Spatial Control over Reactions via Localized Transcription within Membraneless DNA Nanostar Droplets DOI

Eli Kengmana,

Elysse Ornelas-Gatdula,

Kuan-Lin Chen

et al.

Journal of the American Chemical Society, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 20, 2024

Biomolecular condensates control where and how fast many chemical reactions occur in cells by partitioning reactants catalysts, enabling simultaneous different spatial locations of a cell. Even without membrane or physical barrier, the can affect rates downstream reaction cascades ways that depend on location. Such effects enable systems biomolecular to spatiotemporally orchestrate networks facilitate complex behaviors such as ribosome assembly. Here, we develop system for developing synthetic systems. We localize transcription templates within phase-separated, membraneless DNA nanostar (NS) droplets─programmable, vitro liquid–liquid phase separation substrates localization droplets. When RNA produced droplets is also degraded bulk, droplet-localized creates concentration gradients. Consistent with formation these gradients, toehold-mediated strand displacement involving transcripts are 2-fold slower far from site than when nearby. then demonstrate multiple gradients form be maintained independently occurring tandem, each localized NS droplet types. Our results provide means constructing which spatially controlled need membranes. This provides generally studying exchange products might between protocells.

Language: Английский

A cell-free biosensor signal amplification circuit with polymerase strand recycling DOI
Yueyi Li, Tyler Lucci, Matias Villarruel Dujovne

et al.

Nature Chemical Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 13, 2025

Language: Английский

Citations

1
Structural dynamics-guided engineering of a riboswitch RNA for evolving c-di-AMP synthases DOI Creative Commons
Dian Chen, Jun Li, You Wu

et al.

Science Advances, Journal Year: 2025, Volume and Issue: 11(14)

Published: April 2, 2025

Cyclic diadenosine monophosphate (C-di-AMP) synthases are key enzymes for synthesizing c-di-AMP, a potent activator of the stimulator interferon genes (STING) immune pathway. However, characterizing these has been hampered by lack effective sensors. While c-di-AMP riboswitches, as natural aptamers, hold potential RNA biosensors, their poorly comprehended structural dynamics and inherent "OFF" genetic output pose substantial challenges. To address limitations, we synthesized over 10 fluorophore-labeled samples to probe conformational changes riboswitch at single-molecule level. By integrating dynamic findings with steady-state fluorescence titration, mutagenesis, in vivo assays, strand displacement strategy, transformed aptamer into biosensor. This engineered biosensor reversed its from "ON" upon binding, exhibiting 50-fold improvement detection limit. Leveraging this refined biosensor, developed robust strategy high-throughput evolution synthases.

Language: Английский

Citations

0
Synthetic RNA biology DOI Creative Commons
Beatrix Suess

RNA Biology, Journal Year: 2024, Volume and Issue: 21(1), P. 1 - 2

Published: April 14, 2024

Language: Английский

Citations

3
Insights into bacterial metabolism from small RNAs DOI
Kai Papenfort, Gisela Storz

Cell chemical biology, Journal Year: 2024, Volume and Issue: 31(9), P. 1571 - 1577

Published: Aug. 1, 2024

Language: Английский

Citations

3
Induction of bacterial expression at the mRNA level by light DOI Creative Commons
Américo Tavares Ranzani, K Wolburg Buchholz, Marius Blackholm

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(16), P. 10017 - 10028

Published: Aug. 10, 2024

Abstract Vital organismal processes, including development, differentiation and adaptation, involve altered gene expression. Although expression is frequently controlled at the transcriptional stage, various regulation mechanisms operate downstream levels. Here, we leverage photoreceptor NmPAL to optogenetically induce RNA refolding translation of bacterial mRNAs. Blue-light-triggered binding disrupts a cis-repressed mRNA state, thereby relieves obstruction initiation, upregulates Iterative probing optimization circuit, dubbed riboptoregulator, enhanced induction 30-fold. Given action level, riboptoregulator can differentially regulate individual structural genes within polycistronic operons. Moreover, it orthogonal be wed with other gene-regulatory circuits for nuanced more stringent gene-expression control. We thus advance pAurora2 circuit that combines translational increase by >1000-fold. The strategy stands upgrade numerous regulatory widely applies control in microbial biotechnology, synthetic biology materials science.

