SEQUENCE-SPECIFIC RECOGNITION OF DNA BY DIMER MOTIFS

描述（由申请人提供）：申请继续资助一个项目，该项目已资助三年以上，并支持核酸靶向药物设计和合成以及核酸复合物生物物理化学方面的合作实验室。根据初始资助下获得的结果，很明显杂环阳离子的堆叠二聚体代表了一种强大的新基序，用于特异性、强识别混合碱基对DNA序列和抑制蛋白质-DNA复合物。这些化合物毒性低，具有优异的生物活性，该类化合物将进入III期临床试验。由于双螺旋的两条链包含不同的化学信息，识别DNA的化合物如果能同时读取两条链，就能以最高的特异性识别DNA。基于这些观察，我们的假设是，堆叠的二聚体识别DNA的设计杂环阳离子提供了独特的机会，开发新的类别的药物，广泛的选择性分子识别的双链体和抑制DNA-蛋白质复合物。这样的二聚体具有开发为新型治疗剂、生物技术试剂、控制细胞基因表达的试剂和抑制特定蛋白质-DNA复合物的显著潜力。我们已经设计并正在研究两个二聚体堆叠图案，以新的和不同的方式识别小沟。一个系统正在开发，以抑制bZIP转录因子，如Fos/Jun癌蛋白，而第二个系统将靶向小沟HMGA癌蛋白。我们将制备和研究化合物，（i）通过使用各种杂环增加二聚体系统的序列识别能力;（ii）通过延长二聚体的长度来延长读取的碱基序列的长度;（iii）通过制备共价二聚体来增强结合的亲和力和特异性。化合物-DNA复合物的特征在于具有强大的生物物理方法阵列，包括NMR和X射线;酶和化学足迹;生物传感器SPR和ITC。在最基本的水平上，杂环二聚体系统将提供DNA识别的分子基础以及它如何受到碱基对化学、溶剂和配体性质的局部相互作用的影响的重要新认识。杂环系统是唯一的基序靶向混合序列的DNA与临床上有用的和细胞渗透剂。

DESCRIPTION (provided by applicant): Continuation funds are requested for a project that has been funded for three+ years and that supports collaborating laboratories in nucleic acid targeted drug design and synthesis and in the biophysical chemistry of nucleic acid complexes. Based on results obtained under initial funding, it is clear that stacked-dimers of heterocyclic cations represent a powerful new motif for specific, strong recognition of mixed base pair DNA sequences and inhibition of protein-DNA complexes. The compounds have low toxicity with excellent biological activity and a compound from this class is set to enter Phase III clinical trials. Since the two strands of the double helix contain different chemical information, compounds that recognize DNA can do so with the highest specificity if they read both strands. Based on these observations our hypothesis is that stacked dimer recognition of DNA by designed heterocyclic cations offers unique opportunities for development of new classes of drugs for broad-based selective molecular recognition of the duplex and inhibition of DNA-protein complexes. Such dimers have significant potential for development as new types of therapeutics, for reagents in biotechnology, as agents for control of cellular gene expression, and for inhibition of specific protein-DNA complexes. We have designed and are studying two dimer-stacking motifs that recognize the minor groove in new and different ways. One system is being developed to inhibit bZlP transcription factors such as the Fos/Jun oncoproteins, while the second system will target the minor groove HMGA oncoproteins. We will prepare and study compounds that (i) increase the sequence recognition capability of the dimer systems by using a variety of heterocycles; (ii) extend the length of the base sequence that is read by extending the length of the dimers; (iii) enhance the affinity and specificity of binding by preparation of covalent dimers. The compound-DNA complexes will be characterized with a powerful array of biophysical methods including NMR and x-ray; enzymatic and chemical footprinting; biosensor-SPR and ITC. At the most fundamental level, the heterocyclic dimer systems will provide significant new understanding of the molecular basis of DNA recognition and how it is affected by the local interplay of base pair chemistry, solvent and ligand properties. The heterocyclic system is the only motif for targeting mixed sequences of DNA with clinically useful and cell permeable agents.