Rational design of tunable pH switches through shadow-strand hybridization-actuated displacement engineering

Area of Science:

• Biochemistry
• Molecular Biology
• Synthetic Biology

Background:

• Local pH variations are crucial in biological processes.
• Developing tunable and selective pH detection methods remains a challenge.
• Existing methods may lack programmability and specificity.

Purpose of the Study:

• To present a novel DNA-based strategy for programmable and selective pH responses.
• To demonstrate the application of shadow-strand hybridization-actuated displacement engineering (SHADE) for pH sensing.
• To enhance in vivo imaging in acidic tumor microenvironments.

Main Methods:

• Utilized shadow strands derived from i-motif-forming sequences to achieve tunable pH responses.
• Employed toehold-mediated strand displacement reactions (TMSDR) for i-motif folding under acidic conditions.
• Incorporated hairpin shadows (HS) with A+-C pairs for alkaline response and aptamer conjugation for cell surface targeting.

Main Results:

• Developed a narrow pH-responsive probe by combining i-motif and HS.
• Achieved significant fluorescence enhancement in acidic tumor microenvironments.
• Demonstrated improved signal-to-noise ratio for in vivo imaging.

Conclusions:

• SHADE offers a programmable approach to pH regulation using TMSDR.
• The SHADE strategy shows potential for manipulating quadruplex architectures and creating responsive components for molecular devices.
• This work advances the field of DNA-based biosensing and molecular engineering.