DNA Droplets: Intelligent, Dynamic Fluid (Adv. Biology 3/2023)

Udono, Hirotake; Gong, Jianya; Sato, Yusuke; Takinoue, Masahiro

doi:10.1002/adbi.202370031

Cited by 4 publications

(5 citation statements)

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“…Excitingly, these DNA-based coacervate-like systems offer a great programmability since the DNA sequences can be precisely adjusted to achieve the desired material and functional properties. [65][66][67][68][69] An increasing number of studies are thus now geared toward demonstrating the potential of these systems as versatile modules in synthetic cells (see Section 4).…”

Section: Coacervation Driven By Specific Interactionsmentioning

confidence: 99%

Coacervate Droplets for Synthetic Cells

2023

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The design and construction of synthetic cells – human‐made microcompartments that mimic features of living cells – have experienced a real boom in the past decade. While many efforts have been geared toward assembling membrane‐bounded compartments, coacervate droplets produced by liquid–liquid phase separation have emerged as an alternative membrane‐free compartmentalization paradigm. Here, the dual role of coacervate droplets in synthetic cell research is discussed: encapsulated within membrane‐enclosed compartments, coacervates act as surrogates of membraneless organelles ubiquitously found in living cells; alternatively, they can be viewed as crowded cytosol‐like chassis for constructing integrated synthetic cells. After introducing key concepts of coacervation and illustrating the chemical diversity of coacervate systems, their physicochemical properties and resulting bioinspired functions are emphasized. Moving from suspensions of free floating coacervates, the two nascent roles of these droplets in synthetic cell research are highlighted: organelle‐like modules and cytosol‐like templates. Building the discussion on recent studies from the literature, the potential of coacervate droplets to assemble integrated synthetic cells capable of multiple life‐inspired functions is showcased. Future challenges that are still to be tackled in the field are finally discussed.

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Section: Coacervation Driven By Specific Interactionsmentioning

confidence: 99%

Coacervate Droplets for Synthetic Cells

2023

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“…Recently, DNA nanotechnology [37] has demonstrated the formation of liquid-like DNA coacervates [24][25][26]28,29,[38][39][40][41][42][43][44][45][46][47][48][49][50] (DNA droplets), which have attracted interest as design-based methods for forming and controlling biopolymer coacervates. DNA nanotechnology relies on the programmability of DNA sequences based on the computational prediction of the thermodynamic stability of base pairing and the physical topology of DNA strings [51][52][53] and has achieved DNA nanostructures, [37,54] DNA hydrogels, [55][56][57][58] and assemblies of DNA nanostructures on lipid membranes or oil-water interfaces.…”

Section: Introductionmentioning

confidence: 99%

“…DNA nanotechnology relies on the programmability of DNA sequences based on the computational prediction of the thermodynamic stability of base pairing and the physical topology of DNA strings [51][52][53] and has achieved DNA nanostructures, [37,54] DNA hydrogels, [55][56][57][58] and assemblies of DNA nanostructures on lipid membranes or oil-water interfaces. [59][60][61][62][63] The established knowledge of DNA nanotechnology has been applied to the design and formation of DNA droplets [49] constructed with branched DNA nanostructures (called DNA motifs or DNA nanostars), [23][24][25][26][38][39][40][41][42][43][45][46][47][48] and multi-block long single-stranded DNA (ssDNA) generated by rolling-circle amplification. [64][65][66] These studies also demonstrated the dynamic behavior of DNA droplets, [50] such as phase separation and the division of two immiscible DNA droplets with orthogonal sequences, [38,39] bubbling of DNA droplets with an enzymatic reaction, [40] disruption of lipid membranes, [41] DNA logic computation, [42] and droplet locomotion.…”

Section: Introductionmentioning

confidence: 99%

Liquid DNA Coacervates form Porous Capsular Hydrogels via Viscoelastic Phase Separation on Microdroplet Interface

Morita,

Sakamoto,

Nomura

et al. 2024

Adv Materials Inter

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Liquid–liquid phase separation (LLPS) droplets of biopolymers are known as functional microdroplets in living cells and have recently been used to construct protocells and artificial cells. The formation of DNA coacervates (also referred to as DNA droplets) from branched DNA nanostructures and the control of their physical properties via DNA nanostructure design are demonstrated previously. For the construction of artificial cells or protocells, however, even though physical effects such as surface tension, wetting, and viscoelasticity are more important in a tiny (micrometer‐sized), confined environment than in a bulk solution environment, they have not been explored yet. This study shows that a tiny, confined environment using a water‐in‐oil (W/O) microdroplet interface modulates the phase separation dynamics of DNA coacervates, leading to micrometer‐sized porous capsular structures. The porous structures are produced via two types of viscoelastic phase separation (VPS) processes in DNA coacervates: i) simple VPS and ii) cluster‐cluster aggregation after VPS. Finally, it is shown that environmental chemical stimulation can manipulate porous capsular DNA hydrogels extracted from W/O microdroplets. These results provide an approach for designing and fabricating artificial cells or protocells with complex structures and physicochemical properties.

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“…This sequencespecificity of DNA bonding has been harnessed to generate a variety of self-assembling programmable materials 5 . These include nanometer-scale structures with precise control of DNA topology such as in DNA origami 6,7 to mesoscale soft materials such as hydrogels 8,9 . In most of these applications, the negative charge on the phosphodiester backbone is neutralized by low valence counterions, and the desired molecular arrangement is achieved by the sequenceprogrammablity of DNA bonding.…”

Section: Introductionmentioning

confidence: 99%

Sequence programmable nucleic acid coacervates

Majumder,

Coupe,

Fakhri

et al. 2024

Preprint

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Nature uses bottom-up self-assembly to build structures with remarkable complexity and functionality. Understanding how molecular-scale interactions translate to macroscopic properties remains a major challenge and requires systems that effectively bridge these two scales. Here, we generate DNA and RNA liquids with exquisite programmability in their material properties. Nucleic acids are negatively charged, and in the presence of polycations, they may condense to a liquid-like state. Within these liquids, DNA and RNA retain sequence-specific hybridization abilities. We show that intermolecular hybridization in the condensed phase cross-links molecules and slows down chain dynamics. This reduced chain mobility is mirrored in the macroscopic properties of the condensates. Molecular diffusivity and material viscosity scale with the intermolecular hybridization energy, enabling precise sequence-based modulation of condensate properties over orders of magnitude. Our work offers a robust platform to create self-assembling programmable fluids and may help advance our understanding of liquid-like compartments in cells.

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DNA Droplets: Intelligent, Dynamic Fluid (Adv. Biology 3/2023)

Cited by 4 publications

References 0 publications

Coacervate Droplets for Synthetic Cells

Coacervate Droplets for Synthetic Cells

Liquid DNA Coacervates form Porous Capsular Hydrogels via Viscoelastic Phase Separation on Microdroplet Interface

Sequence programmable nucleic acid coacervates

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