Sequence-based engineering of dynamic functions of micrometer-sized DNA droplets

Sato, Yusuke; Sakamoto, Tetsuro; Takinoue, Masahiro

doi:10.1126/sciadv.aba3471

Cited by 109 publications

(297 citation statements)

References 44 publications

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“…As mentioned above, in addition to lipid vesicles, membraneless droplets generated from liquid–liquid phase separation [ 104 , 163 ], including polyester microdroplets [ 112 , 113 ], peptide/nucleotide coacervates [ 119 ], DNA droplet-based compartments [ 164 ], DNA liquid crystal coacervates [ 118 , 120 ], and aqueous two-phase systems [ 108 ], have been investigated in more detail in the context of primitive compartments as well. The overwhelming literature of a breadth of primitive compartments shows that the compartments themselves were also likely to have been extremely compositionally diverse and co-existed on early Earth, demonstrating properties that were not all necessarily compatible.…”

Section: Prebiotic Compartment Speciationmentioning

confidence: 99%

Origin of Species before Origin of Life: The Role of Speciation in Chemical Evolution

Jia

Caudan

Mamajanov

2021

Life

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Speciation, an evolutionary process by which new species form, is ultimately responsible for the incredible biodiversity that we observe on Earth every day. Such biodiversity is one of the critical features which contributes to the survivability of biospheres and modern life. While speciation and biodiversity have been amply studied in organismic evolution and modern life, it has not yet been applied to a great extent to understanding the evolutionary dynamics of primitive life. In particular, one unanswered question is at what point in the history of life did speciation as a phenomenon emerge in the first place. Here, we discuss the mechanisms by which speciation could have occurred before the origins of life in the context of chemical evolution. Specifically, we discuss that primitive compartments formed before the emergence of the last universal common ancestor (LUCA) could have provided a mechanism by which primitive chemical systems underwent speciation. In particular, we introduce a variety of primitive compartment structures, and associated functions, that may have plausibly been present on early Earth, followed by examples of both discriminate and indiscriminate speciation affected by primitive modes of compartmentalization. Finally, we discuss modern technologies, in particular, droplet microfluidics, that can be applied to studying speciation phenomena in the laboratory over short timescales. We hope that this discussion highlights the current areas of need in further studies on primitive speciation phenomena while simultaneously proposing directions as important areas of study to the origins of life.

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Section: Prebiotic Compartment Speciationmentioning

confidence: 99%

Origin of Species before Origin of Life: The Role of Speciation in Chemical Evolution

Jia

Caudan

Mamajanov

2021

Life

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“…A DNA nanostar consists of multiple double-stranded DNA arms emanating from a common three-or four-way junction, with each arm terminating in a single-stranded region (a sticky end). Hybridization of sticky ends causes nanostars to bind each other, driving phase separation (24) and the formation of viscoelastic liquids, whose behavior can be controlled through sequence design (25)(26)(27)(28). DNA nanostars condense into a liquid, rather than a crystalline solid or kinetically arrested gel, due to the reduced particle valence (24,29), the labile sticky ends, and the internal particle flexibility induced by the presence of unpaired bases at the junction and near the sticky end (30,31).…”

mentioning

confidence: 99%

Enzymatic degradation of liquid droplets of DNA is modulated near the phase boundary

Saleh

Jeon

Liedl

2020

Proc. Natl. Acad. Sci. U.S.A.

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Biomolecules can undergo liquid–liquid phase separation (LLPS), forming dense droplets that are increasingly understood to be important for cellular function. Analogous systems are studied as early-life compartmentalization mechanisms, for applications as protocells, or as drug-delivery vehicles. In many of these situations, interactions between the droplet and enzymatic solutes are important to achieve certain functions. To explore this, we carried out experiments in which a model LLPS system, formed from DNA “nanostar” particles, interacted with a DNA-cleaving restriction enzyme, SmaI, whose activity degraded the droplets, causing them to shrink with time. By controlling adhesion of the DNA droplet to a glass surface, we were able to carry out time-resolved imaging of this “active dissolution” process. We found that the scaling properties of droplet shrinking were sensitive to the proximity to the dissolution (“boiling”) temperature of the dense liquid: For systems far from the boiling point, enzymes acted only on the droplet surface, while systems poised near the boiling point permitted enzyme penetration. This was corroborated by the observation of enzyme-induced vacuole-formation (“bubbling”) events, which can only occur through enzyme internalization, and which occurred only in systems poised near the boiling point. Overall, our results demonstrate a mechanism through which the phase stability of a liquid affects its enzymatic degradation through modulation of enzyme transport properties.

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“…This characteristic behavior permitted the authors to generate DNA bricks to form more complex scarless structures that adhere effectively. A similar Y-shaped structure was used by Sato [111]. However, the linker was removed, so that the structure's sticky ends would be complementary.…”

Section: Nucleic Acid-derived Polymersmentioning

confidence: 99%

Supramolecular Biopolymers for Tissue Engineering

Pérez-Pedroza

Ávila-Ramírez

Khan

et al. 2021

Advances in Polymer Technology

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Supramolecular biopolymers (SBPs) are those polymeric units derived from macromolecules that can assemble with each other by noncovalent interactions. Macromolecular structures are commonly found in living systems such as proteins, DNA/RNA, and polysaccharides. Bioorganic chemistry allows the generation of sequence-specific supramolecular units like SBPs that can be tailored for novel applications in tissue engineering (TE). SBPs hold advantages over other conventional polymers previously used for TE; these materials can be easily functionalized; they are self-healing, biodegradable, stimuli-responsive, and nonimmunogenic. These characteristics are vital for the further development of current trends in TE, such as the use of pluripotent cells for organoid generation, cell-free scaffolds for tissue regeneration, patient-derived organ models, and controlled delivery systems of small molecules. In this review, we will analyse the 3 subtypes of SBPs: peptide-, nucleic acid-, and oligosaccharide-derived. Then, we will discuss the role that SBPs will be playing in TE as dynamic scaffolds, therapeutic scaffolds, and bioinks. Finally, we will describe possible outlooks of SBPs for TE.

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Sequence-based engineering of dynamic functions of micrometer-sized DNA droplets

Cited by 109 publications

References 44 publications

Origin of Species before Origin of Life: The Role of Speciation in Chemical Evolution

Origin of Species before Origin of Life: The Role of Speciation in Chemical Evolution

Enzymatic degradation of liquid droplets of DNA is modulated near the phase boundary

Supramolecular Biopolymers for Tissue Engineering

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