A survey of physical methods for studying nuclear mechanics and mechanobiology

Abstract

It is increasingly appreciated that the cell nucleus is not only a home for DNA but also a complex material that resists physical deformations and dynamically responds to external mechanical cues. The molecules that confer mechanical properties to nuclei certainly contribute to laminopathies and possibly contribute to cellular mechanotransduction and physical processes in cancer such as metastasis. Studying nuclear mechanics and the downstream biochemical consequences or their modulation requires a suite of complex assays for applying, measuring, and visualizing mechanical forces across diverse length, time, and force scales. Here, we review the current methods in nuclear mechanics and mechanobiology, placing specific emphasis on each of their unique advantages and limitations. Furthermore, we explore important considerations in selecting a new methodology as are demonstrated by recent examples from the literature. We conclude by providing an outlook on the development of new methods and the judicious use of the current techniques for continued exploration into the role of nuclear mechanobiology.

Gradient Nanoconfinement Facilitates Binding of Transcriptional Factor NF-κB to Histone- and Protamine-DNA Complexes

“…The linear relationship between normal stress from channel wall P and volumetric strain of DNA coil Δ V / V can then be written as P = − K ·Δ V / V , where V is the relaxed volume of a DNA coil, Δ V is the volume change caused by nanoconfinement, and K is the bulk modulus. These results indicate that a DNA coil is an elastic object, and the compressive forces exerted by the nanochannel array do not cause structural changes. − …”

The mechanobiology of nuclear phase separation

“…Bulk material properties are more easily measured using active microrheological approaches, which do not rely on assumptions of thermodynamic equilibrium, and provide a direct means of interrogating the bulk material properties of the nucleus and subnuclear structures; these approaches have been reviewed in depth elsewhere. 51 Briefly, these approaches utilize force directly applied to microscopic materials and measurement of the resulting displacement [ Fig. 2(c) ].…”

ANN-aided Mechanophenotyping of Biological Cells Using AFM

“…In experimental data acquisition of cell profiles, image data can be used to note the cell geometry parameters. Here, the cell morphology can be captured using one of the promising reported techniques of combined sideway imaging and vertical light sheet illumination system, which can be integrated with AFM (Beicker et al 2018) or with side-view light-sheet fluorescence microscope imaging (Hobson et al 2021;Wang et al 2020). Subsequently, we can use ImageJ software to acquire cell parameters 𝐿, 𝐶 𝑝 , and 𝐶 𝑐𝑠 along with cell profile elevations (Graybill et al 2021).…”