Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2023.01.29.525851

Amphiphiles formed from synthetic DNA-nanomotifs mimic the dispersal of transcriptional clusters in the cell nucleus

Tschurikow, X.·Gadzekpo, A.·Tran, M. P.·Chatterjee, R.·Sobucki, M.·Zaburdaev, V.·Goepfrich, K.·Hilbert, L.
View original source ↗Export metadata ↓

Abstract

Stem cells exhibit prominent clusters controlling the transcription of genes into RNA. These clusters form by a phase-separation mechanism, and their size and shape are controlled via an amphiphilic effect of transcribed genes. Here, we construct amphiphile-nanomotifs purely from DNA, and achieve similar size and shape control for phase-separated droplets formed from fully synthetic, self-interacting DNA-nanomotifs. Low amphiphile concentrations induce rounding of droplets, followed by splitting and, ultimately, full dispersal at higher concentrations. Super-resolution microscopy data obtained from zebrafish embryo stem cells reveal a comparable transition for transcriptional clusters with increasing transcription levels. Brownian dynamics and lattice simulations further confirm that addition of amphiphilic particles is sufficient to explain the observed changes in shape and size. Our work reproduces key aspects of the complex organization of transcription in biological cells using relatively simple, DNA sequence-programmable nanostructures, opening novel ways to control mesoscopic organization of synthetic nanomaterials. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/525851v2_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1a8cc4borg.highwire.dtl.DTLVardef@fc6651org.highwire.dtl.DTLVardef@a17c74org.highwire.dtl.DTLVardef@1f1cf14_HPS_FORMAT_FIGEXP M_FIG C_FIG

Explore related subjects

synthetic biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Tschurikow, X., Gadzekpo, A., Tran, M. P., Chatterjee, R., Sobucki, M., Zaburdaev, V., Goepfrich, K., Hilbert, L.. 2023-01-29. Amphiphiles formed from synthetic DNA-nanomotifs mimic the dispersal of transcriptional clusters in the cell nucleus. https://doi.org/10.1101/2023.01.29.525851

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Programmable interphyla communication for Staphylococcus aureus by transferability of homoserine lactone sensors between Bacillales bacteria

Staphylococcus aureus is a Gram-positive opportunistic pathogen of the order Bacillales and a frequent member of human-associated microbiomes. Despite its clinical relevance, engineering S. aureus and the communities it inhabits remains limited by a shortage of well-characterized genetic tools for precise control of gene expression and intercellular signaling. Biosensors for homoserine lactones (HSLs) are widely used in Gram-negative bacteria, as HSLs are small, passively diffusible signaling molecules for and their sensors are tightly regulated. Here, we show that synthetically designed HSL sensors using LuxR-family regulators are highly functional in S. aureus. Notably, synthetic designs previously built for the Gram-positive model Bacillus subtilis, a distantly related Bacillales, transferred functionally and establish repurposing the genetic toolbox as an effective strategy for importing these functions into S. aureus. Sensor performance correlated strongly between the two Bacillales, and activation in S. aureus reached 55-fold, exceeding the dynamic range of reported inducible systems. We further demonstrate tightly regulated, programmable interphyla communication between Gram-negative Escherichia coli and S. aureus via HSL signaling. These results provide a new toolset for engineering interbacterial communication and open a route to extending programmable HSL signaling to other tough-to-engineer bacteria.

synthetic biology↗
bioRxiv2026

Creation of genomic chimeras via megabase scale genome expansion

An organism's physiology is controlled by its genomic content. Building genomic chimeras would enable melding of the diverse functions and properties of life. However, prior arts in genome synthesis are limited to reconstituting pre-existing functions within a singular genome rather than combining diverse genomic functions across multiple distinct genomes. Existing methods are also prohibitively expensive, labor intensive, and time consuming, and thus fundamentally not scalable for creating large synthetic chimeric genomes. To address all these limitations, we invented Additive Conjugative-CAST Engineering (ACE) combining conjugation with CRISPR-associated transposition (CAST) to deliver and integrate up to half a genome per step from a donor cell into a precisely defined position in the recipient's genome. We have demonstrated ACE's capability to integrate at least a 2-megabase donor genomic segment in a single step and at least 3 megabase in two consecutive steps. Importantly, we confirmed ACE's generality through the creation of multiple genomic chimeras across species, genus, and at least order barriers. With ACE, we further demonstrate such chimeric organisms, or what we call genome expanded organisms (GEOs), can be stably forged from at least three starting bacterial strains, and can be stably maintained to express all their acquired genomic parts in a single chimera. ACE offers a new paradigm of creating artificial lifeforms to combine desired properties and potentially create novel functions beyond the constraints of nature. ACE also offers a unique perspective to probe unexplored plasticity in genome architecture and expression patterns of novel, massively expanded genomes.

synthetic biology↗
bioRxiv2026

Functional analysis of small-molecule and protein binding domains using monomeric streptavidin-based two-component biosensors

Protein biosensors are important analytical and diagnostic tools that convert molecular recognition into measurable activity. Most common two-component biosensors require two non-competing recognition domains, yet binding affinity and specificity alone do not reliably predict their compatibility with the rest of the biosensor. We report a modular platform that exploits monomeric streptavidin (mSA2) as a surrogate recognition domain, enabling rapid functional evaluation of candidate binders in the context of biosensor scaffold without requiring a second ligand-specific binding protein. We established a chromatography-free protocol for recovering functional mSA2-based biosensor components from Escherichia coli. Using biotinylated small molecules methotrexate and vitamin D3, as well as heart failure protein biomarkers galectin-3 and S100A7 we demonstrate ligand-dependent reporter biosensor activation. The developed platform provides a scalable approach for rapid binder evaluation and biosensor prototyping, streamlining biosensor development using binding domains generated by directed evolution or computational protein design.

synthetic biology↗