Reshaping the Energy Landscape Transforms the Mechanism and Binding Kinetics of DNA Threading Intercalation
Reshaping the Energy Landscape Transforms the Mechanism and Binding Kinetics of DNA Threading Intercalation
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DOI：
10.1021/acs.biochem.7b01036
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发表时间：
2018-02-06
期刊：
影响因子：
2.9
通讯作者：
Williams, Mark C.
中科院分区：
文献类型：
--
作者：
Clark, Andrew G.;Naufer, M. Nabuan;Williams, Mark C.
通过穿线嵌入结合DNA的分子显示出高结合亲和力以及缓慢的解离动力学，这是开发抗癌药物的理想特性。为此，确定导致最佳DNA相互作用的螺纹嵌入剂的特定分子特征至关重要。使用单分子技术，我们量化的小金属有机钌线程嵌入剂（三角洲，三角洲-B）的结合，并比较其结合特性与一个类似的分子具有显着较大的线程部分（三角洲，三角洲-P）。两种分子的结合亲和力是相同的，而结合动力学的比较揭示了Delta，Delta-B的明显更快的动力学。然而，动力学仍然比常规嵌入剂所观察到的慢得多。两个线程嵌入剂的比较表明，结合亲和力是独立调制的嵌入部分和结合动力学调制的线程部分。为了将DNA，Delta，Delta-P穿线，需要一个“锁定机制”，其中DNA双链体的长度增加很大，这是缔合和解离所必需的。相比之下，力依赖性结合动力学的测量结果表明，Δ，Δ-B需要大的DNA长度增加的协会，但没有长度增加从DNA的解离。这与常规嵌入剂形成强烈对比，对于常规嵌入剂，缔合几乎不需要DNA长度变化，但解离必须发生大的DNA长度变化。这一结果说明了与传统插层法相比，DNA穿层插层法具有根本不同的机理，并将为基于DNA穿层插层法的治疗药物的合理设计铺平道路。
Molecules that bind DNA via threading intercalation show high binding affinity as well as slow dissociation kinetics, properties ideal for the development of anticancer drugs. To this end, it is critical to identify the specific molecular characteristics of threading intercalators that result in optimal DNA interactions. Using single-molecule techniques, we quantify the binding of a small metal-organic ruthenium threading intercalator (Delta,Delta-B) and compare its binding characteristics to a similar molecule with significantly larger threading moieties (Delta,Delta-P). The binding affinities of the two molecules are the same, while comparison of the binding kinetics reveals significantly faster kinetics for Delta,Delta-B. However, the kinetics is still much slower than that observed for conventional intercalators. Comparison of the two threading intercalators shows that the binding affinity is modulated independently by the intercalating section and the binding kinetics is modulated by the threading moiety. In order to thread DNA, Delta,Delta-P requires a "lock mechanism", in which a large length increase of the DNA duplex is required for both association and dissociation. In contrast, measurements of the force-dependent binding kinetics show that Delta,Delta-B requires a large DNA length increase for association but no length increase for dissociation from DNA. This contrasts strongly with conventional intercalators, for which almost no DNA length change is required for association but a large DNA length change must occur for dissociation. This result illustrates the fundamentally different mechanism of threading intercalation compared with conventional intercalation and will pave the way for the rational design of therapeutic drugs based on DNA threading intercalation.