Chemical modification, structural and functional study of nucleic acids

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Nucleic acids, molecules in biological systems, are indispensable for the storage and transmission of genetic information. The dynamic nature of these molecules has been well recognized where their functions are associated with changes in conformations. DNA as a form of nucleic acid is commonly known for its right-handed B-form structure in biology. The ability of B-DNA to undergo a switch to the less stable left-handed Z-DNA under various conditions has been known for over 40 years. Accumulating evidence points toward the involvement of Z-DNA in biological processes, including some human diseases. Yet, little is known about the functions of Z-DNA. We will develop modified oligonucleotides, short pieces of nucleic acids, as tools to study this form of DNA. We will first chemically modify oligonucleotides either to stabilize or to suppress Z-DNA formation. Our first approach will provide model systems that mimic the formation of Z-DNA under biological conditions in order to elucidate mechanisms of genetic regulation involving this form of DNA. Modifications to suppress Z-DNA formation will serve as a negative control to validate results from the first approach. We will expand the knowledge on sequence requirements for DNA and related ribonucleic acids (RNA) in their ability to adopt the left-handed Z-structure in order to better understand the propensity of potential Z-structures in DNA and RNA. We will study the pathways of B-/Z-DNA transitions and the transitions driven by torsional stress as a result of DNA unwinding. With the tools developed, we will then study biochemical and biological processes where formation of Z-DNA structures may be implicated. We will investigate a scenario by which halobacteria, which inhabit salty water, cope with the osmotic stress as a result of high salt concentrations by examining the presence of Z-DNA in the bacterial DNA and proteins that bind to Z-DNAs. In human DNA, we will study connections between Z-DNA formation and epigenetics, where changes in organisms are caused by modifications of transcription instead of genetic codes, a unique layer of regulation of gene expression, by examining proteins that bind to potential Z-DNA forming sequences that regulate transcription. Last, we will investigate new regulation of genetic information flow in human genomic DNA that involves the modification of the phosphate backbone by sulfur, leading to the formation of phosphorothioates. While these have been found to have a role in epigenetics in bacteria, nothing is known for other organisms. Overall we propose to take a chemistry approach to study a class of nucleic acids with little-known functions in biological systems. Our study will answer fundamental questions about the structural features of left-handed DNA and provide approaches toward eventual elucidation of its biological relevance. Ultimately, this knowledge of Z-DNA has potential to influence our approaches to biological systems and disease intervention.