UC Davis

DNA structural stability and programmability offer innumerable degrees of freedom for the design and fabrication of DNA-based devices. DNA sequences can adopt complex structures beyond the double helix, and these structures can occur either naturally or artificially. A thorough understanding of the electrical properties of these intricate structures is still lacking and investigating the charge transport in these structures is of fundamental importance for developing DNA-based electronic devices or sensing platforms. This thesis examines the electronic properties of various complex DNA structures and the possibility of electrically identifying conformational differences using the single molecule break junction (SMBJ) method. First, the conductance of an artificial DNA nanostructure, designed using DNA origami approaches, is examined. The single-molecule break junction (SMBJ) approach, which has been leveraged to examine charge transport through a variety of single-molecule devices, has been adopted to obtain the conductance of individual DNA origamis while bridging the gap between the SMBJ’s electrodes. Thermodynamic analysis and molecular dynamic simulations suggest that the DNA origami used in this study is very stable. Also, different SMBJ tapping modes show that the DNA origami is highly conductive compared to double-stranded DNA. Next, we systematically study the naturally occurring noncanonical guanine-quadruplex (G-quadruplex) structures and their transport properties by increasing the number of G-tetrads. We found that the conductance of the G-quadruplex is weakly length-dependent. These results suggest that the dominant transport mechanism is thermally activated hopping. Finally, besides the G-quadruplex’s essential regulatory role in biology, it is also the basis of many genetic diseases. Here, beyond the fundamental studies of DNA complex structures, we compare different tools for detecting G-quadruplex structures. In particular, circular dichroism (CD), gel electrophoresis, and SMBJ were used to detect the presence of G-quadruplex structures. DNA sequences in this study show that the conductance value of the G-quadruplex is one order of magnitude higher than the double-stranded DNA. Therefore, harnessing electrical signals from individual molecules may provide the ultimate detection scheme for G-quadruplex. Taken together, these experiments demonstrate that the structural polymorphism in DNA greatly influences the electronic properties, and one can foresee that complex structures will open doors to a wide variety of applications, including but not limited to molecular switches, sensors, and nanowires.