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Issue 10, 2012
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Interaction of water with the G-quadruplex loop contributes to the binding energy of G-quadruplex to protein

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Abstract

Unlike DNA duplexes that release water upon interaction with protein, the binding of DNA G-quadruplex of the thrombin-binding aptamer (TBA) to thrombin takes up water. Here, to reveal the mechanism of water uptake, we designed four mutants of TBA (ΔT3, ΔT7, ΔT9, ΔT12), in which thymine residues (T3, T7, T9 and T12) were deleted from the loop regions of TBA G-quadruplex. For the mutants the thermodynamics and the osmolyte effects on the interactions with thrombin were investigated. The mutants ΔT3, ΔT9 and ΔT12 decreased the binding constants of the G-quadruplex to thrombin. Furthermore, an osmotic stress analysis indicated that the number of water molecules binding to the complex decreased in the mutants ΔT3 and ΔT9. The decrease in the binding affinity was related to loss of binding of the loop nucleotides to water molecules. Therefore, the interaction between loops of the G-quadruplex and water molecules contributed to the binding energy of G-quadruplex to protein. Our study suggests that water binding is essential for the binding of G-quadruplex to protein.

Graphical abstract: Interaction of water with the G-quadruplex loop contributes to the binding energy of G-quadruplex to protein

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Publication details

The article was received on 16 Jun 2012, accepted on 16 Jul 2012 and first published on 16 Jul 2012


Article type: Paper
DOI: 10.1039/C2MB25234A
Citation: Mol. BioSyst., 2012,8, 2766-2770
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    Interaction of water with the G-quadruplex loop contributes to the binding energy of G-quadruplex to protein

    S. Nagatoishi and N. Sugimoto, Mol. BioSyst., 2012, 8, 2766
    DOI: 10.1039/C2MB25234A

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