Structural DNA nanotechnology with novel components: Nylon-DNA and hydrophobic DNA

DNA is not only genetic material, but also a very capable supramolecular component. Stable branched DNA molecules and DNA crossover molecules have been employed to build DNA nanostructures through sticky-ended cohesion that act as templates and scaffolds for functional molecules that possess interesting optical, electrical and magnetic properties. In order to perform such a role, DNA nanotechnology needs to incorporate novel components.; For my first project, Denaturing Gradient Gel Electrophoresis (DGGE) is used to study how robust PX cohesion is. It is stable up to 55 °C, a robust cohesion tool for DNA nanotechnology.; Second, nylon-DNA was made with a view to controlling the topology of nylon and other polymers of industrial significance. Such a hybrid may be used in structural DNA nanotechnology and as an antiosense agent. Our results have shown that coupling the carboxylic and amine groups to make nylon-like polymer hanging along DNA backbone can stabilize the DNA duplex (above five amide bonds). The nylon-like polymer linking all monomer uridines that result from enzymatic digestion relieves our concern about failure coupling products.; Third, in order to take full advantage of DNA nanostructures as template and scaffolding, a hydrophobic auxiliary is necessary as an add-on to DNA nanostructures so that hydrophobic functional molecules can interact with DNA template through hydrophobic interactions. Single stranded DNA has been shown to wrap and disperse carbon nanotubes, but in highly ordered DNA structures, nucleobases stack inside and are no longer available for hydrophobic interaction. Methyl phosphonate linkages have been used to replace anionic linkages on one side of a DAE molecule to make it hydrophobic. Such a DAE molecule could behave like an amphiphilic molecule and tubes formed from such DAE tiles could have a hydrophobic core. However, our test failed to confirm that notion. We went on to explore the effect on hydrophobicity by recruiting 2'-O-(2-benzyloxy)ethyl ribonucleic acid in DNA structures that provides a benzene ring to interact with hydrophobic species such as carbon nanotubes. However, we met a problem with forming the DNA molecule. Nevertheless, these preliminary results are helpful regarding our ongoing efforts in this vein.