2017). https://doi.org/10.1007/s00438-017-1288-2

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