Occurrence and Function of Hoogsteen Base Pairs in Nucleic Acids

Nucleic acids (DNA and RNA) play essential roles in the central dogma of biology for the storage and transfer of genetic information. The unique chemical and conformational structures of nucleic acids – the double helix composed of complementary Watson-Crick base pairs, provide the structural basis to carry out their biological functions. DNA double helix can dynamically accommodate Watson-Crick and Hoogsteen base-pairing, in which the purine base is flipped by ~180° degrees to adopt syn rather than anti conformation as in Watson-Crick base pairs. There is growing evidence that Hoogsteen base pairs play important roles in DNA replication, recognition, damage or mispair accommodation and repair. Here, we constructed a database for existing Hoogsteen base pairs in DNA duplexes by a structure-based survey from the Protein Data Bank, and structural analyses based on the resulted Hoogsteen structures revealed that Hoogsteen base pairs occur in a wide variety of biological contexts and can induce DNA kinking towards the major groove. As there were documented difficulties in modeling Hoogsteen or Watson-Crick by crystallography, we collaborated with the Richardsons’ lab and identified potential Hoogsteen base pairs that were mis-modeled as Watson-Crick base pairs which suggested that Hoogsteen can be more prevalent than it was thought to be. We developed solution NMR method combined with the site-specific isotope labeling to characterize the formation of, or conformational exchange with Hoogsteen base pairs in large DNA-protein complexes under solution conditions, in the absence of the crystal packing force. We showed that there are enhanced chemical exchange, potentially between Watson-Crick and Hoogsteen, at a sharp kink site in the complex formed by DNA and the Integration Host Factor protein. In stark contrast to B-form DNA, we found that Hoogsteen base pairs are strongly disfavored in A-form RNA duplex. Chemical modifications N1-methyl adenosine and N1-methyl guanosine that block Watson-Crick base-pairing, can be absorbed as Hoogsteen base pairs in DNA, but rather potently destabilized A-form RNA and caused helix melting. The intrinsic instability of Hoogsteen base pairs in A-form RNA endows the N1-methylation as a functioning post-transcriptional modification that was known to facilitate RNA folding, translation and potentially play roles in the epitranscriptome. On the other hand, the dynamic property of DNA that can accommodate Hoogsteen base pairs could be critical to maintaining the genome stability.

Structure, Morphology, and Electrochemical Properties of Transition Metal Oxide, Hydroxide, and Phosphate Nanomaterials for Energy Storage

Energy storage technologies are crucial for efficient utilization of electricity. Supercapacitors and rechargeable batteries are of currently available energy storage systems. Transition metal oxides, hydroxides, and phosphates are the most intensely investigated electrode materials for supercapacitors and rechargeable batteries due to their high theoretical charge storage capacities resulted from reversible electrochemical reactions. Their insulating nature, however, causes sluggish electron transport kinetics within these electrode materials, hindering them from reaching the theoretical maximum. The conductivity of these transition metal based-electrode materials can be improved through three main approaches; nanostructuring, chemical substitution, and introducing carbon matrices. These approaches often lead to unique electrochemical properties when combined and balanced.

Ethanol-mediated solvothermal synthesis we developed is found to be highly effective for controlling size and morphology of transition metal-based electrode materials for both pseudocapacitors and batteries. The morphology and the degree of crystallinity of nickel hydroxide are systematically changed by adding various amounts glucose to the solvothermal synthesis. Nickel hydroxide produced in this manner exhibited increased pseudocapacitance, which is partially attributed to the increased surface area. Interestingly, this morphology effect on cobalt doped-nickel hydroxide is found to be more effective at low cobalt contents than at high cobalt contents in terms of improving the electrochemical performance.

Moreover, a thin layer of densely packed nickel oxide flakes on carbon paper substrate was successfully prepared via the glucose-assisted solvothermal synthesis, resulting in the improved electrode conductivity. When reduced graphene oxide was used for conductive coating on as-prepared nickel oxide electrode, the electrode conductivity was only slightly improved. This finding reveals that the influence of reduced graphene oxide coating, increasing the electrode conductivity, is not that obvious when the electrode is already highly conductive to begin with.

We were able to successfully control the interlayer spacing and reduce the particle size of layered titanium hydrogeno phosphate material using our ethanol-mediated solvothermal reaction. In layered structure, interlayer spacing is the key parameter for fast ion diffusion kinetics. The nanosized layered structure prepared via our method, however, exhibited high sodium-ion storage capacity regardless of the interlayer spacing, implying that interlayer space may not be the primary factor for sodium-ion diffusion in nanostructured materials, where many interstitials are available for sodium-ion diffusion.

Our ethanol-mediated solvothermal reaction was also effective for synthesis of NaTi2(PO4)3 nanoparticles with uniform size and morphology, well connected by a carbon nanotube network. This composite electrode exhibited high capacity, which is comparable to that in aqueous electrolyte, probably due to the uniform morphology and size where the preferable surface for sodium-ion diffusion is always available in all individual particles.

Fundamental understandings of the relationship between electrode microstructures and electrochemical properties discussed in this dissertation will be important to design high performance energy storage system applications.