Multi-dimensional condensation of intracellular biomolecules.

Liquid-liquid phase separation has been recognized as universal mechanisms in living cells for the formation of RNA-protein condensates and ordered lipid domains. These biomolecular condensates or domains nucleate, diffuse and interact with each other across physical dimensions to perform their biological functions. Here we summarize key features of biophysical principles underlying the multi-dimensional condensation of RNA-protein condensates and ordered lipid domains, which are related to nuclear transcription, and signaling on cell membranes.

Nucleation landscape of biomolecular condensates.

All structures within living cells must form at the right time and place. This includes condensates such as the nucleolus, Cajal bodies and stress granules, which form via liquid-liquid phase separation of biomolecules, particularly proteins enriched in intrinsically disordered regions (IDRs). In non-living systems, the initial stages of nucleated phase separation arise when thermal fluctuations overcome an energy barrier due to surface tension.

Properties of repression condensates in living Ciona embryos.

Recent studies suggest that transcriptional activators and components of the pre-initiation complex (PIC) form higher order associations-clusters or condensates-at active loci. Considerably less is known about the distribution of repressor proteins responsible for gene silencing. Here, we develop an expression assay in living Ciona embryos that captures the liquid behavior of individual nucleoli undergoing dynamic fusion events.

Nucleated transcriptional condensates amplify gene expression.

Membraneless organelles or condensates form through liquid-liquid phase separation, which is thought to underlie gene transcription through condensation of the large-scale nucleolus or in smaller assemblies known as transcriptional condensates. Transcriptional condensates have been hypothesized to phase separate at particular genomic loci and locally promote the biomolecular interactions underlying gene expression. However, there have been few quantitative biophysical tests of this model in living cells, and phase separation has not yet been directly linked with dynamic transcriptional outputs.

Universal phase behaviors of intracellular lipid droplets.

Lipid droplets are cytoplasmic microscale organelles involved in energy homeostasis and handling of cellular lipids and proteins. The core structure is mainly composed of two kinds of neutral lipids, triglycerides and cholesteryl esters, which are coated by a phospholipid monolayer and proteins. Despite the liquid crystalline nature of cholesteryl esters, the connection between the lipid composition and physical states is poorly understood.

Suppression of the coffee-ring effect by sugar-assisted depinning of contact line.

Inkjet printing is of growing interest due to the attractive technologies for surface patterning. During the printing process, the solutes are transported to the droplet periphery and form a ring-like deposit, which disturbs the fabrication of high-resolution patterns. Thus, controlling the uniformity of particle coating is crucial in the advanced and extensive applications.

Molecular behavior of DNA in a cell-sized compartment coated by lipids.

The behavior of long DNA molecules in a cell-sized confined space was investigated. We prepared water-in-oil droplets covered by phospholipids, which mimic the inner space of a cell, following the encapsulation of DNA molecules with unfolded coil and folded globule conformations. Microscopic observation revealed that the adsorption of coiled DNA onto the membrane surface depended on the size of the vesicular space.

Emergence of DNA-encapsulating liposomes from a DNA-lipid blend film.

Spontaneous generation of DNA-enclosing liposomes from a DNA-lipid blend film is investigated. The special properties of the lipid vesicles, namely, micrometer size, unilamellarity, and dense polymer encapsulation acquired by the dehydration-rehydration process, are physicochemically revealed. We found that the formation of giant unilamellar vesicles encapsulating DNAs are governed by micropatterns of the films, such as dots and network patterns.

Probability of double-strand breaks in genome-sized DNA by γ-ray decreases markedly as the DNA concentration increases.

By use of the single-molecule observation, we count the number of DNA double-strand breaks caused by γ-ray irradiation with genome-sized DNA molecules (166 kbp). We find that P1, the number of double-strand breaks (DSBs) per base pair per unit Gy, is nearly inversely proportional to the DNA concentration above a certain threshold DNA concentration. The inverse relationship implies that the total number of DSBs remains essentially constant.