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Elucidating the mechanism of the considerable mechanical stiffening of DNA induced by the couple Zn2+/Calix[4]arene-1,3-O-diphosphorous acid

Abstract : The couple Calix[4]arene-1,3-O-diphosphorous acid (C4diP) and zinc ions (Zn 2+) acts as a synergistic DNA binder. Silicon NanoTweezer (SNT) measurements show an increase in the mechanical stiffness of DNA bundles by a factor of >150, at Zn 2+ to C4diP ratios above 8, as compared to Zinc alone whereas C4diP alone decreases the stiffness of DNA. Electroanalytical measurements using 3D printed devices demonstrate a progression of events in the assembly of C4diP on DNA promoted by zinc ions. A mechanism at the molecular level can be deduced in which C4diP initially coordinates to DNA by phosphate-phosphate hydrogen bonds or in the presence of Zn 2+ by Zn 2+ bridging coordination of the phosphate groups. Then, at high ratios of Zn 2+ to C4diP, interdigitated dimerization of C4diP is followed by cross coordination of DNA strands through Zn 2+ /C4diP inter-strand interaction. The sum of these interactions leads to strong stiffening of the DNA bundles and increased inter-strand binding. DNA is one of the key bio-polymers in life, encoding the information required to build organisms. Defects in DNA can occur either via natural mutations or through external damage 1. Such defects are the cause of a vast range of diseases, from Huntington's disease to cancer, although some mutations may be beneficial 2. In recent years, the rise of artificial nanostructures based on DNA often coupled to metal ions, has been pioneered by Seeman 3. Artificial DNA binders present a great interest in the biomedical field 4. They can be used in various ways, such as the transportation of DNA through the cell membrane in transfection or gene therapy 5 for blocking a specific DNA sequence to avoid the transcription of a specific gene 6 or arresting DNA replication in cancer treatment 7. The calix[n]arenes, are well known for their ability to interact with a wide range of biomolecules including amino acids, nucleotides, surfactants, proteins and DNA 8 , leading to a wide panoply of biological applications 9. Cationic calix[n]arene derivatives have been reported to be efficient DNA binders 10. However, such derivatives present several drawbacks in biology, including toxicity due to the destabilization of cellular membranes possessing negative potential or non-specific electrostatic aggregation by negatively charged DNA 11. Protein ligands of DNA (finger zinc proteins, transcription factors, nucleases) interact mainly through conjoint coordination
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Yannick Tauran, Mehmet Tarhan, Laurent Mollet, Jean Gerves, Momoko Kumemura, et al.. Elucidating the mechanism of the considerable mechanical stiffening of DNA induced by the couple Zn2+/Calix[4]arene-1,3-O-diphosphorous acid. Scientific Reports, Nature Publishing Group, 2018, 8 (1), pp.Article number: 1226. ⟨10.1038/s41598-018-19712-4⟩. ⟨hal-02105863⟩



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