Cooperative effects on the compaction of DNA fragments by the nucleoid protein H-NS and the crowding agent PEG probed by Magnetic Tweezers

Cristofalo, Matteo; Marrano, Claudia Adriana; Salerno, Domenico; Corti, Roberta; Cassina, Valeria; Mammola, A.; Sclavi, Bianca; Lagomarsino, Marco Cosentino; Mantegazza, Francesco

doi:10.1016/j.bbagen.2020.129725

Cited by 11 publications

(15 citation statements)

References 79 publications

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“…First, mass conservation implies that as FUS coated DNA is progressively extracted from the condensate, the amount of material in the FUS-dsDNA co-condensate should decrease by corresponding amounts. Second, the dissolution of FUS-dsDNA co-condensates should occur at a constant DNA tension, similar to the constant temperature observed for the transition between liquid and gaseous water (Cristofalo et al ., 2020; Quail et al ., 2020).…”

Section: Resultssupporting

confidence: 56%

“…We speculate that FUS can form dynamic co-condensates with ssDNA because the association of FUS with ssDNA generates a self-interacting polymer which undergoes a globular collapse to form a liquid-like FUS-DNA co-condensate (Halperin and Goldbart, 2000; Polotsky et al ., 2010; Cristofalo et al ., 2020). Here, FUS-FUS or additional FUS-DNA interactions could act like a ‘molecular glue’ when two FUS-coated ssDNA fragments meet, which would prevent their dissociation.…”

Section: Resultsmentioning

confidence: 99%

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Co-condensation of proteins with single- and double-stranded DNA

Renger

Morín

Lemaitre

et al. 2021

Preprint

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SummaryBiomolecular condensates provide distinct compartments that can localize and organize biochemistry inside cells. Recent evidence suggests that condensate formation is prevalent in the cell nucleus. To understand how different components of the nucleus interact during condensate formation is an important challenge. In particular, the physics of co-condensation of proteins together with nucleic acids remains elusive. Here, we use optical tweezers to study how the prototypical prion-like protein Fused-in-Sarcoma (FUS) forms liquid-like assemblies in vitro, by co-condensing together with individual DNA molecules. Through progressive DNA unpeeling, buffer exchange and force measurements, we show that FUS adsorbing in a single layer on DNA effectively generates a sticky FUS-DNA polymer that can collapse to form a liquid-like FUS-DNA co-condensate. Condensation occurs at constant DNA tension for double-stranded DNA, which is a signature of phase separation. We suggest that co-condensation mediated by protein adsorption on nucleic acids is an important mechanism for intracellular compartmentalization.

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Section: Resultssupporting

confidence: 56%

Section: Resultsmentioning

confidence: 99%

Co-condensation of proteins with single- and double-stranded DNA

Renger

Morín

Lemaitre

et al. 2021

Preprint

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“…Screening negative charges with NaCl reduces the Debye length, favoring closer proximity between molecules or nanoparticles. As a crowding agent, PEG acts by different mechanisms but has the same effect . The selection of PEG8000 in the investigation was based on two reasons.…”

Section: Resultsmentioning

confidence: 99%

Combining Dense Au Nanoparticle Layers and 2D Surface-Enhanced Raman Scattering Arrays for the Identification of Mutant Cyanobacteria Using Machine Learning

et al. 2022

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We report the crowding of Au nanoparticles (Au NPs) on a surface-enhanced Raman scattering (SERS) 2D array substrate with high nanoparticle surface coverage in a combined approach for the identification of cyanobacteria with machine learning. By simply using the screening effect of NaCl, the crowding effect of PEG to overcome the repulsion between nanoparticles, and different dithiol chain lengths during the deposition process of Au NPs on a substrate, we provide a general approach to increase the deposition density of nanoparticles on the films over nanodisk-array SERS substrates. The optimized substrate was subsequently utilized for the discrimination of wild-type (WT) and mutant cyanobacteria using SERS and machine learning methods (principal component analysis, logistic model, Gaussian naïve Bayes model, K-nearest-neighbor model, and a support vector classifier model with radial basis function). The best performance to discriminate between WT and mutant cyanobacteria was achieved by using the support vector classifier (SVC) with a positive rate as high as 97% using five repeat tests for the congeneric cells. These results indicate that highly sensitive SERS substrates, in combination with efficient data analysis, can be employed in mutant identification by SERS, enabling high-throughput screening in the current biological research.

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“…36,37 The rationalization behind the DNA compaction by the neutral polymer PEG is that, highly charged DNA in aqueous solutions is thought to make thermodynamically unfavourable interactions with the polymer. 38 As a result, when PEG is added, the solvent character for DNA alters, initiating the attraction between different segments of DNA. 39 As a consequence, the abrupt contraction of the DNA coil, known as, "coil-globule transition" takes place at a critical PEG concentration.…”

Section: Estimating the Interaction Between Dna And Condensation Agen...mentioning

confidence: 99%

DNA compaction enhances the sensitivity of fluorescence-based nucleic acid assays: a game changer in point of care sensors?

Sudarsan

Prabhu

Prasad

et al. 2023

Analyst

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Cooperative effects on the compaction of DNA fragments by the nucleoid protein H-NS and the crowding agent PEG probed by Magnetic Tweezers

Cited by 11 publications

References 79 publications

Co-condensation of proteins with single- and double-stranded DNA

Co-condensation of proteins with single- and double-stranded DNA

Combining Dense Au Nanoparticle Layers and 2D Surface-Enhanced Raman Scattering Arrays for the Identification of Mutant Cyanobacteria Using Machine Learning

DNA compaction enhances the sensitivity of fluorescence-based nucleic acid assays: a game changer in point of care sensors?

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