Nanomechanical DNA origami pH sensors

Area of Science:

• Nanotechnology
• Biochemistry
• Molecular Biology

Background:

• Nanomechanical DNA origami devices offer precise structural control at the nanoscale.
• pH-responsive DNA structures, like i-motifs, can undergo conformational changes based on protonation.
• Atomic Force Microscopy (AFM) provides high-resolution imaging of single molecules.

Purpose of the Study:

• To develop novel single-molecule pH sensors.
• To investigate the pH-dependent shape transitions of DNA origami nanodevices.
• To demonstrate the utility of AFM for molecular imaging of these transitions.

Main Methods:

• Design and fabrication of DNA origami pliers with specific dimensions.
• Integration of pH-responsive DNA sequences (i-motif forming) into the origami structure.
• High-resolution molecular imaging using Atomic Force Microscopy (AFM) on mica substrates.
• Analysis of structural transitions under varying pH conditions.

Main Results:

• DNA origami pliers exhibit distinct conformations (cross, antiparallel, parallel).
• Introduction of i-motif forming sequences induced a pH-dependent transition from an open cross form to a closed parallel form under acidic conditions.
• AFM successfully imaged these molecular shape transitions with high resolution.
• The observed transitions were directly correlated with changes in pH.

Conclusions:

• The developed DNA origami pliers function as effective single-molecule pH sensors.
• The system demonstrates a clear, imageable response to pH changes at the single-molecule level.
• This approach holds significant potential for advanced molecular sensing applications.