Handhold-Mediated Strand Displacement: A Nucleic Acid Based Mechanism for Generating Far-from-Equilibrium Assemblies...

Area of Science:

• Biotechnology
• DNA Nanotechnology
• Polymer Science

Background:

• Sequence-controlled polymer assembly traditionally relies on equilibrium-driven templating.
• Biological systems utilize transient interactions for non-equilibrium templating, which is challenging to replicate artificially.
• Existing DNA nanotechnology methods often rely on product stability at equilibrium, limiting out-of-equilibrium applications.

Purpose of the Study:

• To introduce a novel DNA-based reaction mechanism for producing out-of-equilibrium polymer assemblies.
• To decouple reaction drive and specificity in templating processes.
• To enable DNA nanotechnology to achieve greater complexity, mirroring biological systems.

Main Methods:

• Development and application of handhold-mediated strand displacement (HMSD) reaction mechanism.
• Kinetic analysis of 98 different HMSD systems to quantify handhold efficiency.
• Demonstration of templating selective DNA duplex assembly from a pool of alternatives using HMSD.

Main Results:

• Handholds in HMSD accelerate strand displacement by up to four orders of magnitude.
• Handholds are transient and not sequestered in the final product, enabling non-equilibrium outcomes.
• HMSD successfully templated the selective assembly of specific DNA duplexes, yielding far-from-equilibrium products.

Conclusions:

• HMSD provides a powerful tool for engineering artificial systems capable of non-equilibrium templating.
• This mechanism overcomes limitations of equilibrium-based DNA reactions for complex sequence control.
• HMSD advances DNA nanotechnology towards mimicking the dynamic processes found in biological polymer biogenesis.