How can macromolecular crowding inhibit biological reactions? The enhanced formation of DNA nanoparticles

Hou, Sen; Trochimczyk, Piotr; Sun, Lili; Wiśniewska, Agnieszka; Kalwarczyk, Tomasz; Zhang, Xuzhu; Wielgus‐Kutrowska, Beata; Bzowska, Agnieszka; Hołyst, Robert

doi:10.1038/srep22033

Cited by 20 publications

(12 citation statements)

References 23 publications

(35 reference statements)

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“…These effects are attributed to the volume exclusion that increases the effective concentrations of the molecules participating in the reaction. On the other hand, other biological reactions show lower rates upon macromolecular crowding [19,45]. Here, we describe an effect of macromolecular crowding at the cellular level in which integrin-dependent cell adhesion is enhanced.…”

Section: Discussionmentioning

confidence: 88%

Extracellular fluid viscosity enhances liver cancer cell mechanosensing and migration

et al. 2018

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The extracellular fluid (ECF) is a crowded environment containing macromolecules that determine its characteristic density, osmotic pressure, and viscosity, which greatly differ between tissues. Precursors and products of degradation of biomaterials enhance ECF crowding and often increase its viscosity. Also, increases in ECF viscosity are related to mucin-producing adenocarcinomas. However, the effect of ECF viscosity on cells remains largely unexplored. Here we show that viscosity-enhancing polymer solutions promote mesenchymal-like cell migration in liver cancer cell lines. Also, we demonstrate that viscosity enhances integrin-dependent cell spreading rate and causes actin cytoskeleton re-arrangements leading to larger cell area, nuclear flattening, and nuclear translocation of YAP and β-catenin, proteins involved in mechanotransduction. Finally, we describe a relationship between ECF viscosity and substrate stiffness in determining cell area, traction force generation and mechanotransduction, effects that are actin-dependent only on ≤ 40 kPa substrates. These findings reveal that enhancing ECF viscosity can induce major biological responses including cell migration and substrate mechanosensing.

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Section: Discussionmentioning

confidence: 88%

Extracellular fluid viscosity enhances liver cancer cell mechanosensing and migration

et al. 2018

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“…5B). The detailed mechanism for this aggregation is of great interest since previous studies have demonstrated that macromolecular crowding could cause a phase separation that controls enzymatic activities (20,37,38). Surprisingly, this aggregation did not affect transcription rates and yields.…”

Section: Resultsmentioning

confidence: 96%

The effect of macromolecular crowding on single-round transcription by E. coli RNA polymerase

Chung

Lerner

Jin

et al. 2017

Preprint

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Biological reactions in the cellular environment differ physicochemically from those performed in dilute buffer solutions due to, in part, slower diffusion of various components in the cellular milieu, increase in their chemical activities, and modulation of their binding affinities and conformational stabilities. In vivo transcription is therefore expected to be strongly influenced by the 'crowdedness' of the cell. Previous studies of transcription under macromolecular crowding conditions have focused mainly on multiple cycles of RNAP-Promoter associations, assuming that the association is the rate-determining step of the entire transcription process. However, recent reports demonstrated that late initiation and promoter escape could be the rate-determining steps for some promoter DNA sequences. The investigation of crowding effects on these steps under single-round conditions is therefore crucial for better understanding of transcription initiation in vivo. Here, we have implemented an in vitro transcription quenched-kinetics single-molecule assay to investigate the dependence of transcription reaction rates on the sizes and concentrations of crowders. Our results demonstrate an expected slowdown of transcription kinetics due to increased viscosity, and an unexpected enhancement in transcription kinetics by large crowding agents (at a given viscosity). More importantly, the enhancement's dependence on crowder size significantly deviates from hard-sphere model (scaled-particle theory) predictions, commonly used for description of crowding effects. Our findings shed new light on how enzymatic reactions are affected by crowding conditions in the cellular milieu.

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“…DNA molecules are apart from each other in normal solution, due to the electrostatic repulsive force. Macromolecular crowding, causes a strong depletion effect, exerts an attractive force between the DNA molecules [36]. The crowded effects may be mimicked in vitro by adding high concentrations of an inert molecule such as polyethylene glycol or ficoll.…”

Section: Resultsmentioning

confidence: 99%

Synthesis and Assessment of DNA/Silver Nanoclusters Probes for Optimal and Selective Detection of Tristeza Virus Mild Strains

et al. 2016

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Citrus Tristeza virus (CTV) is one of the most destructive pathogens worldwide that exist as a mixture of malicious (Sever) and tolerable (Mild) strains. Mild strains of CTV can be used to immunize healthy plants from more Severe strains damage. Recently, innovative methods based on the fluorescent properties of DNA/silver nanoclusters have been developed for molecular detection purposes. In this study, a simple procedure was followed to create more active DNA/AgNCs probe for accurate and selective detection of Tristeza Mild-RNA. To this end, four distinct DNA emitter scaffolds (C12, Red, Green, Yellow) were tethered to the Mild capture sequence and investigated in various buffers in order to find highly emissive combinations. Then, to achieve specific and reliable results, several chemical additives, including organic solvents, PEG and organo-soluble salts were used to enhance control fluorescence signals and optimize the hybridization solution. The data showed that, under adjusted conditions, the target sensitivity is enhanced by a factor of five and the high discrimination between Mild and Severe RNAs were obtained. The emission ratio of the DNA/AgNCs was dropped in the presence of target RNAs and I0/I intensity linearly ranged from 1.5 × 10(-8) M to 1.8 × 10(-6) M with the detection limit of 4.3 × 10(-9) M.

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How can macromolecular crowding inhibit biological reactions? The enhanced formation of DNA nanoparticles

Cited by 20 publications

References 23 publications

Extracellular fluid viscosity enhances liver cancer cell mechanosensing and migration

Extracellular fluid viscosity enhances liver cancer cell mechanosensing and migration

The effect of macromolecular crowding on single-round transcription by E. coli RNA polymerase

Synthesis and Assessment of DNA/Silver Nanoclusters Probes for Optimal and Selective Detection of Tristeza Virus Mild Strains

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