Language: Английский

Citations

3
Bacterial Metallostasis: Metal Sensing, Metalloproteome Remodeling, and Metal Trafficking DOI Creative Commons
Daiana A. Capdevila, Johnma J. Rondón, Katherine A. Edmonds

et al.

Chemical Reviews, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 10, 2024

Transition metals function as structural and catalytic cofactors for a large diversity of proteins enzymes that collectively comprise the metalloproteome. Metallostasis considers all cellular processes, notably metal sensing, metalloproteome remodeling, trafficking (or allocation) ensure functional integrity adaptability Bacteria employ both protein RNA-based mechanisms sense intracellular transition bioavailability orchestrate systems-level outputs maintain metallostasis. In this review, we contextualize metallostasis by briefly discussing specialized roles play in biology. We then offer comprehensive perspective on metalloregulatory metal-sensing riboswitches, defining general principles within each sensor superfamily capture how specificity is encoded sequence, selectivity can be leveraged downstream synthetic biology biotechnology applications. This followed discussion recent work highlights selected outputs, including remodeling allocation metallochaperones to client compartments. close places where more needed fill gaps our understanding

Language: Английский

Citations

2
Fluorogenic RNA-Based Biosensors of Small Molecules: Current Developments, Uses, and Perspectives DOI Creative Commons
Janine Kehrli, Claire Husser, Michaël Ryckelynck

et al.

Biosensors, Journal Year: 2024, Volume and Issue: 14(8), P. 376 - 376

Published: Aug. 1, 2024

Small molecules are highly relevant targets for detection and quantification. They also used to diagnose monitor the progression of disease infectious processes track presence contaminants. Fluorogenic RNA-based biosensors (FRBs) represent an appealing solution problem detecting these targets. combine portability molecular systems with sensitivity multiplexing capacity fluorescence, as well exquisite ligand selectivity RNA aptamers. In this review, we first present different sensing reporting aptamer modules currently available design FRB, together main methodologies discover new specificities. We next introduce discuss how both can be functionally connected prior exploring applications which FRB have been used. Finally, conclude by discussing using alternative nucleotide chemistries may improve properties further widen their application scope.

Language: Английский

Citations

1
An engineering perspective on transcription, translation and their regulation DOI Open Access
Jarosław Śmieja

Postępy Biochemii, Journal Year: 2024, Volume and Issue: 70(1), P. 88 - 94

Published: March 18, 2024

Information coded in DNA is replicated, modified and transmitted from the origins of protein-based life. Analogies these processes to information processing, transmission storage computer systems straightforward can be utilized both analysis biological data development biologically based technical systems. Transcription translation are regulated by extremely complex regulatory networks, providing control cell growth, cycle cellular responses stress. As such, they constitute engineering exerting their actions at many levels time scale spatial organization. This work presents an perspective on DNA-related processing biochemical process living cells, followed a review two-way crosstalk between biology.

Language: Английский

Citations

0
Therapeutic applications of RNA nanostructures DOI Creative Commons
Theresa Yip, Xiaodong Qi,

Hao Yan

et al.

RSC Advances, Journal Year: 2024, Volume and Issue: 14(39), P. 28807 - 28821

Published: Jan. 1, 2024

Non-immunogenic RNA nanostructures are functionalized for/with RNAi, mRNA, ribozymes, CRISPR, and small molecule drugs. Immunogenic designed as immunostimulants cancer vaccine platforms. Created in Biorender.com.

Language: Английский

Citations

0
RNA-DCGen: Dual Constrained RNA Sequence Generation with LLM-Attack DOI

Haz Sameen Shahgir,

Md. Rownok Zahan Ratul, Md Toki Tahmid

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 25, 2024

Abstract Designing RNA sequences with specific properties is critical for developing personalized medications and therapeutics. While recent diffusion flow-matching-based generative models have made strides in conditional sequence design, they face two key limitations: specialization fixed constraint types, such as tertiary structures, lack of flexibility imposing additional conditions beyond the primary property interest. To address these challenges, we introduce RNA-DCGen, a generalized framework generation that adaptable to any structural or functional through straightforward finetuning an language model (RNA-LM). Additionally, RNA-DCGen can enforce on generated by fixing conserved regions. On conditioned distance maps, generates average R 2 score 0.625 compared random only 0.118 over 250 generations judged separate more capable RNA-LM. When secondary achieves F1 0.4 against baseline 0.006.

Language: Английский

Citations

0