Introducing a new paradigm of "socket-plug" complementarity for specific DNA-DNA recognition and binding

Nucleic acids have proved to be powerful building blocks in nanotechnology owing to their highly predictable and controllable self-assembling property. The classical Watson-Crick complementarity has been utilized to build complex 2D and 3D architectures and nanodevices. In addition to the iconic double helix generated from Watson-Crick strand pairing, DNAs are also known to be able to form alternative pairing schemes, giving rise to form DNA triplexes and G-quadruplexes, which in turn introduce novel possibilities for the engineering of DNA architectures. Herein, we describe a class of "sticky-ended" DNA triplex-quadruplex (TQ) composites that recognize and bind to each other via a wholly new paradigm of so-called "socket-plug" (as opposed to Watson-Crick) complementarity. The formation of these "socket-plug" hybrid composites is dependent on the presence of specific counterions under modestly acidic pH; the structures can in turn be disassembled by changes to either one of these requirements. Using gel electrophoresis and Förster Resonance Energy Transfer experiments, I have demonstrated the formation of different "socket-plug" hybrids in the presence of K+ versus Na+ counter-cations. Such a sensitivity to specific counterions is predicted to be a highly useful hybridization property, that will find wide application in nanotechnology, bioanalytical chemistry, as well as in other fields.