Environmentally Controlled Oscillator with Triplex Guided Displacement of DNA Duplexes

Area of Science:

• Structural DNA nanotechnology
• DNA self-assembly
• Molecular engineering

Background:

• DNA triplexes offer pH-responsive reconfiguration for dynamic nanostructures.
• Combining pH-induced triplex formation with strand displacement is key in DNA nanotechnology.

Purpose of the Study:

• To demonstrate pH-driven displacement of triplex-forming oligonucleotides (TFOs) by DNA duplexes.
• To explore cyclic molecular oscillations using this duplex/triplex system.
• To implement and verify this system on 2D DNA origami for binary data representation.

Main Methods:

• Utilized pH alteration to trigger triplex-forming oligonucleotide (TFO) binding and displacement.
• Employed toehold-mediated strand displacement with a DNA duplex to displace TFOs.
• Investigated the effect of toehold length on the displacement efficiency.
• Implemented the system on 2D DNA origami structures representing binary digits.
• Verified conformational changes using atomic force microscopy.

Main Results:

• Demonstrated that a DNA duplex can displace TFOs from a triplex structure via pH alteration and toehold assistance.
• Showcased cyclic oscillations between two molecular formations controlled by pH changes.
• Successfully implemented binary digit representation (0 or 1) on DNA origami using this mechanism.
• Confirmed oscillatory conformational changes via atomic force microscopy.

Conclusions:

• pH-controlled duplex/triplex interactions provide a novel method for dynamic DNA nanostructure reconfiguration.
• This system enables environmentally responsive molecular switches and potential for data storage applications.
• The demonstrated cyclic oscillations on DNA origami highlight its utility in advanced nanotechnology.