Programmable pH-responsive DNA inter-strand matching (PRISM) for precision molecular band-pass actuation

Precise sensing of narrow physiological pH ranges is important for accurate molecular regulation in complex biological environments. Traditional pH-responsive systems generally rely on monotonic off-to-on switching, making it difficult to distinguish subtle differences in tumor microenvironment pH (6.5-6.8) from neutral healthy tissues or highly acidic lysosomal compartments.

We developed PRISM (pH-Responsive DNA Inter-Strand Matching), a universal and DNA-based strategy that functions as a programmable molecular band-pass filter. PRISM combines two antagonistic regulatory domains-an i-motif-mediated low-pH OFF module and a C-A mismatch-mediated high-pH OFF module-within a three strand framework. Through sequence-level thermodynamic design, the system defines a controllable operational window that enables non-monotonic molecular actuation.

Systematic characterization showed that PRISM generated band-pass signal responses with tunable operational range. The platform was successfully applied to high-contrast imaging of subtle pH gradients on HeLa cell surfaces, enabling effective discrimination of tumor microenvironment from both neutral and highly acidic environments. In addition, PRISM enabled allosteric regulation of fluorogenic DNA Lettuce aptamers and enabled logic gated control of CRISPR/Cas13a activity by integrating synthetic DNA modules with the intrinsic pH responsiveness of enzymes.

Beyond conventional monotonic switching toward precise windowed regulation, PRISM offers a modular and biocompatible strategy for the development of intelligent theranostic platforms. This strategy facilitates high-fidelity diagnostic imaging and localized therapeutic activation within subtle pathological microenvironments without the need for complex bioconjugation.