Chemical modification, structural and functional study of nucleic acids

核酸是生物系统中不可缺少的分子，是遗传信息的储存和传递。这些分子的动态性质已经得到很好的认可，其中它们的功能与构象的变化有关。DNA作为核酸的一种形式，在生物学中通常以其右手B型结构而闻名。B-DNA在各种条件下转换为不太稳定的左手Z-DNA的能力已经被发现了40多年。越来越多的证据表明Z-DNA参与了生物过程，包括一些人类疾病。然而，人们对Z-DNA的功能知之甚少。我们将开发经过修饰的寡核苷酸，即核酸的短片段，作为研究这种形式的DNA的工具。我们将首先化学修饰寡核苷酸以稳定或抑制Z-DNA的形成。我们的第一种方法将提供模拟在生物条件下形成Z-DNA的模型系统，以阐明涉及这种形式的DNA的遗传调控机制。抑制Z-DNA形成的修饰将用作阴性对照，以验证第一种方法的结果。我们将扩大对DNA和相关核糖核酸（RNA）的序列要求的知识，以更好地理解DNA和RNA中潜在Z结构的倾向。我们将研究B-/Z-DNA转换的途径以及由于DNA解旋而引起的扭转应力驱动的转换。随着工具的开发，我们将研究可能涉及Z-DNA结构形成的生物化学和生物学过程。我们将调查的情况下，其中嗜盐菌，居住在盐水中，科普渗透胁迫，由于高盐浓度的细菌DNA和蛋白质结合到Z-DNA中的Z-DNA的存在下进行检查。在人类DNA中，我们将研究Z-DNA形成和表观遗传学之间的联系，其中生物体的变化是由转录的修改而不是遗传密码引起的，这是一个独特的基因表达调控层，通过检查与潜在的Z-DNA形成序列结合的蛋白质来调节转录。最后，我们将研究人类基因组DNA中遗传信息流的新调控，该调控涉及硫对磷酸骨架的修饰，导致硫代磷酸酯的形成。虽然已经发现这些在细菌的表观遗传学中起作用，但对其他生物体一无所知。 总的来说，我们建议采取化学方法来研究一类在生物系统中具有鲜为人知功能的核酸。我们的研究将回答关于左手DNA结构特征的基本问题，并提供最终阐明其生物学相关性的方法。最终，Z-DNA的知识有可能影响我们对生物系统和疾病干预的方法。

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.