Effectively controlling the structures of DNA and RNA is crucial for their functional utilization in material development, biological regulation, and medical applications. Here, we present a gain-of-function strategy for controlling DNA and RNA structures using an inverse electron-demand Diels-Alder (IEDDA) based click-to-release reaction. By incorporating click reaction-cleavable caged moiety into oligonucleotides, we disrupt activated base pairs, allowing controlled release of biofunctional higher-order nucleic acid structures. This click-to-release caged DNA was employed to control DNA duplex formation. Next, we demonstrated the utility of "click-to-release" strategy for regulated release of Z-DNA or Z-RNA and bind associated proteins. In addition, the approach was used to manipulated G-quadruplex formation in vitro and in vivo, enabling visual detection of G-quadruplex using BVE-caged DNA with fluorescent dye. Furthermore, we demonstrated the utility of click-to-release caged DNA for Quantum Dots (QDs) functionalization, enabling precise molecular imaging for cancer diagnosis. Finally, we developed a click-to-release controllable nucleic acid aptamer for precise blood clotting regulation and anticoagulation therapy. This strategy provides moderate kinetics, excellent orthogonality, and biocompatibility. It establishes a new pathway towards control of nucleic acid structures and functions, which has promising applications in various biological procedures and nucleic acid medicines.