Chemical modification, structural and functional study of nucleic acids

核酸是生物系统中的分子，对于遗传信息的存储和传输是不可或缺的。人们已经很好地认识到这些分子的动态性质，因为它们的功能与构象的变化有关。DNA作为核酸的一种形式，在生物学上因其右旋B型结构而广为人知。B-DNA在各种条件下转换为不太稳定的左撇子Z-DNA的能力已经被人们知道了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。我们将开发修饰的寡核苷酸，即短的核酸片段，作为研究这种形式的DNA的工具。我们将首先对寡核苷酸进行化学修饰，以稳定或抑制Z-DNA的形成。我们的第一种方法将提供模拟生物条件下Z-DNA形成的模型系统，以阐明涉及这种形式DNA的遗传调控机制。抑制Z-DNA形成的修饰将作为阴性对照来验证第一种方法的结果。我们将扩大关于DNA和相关核糖核酸(RNA)采用左手Z-结构的能力的序列要求的知识，以便更好地了解DNA和RNA中潜在的Z-结构的倾向。我们将研究B-/Z-DNA转变的途径，以及由于DNA解旋而导致的扭应力驱动的转变。有了开发的工具，我们将研究可能涉及Z-DNA结构形成的生化和生物过程。我们将通过检测细菌DNA和与Z-DNA结合的蛋白质中Z-DNA的存在，来研究生活在咸水中的盐杆菌应对高盐浓度造成的渗透胁迫的情况。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，在表观遗传学中，生物体的变化是由转录的修改而不是遗传密码引起的，遗传密码是基因表达的独特调节层，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节，涉及硫磺修饰磷酸盐骨架，导致硫代硫酸盐的形成。虽然这些已经被发现在细菌的表观遗传学中起到了作用，但对其他生物却一无所知。总体而言，我们建议采用化学方法来研究一类在生物系统中功能鲜为人知的核酸。我们的研究将回答有关左撇子DNA结构特征的基本问题，并为最终阐明其生物学相关性提供方法。最终，这种对Z-DNA的了解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.