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

Resource type
Thesis type
(Thesis) M.Sc.
Date created
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.
100 pages.
Copyright statement
Copyright is held by the author(s).
This thesis may be printed or downloaded for non-commercial research and scholarly purposes.
Supervisor or Senior Supervisor
Thesis advisor: Sen, Dipankar
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