Date of Award




Document Type

Master's Thesis

Degree Name

Master of Science (MS)


Department of Chemistry

Content Description

1 online resource (vi, 27 pages) : illustrations (some color)

Dissertation/Thesis Chair

Paul F Agris

Committee Members

Igor K Lednev, Charles P Scholes


DNA, Self-assembly (Chemistry), Nanostructured materials

Subject Categories



A thermodynamic and structural analysis of DNA nanostructures was performed, following the replacement of the unpaired thymine bases within a central loop to determine their effect on the self-assembly process. Specifically this study focused on DNA cross-tile nanostructures. Self-assembly of DNA cross-tiles occurs by means of Watson-crick base-pairing interactions between designed single-stranded DNAs from which lattice structures assemble through sticky-end cohesion. These cross-tile structures were constructed from nine single-stranded DNAs and consisted of a central loop containing 16 unpaired thymine bases, four shell strands, and four arms. Modifications were introduced to replace the central unpaired thymine base loop. The modifications used were ribouridine, 2'-O-methyluridine and abasic. The thermodynamic profile and structural base-stacking contributions were assessed using UV thermal denaturation and circular dichroism, respectively. As a result of altering the unpaired region of the tiles, there were significant changes in the thermodynamic and structural properties of the lattice formation. Therefore disrupting normal lattice formation by altering the unpaired central loop allows for a large possibility of uses for cross-tiles, such as designs for biosensing devices.

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