Abstract
Molecular simulations suggest that the stability of a folded macromolecule increases in a confined space due to entropic effects. However, due to the interactions between the confined molecular structure and the walls of the container, clear-cut experimental evidence for this prediction is lacking. Here, using DNA origami nanocages, we show the pure effect of confined space on the property of individual human telomeric DNA G-quadruplexes. We induce targeted mechanical unfolding of the G-quadruplex while leaving the nanocage unperturbed. We find that the mechanical and thermodynamic stabilities of the G-quadruplex inside the nanocage increase with decreasing cage size. Compared to the case of diluted or molecularly crowded buffer solutions, the G-quadruplex inside the nanocage is significantly more stable, showing a 100 times faster folding rate. Our findings suggest the possibility of co-replicational or co-transcriptional folding of G-quadruplex inside the polymerase machinery in cells.
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Acknowledgements
This project was supported by the Japan Society for the Promotion of Science (JSPS) and the National Science Foundation (NSF) under the JSPS-NSF International Collaborations in Chemistry (ICC) (CHE-1415883, to H.S. and H.M.). H.M. acknowledges support from NSF (CHE-1609504). M.E. acknowledges supports from JSPS KAKENHI (grant nos. 24104002, 15H03837 and 16K14033).
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H.M. and H.S. conceived the project. H.M., H.S., M.E. and P.S. designed experiments. H.M. supervised mechanical unfolding experiments. H.S. and M.E. supervised origami synthesis and characterization. P.S. performed mechanical unfolding experiments and prepared origami constructs. P.S. and H.M. carried out data analyses. S.J. performed mechanical unfolding experiments. T.E. and K.H. prepared and characterized origami constructs. H.M., P.S., M.E. and H.S. co-wrote the manuscript.
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Shrestha, P., Jonchhe, S., Emura, T. et al. Confined space facilitates G-quadruplex formation. Nature Nanotech 12, 582–588 (2017). https://doi.org/10.1038/nnano.2017.29
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DOI: https://doi.org/10.1038/nnano.2017.29
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