Quantitative Analysis of the Effect of Fluorescent Labels on DNA Strand Displacement Reaction DOI Creative Commons

Masato Toyonari,

Kaori Aso,

Takashi Nakakuki

et al.

Micromachines, Journal Year: 2024, Volume and Issue: 15(12), P. 1466 - 1466

Published: Nov. 30, 2024

DNA chemical reaction networks can perform complex information processing through careful design of kinetics, which involves the network structure, rate constants, and initial concentrations. The toehold-mediated strand displacement (TMSDR) is a key mechanism in creating circuits, offering rational approach by integrating individually designed TMSDRs. Tools such as VisualDSD NUPACK facilitate efficient these systems allowing precise tuning parameters. However, discrepancies between simulated experimental results occur, often due to modification reporter molecules. Recently, fluorophore dyes quenchers were found significantly impact dynamics irreversible TMSDRs, altering them nearly two orders magnitude. on varies with site reporters. This study examines mechanisms modifications affecting reversible influencing transient steady-state characteristics. crucial for circuit design, integrates Our findings indicate that modifying fluorescent dye quencher an appropriate distance apart (e.g., toehold length) minimize adverse effects while ensuring effective FRET, therefore improving accuracy verification systems.

Language: Английский

RSTA: A reversible signal transmission architecture for breaking the limitation of unidirectional transmission DOI
Xin Liu, Shuang Cui, Xun Zhang

et al.

Chemical Engineering Journal, Journal Year: 2025, Volume and Issue: unknown, P. 162237 - 162237

Published: April 1, 2025

Language: Английский

Citations

0
Quantitative Analysis of the Effect of Fluorescent Labels on DNA Strand Displacement Reaction DOI Creative Commons

Masato Toyonari,

Kaori Aso,

Takashi Nakakuki

et al.

Micromachines, Journal Year: 2024, Volume and Issue: 15(12), P. 1466 - 1466

Published: Nov. 30, 2024

DNA chemical reaction networks can perform complex information processing through careful design of kinetics, which involves the network structure, rate constants, and initial concentrations. The toehold-mediated strand displacement (TMSDR) is a key mechanism in creating circuits, offering rational approach by integrating individually designed TMSDRs. Tools such as VisualDSD NUPACK facilitate efficient these systems allowing precise tuning parameters. However, discrepancies between simulated experimental results occur, often due to modification reporter molecules. Recently, fluorophore dyes quenchers were found significantly impact dynamics irreversible TMSDRs, altering them nearly two orders magnitude. on varies with site reporters. This study examines mechanisms modifications affecting reversible influencing transient steady-state characteristics. crucial for circuit design, integrates Our findings indicate that modifying fluorescent dye quencher an appropriate distance apart (e.g., toehold length) minimize adverse effects while ensuring effective FRET, therefore improving accuracy verification systems.

Language: Английский

Citations

0