Nonspecific characteristics of macromolecules create specific effects in living cells

Abstract

Recently, the important role of microphase separation in living cells has been attracting considerable interest in relation to cell organization and function. For example, many studies have focused on liquid-liquid phase separation (LLPS) as a very plausible mechanism for the presence of membraneless organelles. To confirm the role of phase separation in living cells, experimental studies on models and/or reconstructed systems are needed. In this short review, we discuss current paradigms of LLPS and provide some example "review data" to demonstrate particular points relating to the specific localization of biological macromolecules like DNAs and actin proteins with spontaneous domain formation in microdroplets emerging in an aqueous two-phase system (ATPS) (we use polyethylene glycol (PEG)/dextran (DEX)-a binary polymer solution). We also suggest that phase separation and transition may play basic roles in regulation of the biochemical reactivity of individual long genomic DNAs.

Emergence of uniform linearly-arranged micro-droplets entrapping DNA and living cells through water/water phase-separation

“…Figure 2 b shows that the epithelial cells are localized on the interface of the w/w droplets, where fluorescence is emitted by mCherry expressed inside the cells. A similar localization of RBC and epithelial cells for w/w droplets in a PEG/DEX solution was observed under non-confinement conditions in the 3D experimental system as recently reported 33 , 34 . Figure 2 c shows the generation of the droplet array entrapping DNA molecules, where DNAs are stained by YOYO-1.…”

Transcription Factors as Evolvable Biosensors

“…Yoshikawa and his colleagues have demonstrated that double-stranded DNA (dsDNA) undergo soluble/insoluble transition as a first-order phase transition. This sharp transition can be induced by various chemical stimuli, including polycations, neutral polymers, divalent/trivalent cations, and even polyanions 52 . Eukaryotic chromosomes are known to be organized in numerous micrometer-sized DNA "puffs" that are approximately 1 megabase in length 53 ; it is physically possible that small changes in the local chemical environment induce the phase separation of each individual puff independently.…”

“…But considering the highly condensed cellular environment, the demonstrations by the Yoshikawa group, and the growing evidence for the existence and biological function of membrane-less organelle64 , it is likely that solution properties of biomolecules should have the evolvability of TF-biosensors. By considering the designed biomolecules' physicochemical dynamics, including aggregative65 , kinetic, and phase separational52,55,64 , directed evolutionists can maximize the evolvability of the TF-biosensors.15H04189, 15K14228, 16H 06450]. D.U.…”

Biophysical Reviews: 2020—looking back, going forward

“…The bulk of the Special Issue was composed of numerous review articles (forty-five) chosen from the nearly thirty separate sections of the BSJ’s national society meeting. A short selection of these (many) interesting review articles includes those dealing with the biophysics of chromatin (Ashwin et al 2020 ; Kumar and Kono 2020 ); optogenetics (Kandori 2020 ); computational structure prediction (Kinoshita and Hayashi 2020 ; Leitner and Yamamoto 2020 ; Tsuchiya and Tomii 2020 ); physical biochemistry (Tsumoto et al 2020 ); molecular motors (Li and Toyabe 2020 ; Loutschko and Flechsig 2020 ; Noji et al 2020 ); membrane protein interaction (Moghal et al 2020 ); novel scattering, structural and imaging techniques (Nakasako et al 2020 ; Uchihashi and Ganser 2020 ; Yamaoki et al 2020 ; Yokoyama et al 2020 ); cellular biophysics (Okazaki et al 2020 ; Yasuda 2020 ); biophysical thermochemistry (Fukuyama and Maeda 2020 ; Suzuki and Plakhotnik 2020 ); and biophysical theory (Leitner and Yamamoto 2020 ; Uda 2020 ).…”