DNA tetraplexes-based toehold activation for controllable DNA strand displacement reactions

Area of Science:

• Biochemistry
• Molecular Biology
• Nanotechnology

Background:

• Dynamic DNA devices often rely on toehold-mediated strand displacement.
• Current methods are limited by double-stranded hybridization and lack versatile control.
• A need exists for enhanced control over DNA strand displacement kinetics.

Purpose of the Study:

• To propose a novel toehold activation strategy for dynamic DNA devices.
• To enable fine control over DNA strand displacement rates using environmental stimuli.
• To expand the design principles for responsive molecular devices.

Main Methods:

• Designed a toehold activation strategy using DNA tetraplexes (G-quadruplex or i-motif).
• Incorporated a complementary single-stranded segment (CS) attached to G-rich/C-rich segments.
• Modulated G-quartet/C·C(+) numbers and CS lengths to tune kinetics.

Main Results:

• Achieved fine control of DNA strand displacement rates over two orders of magnitude.
• Demonstrated tunability through adjustment of environmental stimuli concentrations.
• Successfully expanded the design rules for dynamic DNA devices.

Conclusions:

• The proposed tetraplex-based toehold activation strategy offers enhanced control over DNA strand displacement.
• This approach allows for the development of diverse molecular devices responsive to environmental cues.
• The strategy broadens the toolkit for engineering sophisticated DNA-based nanomachinery.