Category Archives: Publicaciones

Nanorheology of living cells measured by AFM-based force–distance curves

Pablo D. Garcia, Carlos R. Guerrero and Ricardo Garcia

Abstract: Mechanobiology aims to establish functional relationships between the mechanical state of a living a cell
and its physiology. The acquisition of force–distance curves with an AFM is by far the dominant method to characterize the nanomechanical properties of living cells. However, theoretical simulations have shown that the contact mechanics models used to determine the Young’s modulus from a force–distance curve could be off by a factor 5 from its expected value. The semi-quantitative character arises from the lack of a theory that integrates the AFM data, a realistic viscoelastic model of a cell and its finitethickness. Here, we develop a method to determine the mechanical response of a cell from a force–distance curve. The method incorporates bottom-effect corrections, a power-law rheology model and the deformation history of the cell. It transforms the experimental data into viscoelastic parameters of the cell as a function of the indentation frequency. The quantitative agreement obtained between the experiments performed on living fibroblast cells and the analytical theory supports the use of force–distance curves to measure the nanorheological properties of cells.

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Double-stranded RNA bending by AU-tract sequences

Alberto Marin-Gonzalez, Clara Aicart-Ramos, Mikel Marin-Baquero, Alejandro Martín-González, Maarit Suomalainen, Abhilash Kannan, J. G. Vilhena, Urs F. Greber, Fernando Moreno-Herrero and Rubén Pérez.

Abstract: Sequence-dependent structural deformations of the DNA double helix (dsDNA) have been extensively
studied, where adenine tracts (A-tracts) provide a striking example for global bending in the molecule. In
contrast to dsDNA, much less is known about how the nucleotide sequence affects bending deformations
of double-stranded RNA (dsRNA). Using all-atom microsecond long molecular dynamics simulations we
found a sequence motif consisting of alternating adenines and uracils, or AU-tracts, that bend the dsRNA
helix by locally compressing the major groove. We experimentally tested this prediction using atomic force
microscopy (AFM) imaging of long dsRNA molecules containing phased AU-tracts. AFM images revealed a
clear intrinsic bend in these AU-tracts molecules, as quantified by a significantly lower persistence length
compared to dsRNA molecules of arbitrary sequence. The bent structure of AU-tracts here described might
play a role in sequence-specific recognition of dsRNAs by dsRNA-interacting proteins or impact the folding
of RNA into intricate tertiary and quaternary structures.

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