Nanomechanical DNA resonators for sensing and structural analysis of DNA-ligand complexes

Stefano Stassi, Monica Marini, Marco Allione, Sergei Lopatin, Domenico Marson, Erik Laurini, Sabrina Pricl, Candido Fabrizio Pirri, Carlo Ricciardi () and Enzo Fabrizio ()
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Stefano Stassi: Politecnico di Torino, Corso Duca Degli Abruzzi, 24
Monica Marini: Politecnico di Torino, Corso Duca Degli Abruzzi, 24
Marco Allione: King Abdullah University of Science and Technology
Sergei Lopatin: King Abdullah University of Science and Technology
Domenico Marson: Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS) – DEA, University of Trieste
Erik Laurini: Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS) – DEA, University of Trieste
Sabrina Pricl: Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS) – DEA, University of Trieste
Candido Fabrizio Pirri: Politecnico di Torino, Corso Duca Degli Abruzzi, 24
Carlo Ricciardi: Politecnico di Torino, Corso Duca Degli Abruzzi, 24
Enzo Fabrizio: King Abdullah University of Science and Technology

Nature Communications, 2019, vol. 10, issue 1, 1-10

Abstract: Abstract The effect of direct or indirect binding of intercalant molecules on DNA structure is of fundamental importance in understanding the biological functioning of DNA. Here we report on self-suspended DNA nanobundles as ultrasensitive nanomechanical resonators for structural studies of DNA-ligand complexes. Such vibrating nanostructures represent the smallest mechanical resonator entirely composed of DNA. A correlative analysis between the mechanical and structural properties is exploited to study the intrinsic changes of double strand DNA, when interacting with different intercalant molecules (YOYO-1 and GelRed) and a chemotherapeutic drug (Cisplatin), at different concentrations. Possible implications of our findings are related to the study of interaction mechanism of a wide category of molecules with DNA, and to further applications in medicine, such as optimal titration of chemotherapeutic drugs and environmental studies for the detection of heavy metals in human serum.

Date: 2019
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DOI: 10.1038/s41467-019-09612-0

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