Micromachines, Год журнала: 2024, Номер 15(12), С. 1466 - 1466

Опубликована: Ноя. 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.

Язык: Английский