Deciphering the structure and dynamics of non-canonical DNA implicated in cancer

项目摘要 这项拟议的研究将通过提供新的治疗方案来提高抗癌疗法的选择性和疗效。 关于非规范核酸结构，G-四链体（GQ）和i-基序的知识，以及它们的细节 与小分子配体的相互作用。生物信息学研究已经确定了10700，000个具有GQ的序列， 在人类基因组中形成潜力。富含C的相反链被提议形成i基序。现在有 令人信服的生物学证据表明，GQ和i-基序在体内形成，并且这些结构相互补充 另一个是调节各种癌症相关的生物过程。GQ核酸一直坚定地 作为癌症的重要治疗靶点。同样的证据表明， 积累。已经鉴定出选择性结合GQ DNA和RNA以及i基序的小分子， 并且一些已经显示出抑制肿瘤细胞生长;然而，这种抑制的确切机制 不知道。此外，选择性i基序配体的数量很低。这些配体最终可能成为 用于癌症干预的先导化合物上级常规诱变疗法。 以核酸为中心的药物发现计划受到GQ和i基序的有限结构信息的困扰， 尤其是在配体存在下。到目前为止，还没有i-基序-配体复合物的结构被报道。 由于GQ和i基序两者的高度结构多样性，它们的矛盾性， 生物学功能，以及我们有限的靶向其特定折叠拓扑结构的能力（例如，平行与反平行 GQ）。 为了应对这些挑战，我们建议对端粒进行全面的晶体学研究， 和癌基因启动子GQ和i-基序，两者单独或与新的和可商购获得的 选择性小分子配体。为GQ和i-基序提供稳定性的相互作用的多样性将是 测定配体结合位点的详细信息，以及配体的化学和结构特征 其亲和性和选择性将被鉴定。这项工作将得到光谱和 配体结合的热力学参数的量热研究。对于GQ DNA来说， 探索，结构研究将补充配体辅助GQ折叠的严格动力学探索。 动力学信息可以帮助我们确定GQ形成的时间尺度，从而确定可以 受到这些结构的影响。总的来说，拟议的工作将加强我们对 GQ和i-motif结构可塑性的研究，为药物发现平台提供坐标，揭示了 配体对特定DNA或RNA靶点的选择性，并指导新型抗癌疗法的设计， 为斯沃斯莫尔学院的本科生提供转型培训。

PROJECT SUMMARY The proposed research will improve the selectivity and efficacy of anticancer therapies by contributing new knowledge about non-canonical nucleic acid structures, G-quadruplexes (GQ) and i-motifs, and details of their interactions with small-molecule ligands. Bioinformatics studies have identified 700,000 sequences with GQ- forming potential in the human genome. The C-rich opposite strands are proposed to form i-motifs. There is now convincing biological evidence that GQs and i-motifs form in vivo and that these structures complement each other in regulating a variety of cancer-related biological processes. GQ nucleic acids have been firmly established as an important therapeutic target for cancer. The same evidence for i-motifs is steadily accumulating. Small molecules that bind selectively to GQ DNA and RNA and to i-motifs have been identified, and some have been shown to inhibit tumor cells growth; however, exact mechanisms underlying this inhibition are not known. Additionally, the number of selective i-motif ligands is low. Such ligands may ultimately become lead compounds for cancer intervention superior to conventional mutagenetic therapies. Nucleic acid-centered drug discovery programs suffer from limited structural information for GQs and i-motifs, especially in the presence of ligands. As of now, no structure of an i-motif-ligand complex has been reported. The situation is further complicated by high structural diversity of both GQs and i-motifs, their contradictory biological functions, and our limited ability to target their specific folding topology (e.g., parallel vs antiparallel GQs). To address these challenges, we propose to perform comprehensive crystallographic investigation of telomeric and oncogene promoter GQs and i-motifs, both alone and in complex with novel and commercially available selective small-molecule ligands. The diversity of interactions which provide stability to GQs and i-motifs will be determined. The details of ligand binding sites, as well as chemical and structural features of ligands essential for their affinity and selectivity will be identified. This work will be complemented by spectroscopic and calorimetric studies of the thermodynamic parameters of ligand binding. For GQ DNA, that is much more explored, structural studies will be complemented by rigorous kinetic exploration of ligand-assisted GQ folding. Kinetic information can help us identify the timescale of GQ formation and, thus, biological processes that can be affected by the presence of these structures. Collectively, the proposed work will enhance our understanding of GQ and i-motif structural plasticity, supply coordinates for drug discovery platforms, shed light on the origin of ligand selectivity for a specific DNA or RNA target, and guide the design of novel anticancer therapies all while providing transformative training to Swarthmore undergraduates.