Dissipative Gated and Cascaded DNA Networks

Area of Science:

• Supramolecular Chemistry
• Chemical Kinetics
• Molecular Engineering

Background:

• Out-of-equilibrium systems are crucial for complex molecular functions.
• Nucleic acid nanotechnology offers precise control over molecular assembly.
• Enzyme-mediated reactions can drive dynamic molecular processes.

Purpose of the Study:

• To design and characterize nucleic acid-based dissipative networks.
• To demonstrate fuel-triggered activation, gated operation, and cascading behavior.
• To investigate intercommunication and feedback mechanisms within these networks.

Main Methods:

• Utilized nucleic acid fuels and the nicking enzyme Nt.BbvCI to drive dissipative networks.
• Employed fluorophore-labeled strands and Förster Resonance Energy Transfer (FRET) to monitor supramolecular intermediates.
• Incorporated inhibitors for selective gated operation and studied strand-transfer/feedback for cascading.

Main Results:

• Successfully constructed functional modules activated by nucleic acid fuels, forming transient supramolecular intermediates.
• Demonstrated selective, gated dissipative operation using inhibitors (I1 or I2).
• Achieved intercommunication and cascading between two dissipative networks via strand-transfer and feedback.

Conclusions:

• Nucleic acid dissipative networks can be precisely controlled and programmed for complex dynamic behaviors.
• The developed systems exhibit tunable transient patterns predictable by kinetic models and simulations.
• This work provides a foundation for building sophisticated, enzyme-driven molecular machines and responsive materials.