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A protein-DNA surface hydrogel mechanically reinforces the cell nucleus and protects the genome
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A protein-DNA surface hydrogel mechanically reinforces the cell nucleus and protects the genome

Ramesh Adakkattil, Pranay Mandal, Yahor Savich +7 more
August 2025
 ·
bioRxiv
 ·
DOI 
10.1101/2025.05.21.655270
94
%
Reproducible
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This paper passed independent validation.
QED's automated review checked the evidence supporting each claim, the statistical methods, and whether the results are reproducible from the data provided.

It ranks in the top 1% of preprints assessed in Biophysics this quarter.
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Why this is interesting

By showing that a pre-stressed BAF-LEM2 protein-DNA surface hydrogel actively shields DNA beyond its 65 pN melting threshold and quantitatively recapitulates nuclear mechanics in living cells, this work redefines biomolecular condensates as load-bearing genome protectors.

Author perspective

What is the most important insight, discovery, or finding from your paper that you would like other scientists to know?
“

We show that the genome is coated by a hydrogel-like surface layer assembled from chromatin and inner nuclear membrane proteins. This structure acts as a mechanical shock absorber that strengthens the nucleus, maintains its shape, and shields DNA from force-induced damage. By combining reconstitution, optical tweezers, cryo-electron microscopy, and cell biology, we reveal a previously unrecognized physical mechanism by which cells organize and mechanically safeguard their genomes. Our findings uncover a new principle of nuclear self-organization and genome protection.

”
Alexander von Appen

QED claims analysis

Summary

The nuclear envelope proteins BAF and LEM2 form a pre-stressed surface hydrogel through multivalent protein-DNA co-condensation that mechanically reinforces the nucleus by shielding DNA beyond its melting point at 65 pN and generating a load-dependent stiffening response, with disruption of this system leading to reduced nuclear mechanical integrity and increased DNA damage under mechanical stress.

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Main Claim 1 –

BAF and LEM2 phase-separate into multivalent protein–DNA co-condensates

Supporting evidence

  • BAF, LEM2 and DNA co-enrich at the nuclear envelope
Main Claim 2 –

BAF–LEM2–DNA co-condensates shield DNA beyond 65 pN melting

Supporting evidence

  • Co-condensates lower internal DNA tension via force redistribution
  • Co-condensates prevent DNA melting at high tension inside condensate
Main Claim 3 –

BAF–LEM2 assembly on stressed DNA generates tension-dependent reinforcement

Supporting evidence

  • BAF–LEM2 increases DNA stiffness without altering rest length
Main Claim 4 –

LEM2 depletion softens nuclear surface and increases nuclear asphericity

Supporting evidence

  • 14-nm nucleosome-excluding inner nuclear membrane layer supports surface hydrogel
  • LEM2 depletion increases nuclear surface area and asphericity
  • BAF depletion more strongly disrupts nuclear mechanics and morphology

Abstract

The nuclear envelope protects the genome from mechanical stress during processes such as migration, division, and compression, but how it buffers forces at the scale of DNA remains unclear. Here, we utilize optical tweezers to show that a multivalent protein–DNA co-condensate containing the nuclear envelope protein LEM2 and the DNA-binding protein BAF shield DNA beyond its melting point at 65 pN. Under load, their collective assembly induces an unconventional DNA stiffening effect that provides mechanical reinforcement, dependent on the intrinsically disordered region (IDR) of LEM2. At the nuclear surface, these components form an elastic surface hydrogel in which LEM2 IDR-IDR interactions contract the surface hydrogel relative to its relaxed state, introducing a pre-stress in the lamin network. Inside cells, this surface hydrogel model can recapitulate elastic properties of the nuclear envelope measured via AFM indentation experiments as well as nuclear morphology, using parameters obtained at the molecular scale by use of optical tweezers. Disruption of the surface hydrogel increases DNA damage and micronuclei formation during nuclear deformation. These findings reveal a load-bearing, mesoscale surface hydrogel that reinforces the nucleus and expands the functional repertoire of biomolecular condensates to include DNA protection under mechanical stress.

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