Role of Tensile Stress in DNA Nanoresonators for Epigenetic Studies

Creators: Legittimo, Francesca; Marini, Monica; Stassi, Stefano; Tortello, Mauro; Sader, John E.¹; Ashby, Paul D.; Rad, Behzad; Ralston, Corie Y.; Di Fabrizio, Enzo; Ricciardi, Carlo

1. California Institute of Technology

Abstract

The evaluation of epigenetic features such as DNA methylation is becoming increasingly important in many biochemical processes like gene expression and transcription as well as in several diseases like schizophrenia or diabetes. Here, we report that self-assembled nanomechanical resonators entirely composed of DNA molecules can be used to explore gross changes in DNA methylation levels (0–25–50%), while careful control of tensile stress is needed to reduce the variability of resonance frequency for rigorous quantification. The effect of the tensile stress retained by the suspended DNA nanoresonators on the application of the technique is extensively explored using a combination of laser Doppler vibrometry and atomic force spectroscopy. DNA nanoresonators are real-time, label-free sensors and could avoid chemical functionalization and sample amplification. Therefore, they may represent in the future a key complementary routine tool for global DNA methylation analysis needed to evaluate the consequences of environmental stresses on the human genome.

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Acknowledgement

This publication is part of the project NODES, which has received funding from the MUR–M4C2 1.5 of PNRR with grant agreement no. ECS00000036. This research has been cofunded by European Union - Next Generation EU Programme within the projects SOE_0000167 and P2022CBHZK (PRIN 2022 PNRR). Work at the Molecular Foundry was supported by the Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

Contributions

F.L. and C.R. conceived the experiment. F.L., M.M., B.R., and C.Y.R. managed the preparation of DNA bundles. F.L. performed all of the measurements. Nanomechanical data were analyzed by S.S., E.D.F., and C.R. AFM data were analyzed by P.D.A. J.E.S. provided the theoretical interpretation of AFM force curves. F.L. wrote the draft and all authors contributed to finalizing the manuscript.

Data Availability

Graphical representation of DNA bundles on SHS; additional experimental results: diameter distribution, modal ratios, AFM procedures and data analysis, and analysis of thermomechanical fluctuations in DNA bundles; and tables with all of the data (PDF)

Conflict of Interest

The authors declare no competing financial interest.

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