Photochemically Triggered, Transient, and Oscillatory Transcription Machineries Guide Temporal Modulation of Fibrinogenesis DOI Creative Commons

Jiantong Dong,

Itamar Willner

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

Published: Dec. 31, 2024

Photochemically triggered, transient, and temporally oscillatory-modulated transcription machineries are introduced. The resulting dynamic circuits implemented to guide photochemically oscillatory modulation of thrombin toward temporal control over fibrinogenesis. One system describes the assembly a reaction module leading triggered formation an active machinery that, in presence RNase H, guides transient activation A second introduces photochemical triggering circuit consisting two coupled machineries, depletion intermediate product. concept is applied develop leads generation anti-thrombin aptamer-modified oscillating product induces rhythmic inhibition thrombin, accompanied by cyclic deactivation fibrinogenesis process. operation computational kinetic models, allowing predict behaviors under different auxiliary conditions. phototriggered circuit-guided examined physiological-like conditions within human plasma environment.

Language: Английский

Dynamic switching circuit modulated by intramolecular conformation transition of DNA translator for versatile fluorescence biosensors DOI
Yuqing Zhang, Chunli Yang, Jiayang He

et al.

Biosensors and Bioelectronics, Journal Year: 2025, Volume and Issue: unknown, P. 117404 - 117404

Published: March 1, 2025

Language: Английский

Citations

0
Oligo‐Adenine Derived Secondary Nucleic Acid Frameworks: From Structural Characteristics to Applications DOI Creative Commons
Yuwei Hu, Itamar Willner

Angewandte Chemie International Edition, Journal Year: 2024, Volume and Issue: 63(45)

Published: Aug. 26, 2024

Abstract Oligo‐adenine (polyA) is primarily known for its critical role in mRNA stability, translational status, and gene regulation. Beyond biological functions, extensive research has unveiled the diverse applications of polyA. In response to environmental stimuli, single polyA strands undergo distinctive structural transitions into secondary configurations, which are reversible upon introduction appropriate counter‐triggers. this review, we systematically summarize recent advances noncanonical structures derived from polyA, including A‐motif duplex, A‐cyanuric acid triplex, A‐coralyne‐A T ⋅ A‐T triplex. The characteristics mechanisms underlying these conformations under specific external stimuli addressed, followed by examples their stimuli‐responsive DNA hydrogels, supramolecular fibre assembly, molecular electronics switches, biosensing bioengineering, payloads encapsulation release, others. A detailed comparison polyA‐derived provided, highlighting features. Furthermore, integrating stimuli‐responsiveness conformational characteristics, advanced material development, such as pH‐cascaded hydrogels fibres exhibiting dynamic adapting cues, introduced. An outlook future developments also discussed. These derived, stimuli‐responsive, enrich arsenal “toolbox”, offering frameworks applications.

Language: Английский

Citations

3
Protein Recruitment to Dynamic DNA-RNA Host Condensates DOI
Mahdi Dizani, Daniela Sorrentino, Siddharth Agarwal

et al.

Journal of the American Chemical Society, Journal Year: 2024, Volume and Issue: 146(43), P. 29344 - 29354

Published: Oct. 17, 2024

We describe the design and characterization of artificial nucleic acid condensates that are engineered to recruit locally concentrate proteins interest in vitro. These emerge from programmed interactions nanostructured motifs assembling three DNA strands one RNA strand can include an aptamer domain for recruitment a target protein. Because designed form regardless presence protein, they function as "host" compartments. As model we consider Streptavidin (SA) due its widespread use binding assays. In addition demonstrating protein recruitment, two approaches control onset condensation recruitment. The first approach uses UV irradiation, physical stimulus bypasses need exchanging molecular inputs is particularly convenient emulsion droplets. second transcription, ubiquitous biochemical reaction central development next generation living materials. then show combination transcription degradation leads autonomous dissipative system which host occur transiently condensate size well time scale transition be controlled by level RNA-degrading enzyme. conclude biotinylated beads recruited SA-host condensates, may therefore find immediate separation variety biotin-tagged components.

Language: Английский

Citations

2
Protein recruitment to dynamic DNA-RNA host condensates DOI Creative Commons
Mahdi Dizani, Daniela Sorrentino, Siddharth Agarwal

et al.

