arXiv subjects

Willem Vanderlinden

Publications and source records attributed to Willem Vanderlinden.

5 recordsLinked to original sources

arXiv2026

Yeast condensin acts as a transient intermolecular crosslinker in entangled DNA

Structural-Maintenance-of-Chromosome (SMC) complexes such as condensins organise the folding of chromosomes. However, their role in modulating the entanglement of DNA and chromatin is not fully understood. To address this question, we perform single molecule and bulk characterisation of yeast condensin in entangled DNA. First, we discover that yeast condensin can proficiently bind double-stranded DNA through its hinge domain, in addition to its heads. Through bulk microrheology assays we then discover that physiological concentrations of yeast condensin increase both the viscosity and elasticity of dense solutions of lambda-DNA suggesting that condensin acts as a crosslinker in entangled DNA, stabilising entanglements rather than resolving them and contrasting the popular theoretical picture where SMCs purely drive the formation of segregated, bottle-brush-like chromosome structures. We further discover that the presence of ATP fluidifies the solution -- likely by activating loop extrusion -- but does not recover the viscosity measured in the absence of protein. Finally, we show that the observed rheology can be understood by modelling SMCs as transient crosslinkers in bottle-brush-like entangled polymers. Our findings help us to understand how SMCs affect the dynamics and entanglement of genomes.

cond-mat.soft↗

arXiv2026

The Integration Host Factor is a pH-responsive protein that switches from DNA bending to DNA bridging in acidic biofilm-like conditions

The Integration Host Factor (IHF) is a nucleoid-associated protein critical for both DNA compaction and biofilm stability. While its role in DNA packaging within the cell is well understood, its structural role in scaffolding biofilms is more puzzling and difficult to reconcile with its known DNA bending activity. Here, we investigated how IHF-DNA interactions are modulated across a pH spectrum mimicking the acidic microenvironments of bacterial biofilms. By performing all-atom calculations we discovered that low pHs lead to a change in protonation of IHF residues, which in turn exposes positively charged patches. We then conjectured that these positively charged residues could lead to intermolecular DNA bridging and tested this hypothesis through single-molecule and bulk assays. We discovered that while at physiological pH IHF mostly bends DNA, at pH < 5 there is clear evidence of IHF-mediated intermolecular crosslinking. Our results demonstrate that pH significantly modulates IHF-DNA interactions and explains the structural role played by IHF in supporting biofilm mechanics through intermolecular crosslinking.

cond-mat.soft↗

arXiv2023

Single-Molecule Morphology of Topologically Digested Olympic Networks

The kinetoplast DNA (kDNA) is the archetype of a two-dimensional Olympic network, composed of thousands of DNA minicircles and found in the mitochondrion of certain parasites. The evolution, replication and self-assembly of this structure are fascinating open questions in biology that can also inform us how to realise synthetic Olympic networks in vitro. To obtain a deeper understanding of the structure and assembly of kDNA networks, we sequenced the Crithidia fasciculata kDNA genome and performed high-resolution Atomic Force Microscopy (AFM) and analysis of kDNA networks that had been partially digested by selected restriction enzymes. We discovered that these topological perturbations lead to networks with significantly different geometrical features and morphologies with respect to the unperturbed kDNA, and that these changes are strongly dependent on the class of DNA circles targeted by the restriction enzymes. Specifically, cleaving maxicircles leads to a dramatic reduction in network size once adsorbed onto the surface, whilst cleaving both maxicircles and a minor class of minicircles yields non-circular and deformed structures. We argue that our results are a consequence of a precise positioning of the maxicircles at the boundary of the network, and we discuss our findings in the context of kDNA biogenesis, design of artificial Olympic networks and detection of in vivo perturbations.

cond-mat.soft↗

arXiv2022

Doubly Stabilized Perovskite Nanocrystal Luminescence Downconverters

Halide perovskite nanocrystals (NCs) have emerged as a promising material for applications ranging from light-emitting diodes (LEDs) to solar cells and photodetectors. Still, several issues impede the realization of the nanocrystals' full potential, most notably their susceptibility to degradation from environmental stress. This work demonstrates highly stable perovskite nanocrystals (NCs) with quantum yields as high as 95 % by exploiting a ligand-assisted copolymer nanoreactor-based synthesis. The organic ligands thereby serve a dual function by enhancing the uptake of precursors and passivating the NCs. The polymer micelles and ligands thus form a double protection system, shielding the encapsulated NCs from water-, heat- and UV-light-induced degradation. We demonstrate the optoelectronic integrability by incorporating the perovskite NCs as spectrally pure downconverters on top of a deep-blue-emitting organic LED. These results establish a way of stabilizing perovskite NCs for optoelectronics while retaining their excellent optical properties.

physics.app-ph↗

arXiv2019

Polymer Nanoreactors Shield Perovskite Nanocrystals from Degradation

Halide perovskite nanocrystals (NCs) have shown impressive advances, exhibiting optical properties that outpace conventional semiconductor NCs, such as near-unity quantum yields and ultrafast radiative decay rates. Nevertheless, the NCs suffer even more from stability problems at ambient conditions and due to moisture than their bulk counterparts. Herein, we report a strategy of employing polymer micelles as nanoreactors for the synthesis of methylammonium lead trihalide perovskite NCs. Encapsulated by this polymer shell, the NCs display strong stability against water degradation and halide ion migration. Thin films comprising these NCs exhibit a more than 15-fold increase in lifespan in comparison to unprotected NCs in ambient conditions and even survive over 75 days of complete immersion in water. Furthermore, the NCs, which exhibit quantum yields of up to 63% and tunability of the emission wavelength throughout the visible range, show no signs of halide ion exchange. Additionally, heterostructures of MAPI and MAPBr NC layers exhibit efficient Förster resonance energy transfer (FRET), revealing a strategy for optoelectronic integration.

cond-mat.mtrl-sci↗