DNA branch migration reactions through photocontrollable toehold formation

Area of Science:

• Biochemistry
• Nanotechnology
• Molecular Biology

Background:

• Strand displacement cascades are vital for creating dynamic DNA nanostructures.
• Toehold-mediated DNA branch migration is key for these structures.
• Controlling the formation of pure 1:1 DNA duplexes with toeholds remains a challenge.

Purpose of the Study:

• To introduce a novel photocontrolled method for toehold formation.
• To enable precise control over the ratio and formation of DNA duplexes.
• To facilitate the construction of light-responsive DNA nanostructures.

Main Methods:

• Utilizing photocleavage of 2-nitrobenzyl linker-embedded DNA hairpin precursors.
• Employing UV light irradiation (λ ≈ 365 nm) to cleave the linker.
• Demonstrating subsequent toehold-mediated DNA branch migration reactions, such as hybridization chain reactions.

Main Results:

• Achieved complete cleavage of the nitrobenzyl linker upon UV irradiation.
• Successfully formed pure 1:1 DNA duplexes with toehold structures.
• Demonstrated that toehold amount is controllable by UV irradiation dose.
• Validated the use of these toehold structures in DNA hybridization chain reactions.

Conclusions:

• A new photocontrolled toehold formation method has been established.
• This method allows for precise control over toehold structures in DNA nanostructures.
• The technique offers broad applications in building light-controllable dynamic DNA nanostructures and circuits.