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

Stassi, Stefano; Marini, Monica; Allione, Marco; Lopatin, Sergei; Marson, Domenico; Laurini, Erik; Pricl, Sabrina; Pirri, Candido Fabrizio; Ricciardi, Carlo; Di Fabrizio, Enzo

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. Intercalating molecules can significantly change the conformation of DNA. Here, the authors fabricated resonators fully composed of DNA forming bundles between microfabricated pillars to study the vibration property of the DNA bundles with/without intercalant molecules.

Nature Communications, 2019, Vol 10, Issue 1, pN.PAG

2041-1723

Academic Journal

10.1038/s41467-019-09612-0