Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acsami.6c00347

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1002/cbic.202500927

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Language：English   Publishing type：Research paper (scientific journal)  

DNA condensate droplets (hereafter referred to as DNA condensates), which arise from specific interactions between sticky ends embedded in multi-arm DNA nanostructures, hold significant promise as programmable smart materials. However, from an engineering standpoint, the controlled preparation of DNA condensates with uniform size and a well-defined structure remains a major challenge due to the stochastic nature of the condensation process. This study presents a novel approach that employs vibration-induced local vortices (VILV) within a microfluidic platform to achieve spatial control over DNA condensate dimensions and enable their parallel generation. A key advantage of this platform is its ability to support direct observation and real-time tracking of structural morphology and dynamics. Through flow-field analysis of the VILV system, we demonstrate that uniform microvortices serve as semi-closed compartments, wherein DNA molecules confined within each vortex space rapidly aggregate and relax into uniform spherical condensate droplets. By modulating parameters such as DNA concentration and micropillar dimensions, the VILV platform not only enables systematic control of condensate size but also facilitates the construction of complex, multicomponent "patchy" condensates with consistent morphology. This platform provides a robust and scalable tool for studying liquid-liquid phase separation (LLPS) and offers broad potential for applications in the bottom-up synthesis of condensed molecular systems.

DOI： 10.1039/d5mh01304f

PubMed

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1039/d5mh01304f

Web of Science

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Language：English   Publishing type：Research paper (scientific journal)  

<jats:title>Abstract</jats:title>
<jats:p>
Soil is a suitable habitat for various microorganisms. These soil microorganisms establish complex social relationships and build biogeochemical cycles, such as carbon or nitrogen cycles, which synthesize plant nutrients and greenhouse gases. Clarifying microbial activities inside the soil is essential for agricultural and environmental fields. One of critical factors influencing bacterial activity in soil is the physical structure of the soil built by soil aggregates. The size distribution of soil aggregates widely ranges from µm to mm and creates pores with various sizes that act as pathways for air, water, and nutrients and affect microbial activities. Although it is known that pore size in soil is important for bacterial activity, how the pore size distribution affects bacterial activity remains unclear. The pore size distribution is considered to affect the movement of bacteria within the soil as well as that of air, water, and nutrients. Therefore, further investigation into the relationship between the size distribution of micrometer-sized pores in soil and the bacterial movement in micrometer space is required to understand bacterial activity in soil. In this study, we investigated the dependence of fractally distributed pore size distributions (from micrometers to millimeters) on bacterial activity, especially bacterial growth, using a polydimethylsiloxane culture device and numerical simulations. We fabricated a culture device with 2 μm depth with the pillars arranged fractally or periodically to represent soil particles and pore size distributions.
<jats:italic>Escherichia coli</jats:italic>
was cultured for 20 h in a culture device, and the results showed that final amount of
<jats:italic>E. coli</jats:italic>
was significantly higher in the device with the pillars arranged fractally than in the one with pillars arranged in an array. Bacterial growth was simulated in a two-dimensional space with pillars. The results also showed clear relationships among bacterial growth, movement, and pillar arrangement. Our findings provide insights into microbial activity inside complex physical structures such as soils.
</jats:p>

DOI： 10.1038/s41598-025-23995-9

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Publishing type：Research paper (scientific journal)   Publisher：Wiley  

Abstract

DNA nanostar hydrogels are a novel class of biocompatible and programmable materials with promising applications as a cell matrix for tissue engineering or cancer diagnosis. Yet, precise isolation of specific cell types with these hydrogels has remained elusive without specific interaction between DNA and cell membrane. Here, a DNA nanostar hydrogel–based method is reported for cell isolation, achieved by interfacing living cells with the hydrogel via an antibody‐functionalized DNA motif. As a proof of concept, epithelial cell adhesion molecule (EpCAM)‐positive cells are isolated—a model of circulating tumor cells—whose separation from white blood cells is crucial for early cancer diagnosis. By optimizing the antibody‐DNA conjugate, a specific binding is achieved between target cells and the DNA gel, enabling the capture of up to 90% of cells. The cells are selectively enriched from a mixture of different cell types using parallelized and iterative capture. The cells recover by dissociating the gel using strand displacement, retain their viability and capacity to proliferate, which supports their future use for culture or analysis. This generalizable method allows coupling of any cell type to DNA gels —supporting future applications ranging from cancer research to recapitulate cellular tumor models in vitro or regenerative medicine to grow designer tissues.

DOI： 10.1002/admi.202500619

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Publishing type：Research paper (scientific journal)  

DOI： 10.1038/s41428-025-01050-8

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/jacsau.5c00568

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acssynbio.4c00709

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Publishing type：Research paper (scientific journal)  

DOI： 10.1039/D5LF00131E

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Language：English   Publishing type：Research paper (scientific journal)  

Aqueous two-phase systems (ATPS) of dextran and polyethylene glycol (PEG) enable the purification of DNA structures such as DNA origami and DNA nanotubes in times as short as 10 min. This method, which has recovery yields >90% for a typical DNA origami, owes its efficiency to the highly selective partition of the DNA structures in the dextran phase of these emulsions. This purification method is carried out in conditions that promote the structural stability of these structures, making it particularly suitable for DNA nanotechnology. In this protocol, we will describe the materials and methods for purifying DNA origami and quantifying the purification yield by agarose electrophoresis and image analysis.

DOI： 10.1007/978-1-0716-4394-5_2

PubMed

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