UC San Diego

DNA and RNA have become of interest in nanotechnology applications due to nucleic acids’ ability to encode folding and programmable self-assembly primarily through base paring. A versatile kit of robust polygonal nanoshapes self-assembling from DNA and RNA modules provide a novel framework to integrate a combination of RNA motifs as architectural joints and DNA building blocks as functional modules. The RNA-DNA hybrid nanostructure provides the platform for application in molecular recognition, sensor and catalyst development in addition to protein interaction studies. The design, assembly and characterization of RNA-DNA hybrid structures has been established, methods for chemical modification of DNA components are being explored.

DNA components of RNA-DNA nanostructures were modified to carry diverse functional groups by targeting abasic sites in DNA helices with a selective ligand, amiloride. Amiloride was explored as a possible non-covalent ligand that targets abasic sites within DNA duplexes. Amiloride derivatives were synthesized with various side chain linkers and substituents to test binding within RNA-DNA hybrid nanostructures and expand diverse application of DNA modules.