biostudies-literatureHan XChongqing Medical UniversityNational key R&D Program of ChinaNational Natural Science Foundation of Chinagkaf849https://www.ebi.ac.uk/biostudies/studies/S-EPMC12412784biostudies-literatureUnknown53(17)Local pH variations play a pivotal role in numerous critical biological processes. However, achieving the tunability and selectivity of pH detection remains a challenge. Here, we present a DNA-based strategy that enables programmable and selective pH responses, which is termed shadow-strand hybridization-actuated displacement engineering (SHADE). The tunability of pH responses is accomplished via rational manipulations of shadow strands derived from the i-motif-forming sequence. Shadow strands, which can be considered the "nucleic acid molecular chaperones," assist in the folding of i-motif structure under acidic conditions via toehold-mediated strand displacement reactions (TMSDR). The response to alkaline conditions is achieved through a hairpin shadow (HS) containing A+-C pairs in stem.Nucleic acids researchRational design of tunable pH switches through shadow-strand hybridization-actuated displacement engineering.PMC1241278482172369BJRC2025052022YFC2603800Liu XJiang JYang GXie GDong XGuo YZhang YHan XLin XWang WZhang LYu HfalseRational design of tunable pH switches through shadow-strand hybridization-actuated displacement engineering.Local pH variations play a pivotal role in numerous critical biological processes. However, achieving the tunability and selectivity of pH detection remains a challenge. Here, we present a DNA-based strategy that enables programmable and selective pH responses, which is termed shadow-strand hybridization-actuated displacement engineering (SHADE). The tunability of pH responses is accomplished via rational manipulations of shadow strands derived from the i-motif-forming sequence. Shadow strands, which can be considered the "nucleic acid molecular chaperones," assist in the folding of i-motif structure under acidic conditions via toehold-mediated strand displacement reactions (TMSDR). The response to alkaline conditions is achieved through a hairpin shadow (HS) containing A+-C pairs in stem.2025-01-01T00:00:00Z2025 Sep2026-06-01T13:58:06.223Z2026-04-08T13:18:57.533ZS-EPMC124127844092375710.1093/nar/gkaf849