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

Published: June 4, 2024

Abstract We describe the design and characterization of artificial nucleic acid condensates that are engineered to recruit locally concentrate proteins interest in vitro . These emerge from programmed interactions nanostructured motifs assembling three DNA strands one RNA strand can include an aptamer domain for recruitment a target protein. Because designed form regardless presence protein, they function as “host” compartments. As model protein we consider streptavidin (SA) due its widespread use binding assays, thus host presented here could find immediate physical separation variety biotin-tagged components. In addition demonstrating recruitment, two approaches control onset condensation recruitment. The first approach uses UV irradiation, stimulus bypasses need exchanging molecular inputs is particularly convenient emulsion droplets. second transcription, ubiquitous biochemical reaction central development next generation living materials. finally show combination transcription degradation leads autonomous dissipative system which occur transiently, condensate size well timescale transient be controlled by level degrading enzyme. For Table Contents Only

Language: Английский

Citations

0
Oligo‐Adenine Derived Secondary Nucleic Acid Frameworks: From Structural Characteristics to Applications DOI Creative Commons
Yuwei Hu, Itamar Willner

Angewandte Chemie, Journal Year: 2024, Volume and Issue: 136(45)

Published: Aug. 26, 2024

Abstract Oligo‐adenine (polyA) is primarily known for its critical role in mRNA stability, translational status, and gene regulation. Beyond biological functions, extensive research has unveiled the diverse applications of polyA. In response to environmental stimuli, single polyA strands undergo distinctive structural transitions into secondary configurations, which are reversible upon introduction appropriate counter‐triggers. this review, we systematically summarize recent advances noncanonical structures derived from polyA, including A‐motif duplex, A‐cyanuric acid triplex, A‐coralyne‐A T ⋅ A‐T triplex. The characteristics mechanisms underlying these conformations under specific external stimuli addressed, followed by examples their stimuli‐responsive DNA hydrogels, supramolecular fibre assembly, molecular electronics switches, biosensing bioengineering, payloads encapsulation release, others. A detailed comparison polyA‐derived provided, highlighting features. Furthermore, integrating stimuli‐responsiveness conformational characteristics, advanced material development, such as pH‐cascaded hydrogels fibres exhibiting dynamic adapting cues, introduced. An outlook future developments also discussed. These derived, stimuli‐responsive, enrich arsenal “toolbox”, offering frameworks applications.

Language: Английский

Citations

0
Directing Nanoparticle Organization in Response to Diverse Chemical Inputs DOI
Yan Xiong, Colin Yancey,

Heon-Joon Lee

et al.

Journal of the American Chemical Society, Journal Year: 2024, Volume and Issue: 146(45), P. 30802 - 30812

Published: Oct. 30, 2024

Signaling cascades are crucial for transducing stimuli in biological systems, enabling multiple to regulate a downstream target with precisely controlled timing and amplifying signals through series of intermediary reactions. Developing robust signaling system such capabilities would be pivotal programming complex behaviors synthetic DNA-based molecular devices. However, although "software" as nucleic acid circuits could potentially harnessed relay nanostructure hardware, explorations have been limited. Here, we develop platform variety via messenger-mediated reactions the release reloading gold nanoparticles (AuNPs) 3D DNA framework. In first step, an vitro transcription circuit is engineered sense amplify chemical stimuli, including arbitrary sequences proteins, producing RNA. second RNA releases DNA-coated AuNPs from framework strand displacement reaction. AuNP by separate step driven degradation Our holds promise applications requiring dynamic multiagent control over devices, offering versatile tool advanced device engineering.

Language: Английский

Citations

0
Photochemically Triggered, Transient, and Oscillatory Transcription Machineries Guide Temporal Modulation of Fibrinogenesis DOI Creative Commons

Jiantong Dong,

Itamar Willner

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

Published: Dec. 31, 2024

Photochemically triggered, transient, and temporally oscillatory-modulated transcription machineries are introduced. The resulting dynamic circuits implemented to guide photochemically oscillatory modulation of thrombin toward temporal control over fibrinogenesis. One system describes the assembly a reaction module leading triggered formation an active machinery that, in presence RNase H, guides transient activation A second introduces photochemical triggering circuit consisting two coupled machineries, depletion intermediate product. concept is applied develop leads generation anti-thrombin aptamer-modified oscillating product induces rhythmic inhibition thrombin, accompanied by cyclic deactivation fibrinogenesis process. operation computational kinetic models, allowing predict behaviors under different auxiliary conditions. phototriggered circuit-guided examined physiological-like conditions within human plasma environment.

Language: Английский

Citations

0